PaperBLAST
PaperBLAST Hits for 74 a.a. (DARRKRRNFS...)
Show query sequence
>74 a.a. (DARRKRRNFS...)
DARRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY
KKNIGKAQEEANLY
Running BLASTp...
Found 250 similar proteins in the literature:
EXD_DROME / P40427 Homeobox protein extradenticle; Dpbx from Drosophila melanogaster (Fruit fly) (see 7 papers)
NP_523360 extradenticle, isoform A from Drosophila melanogaster
100% identity, 20% coverage
- function: Transcription factor which acts with the selector homeodomain proteins altering the regulation of downstream target genes such as wingless (wg), teashirt (tsh) and decapentaplegic (dpp), thus affecting segmental identity. Delimits the eye field and prevent inappropriate eye development. Required for proper localization of chordotonal organs within the peripheral nervous system.
subunit: Interacts with Ubx and hth.
disruption phenotype: Weak posterior-directed transformations in all 3 thoracic segments and in the anterior segments of the abdomen. - Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription.
Villarreal-Puente, Hereditas 2024 - GeneRIF: Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription.
- Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity.
Jiménez-Mejía, Hereditas 2022 - GeneRIF: Trimeric complexes of Antp-TBP with TFIIEbeta or Exd modulate transcriptional activity.
- Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS.
Khandelwal, PLoS genetics 2017 - GeneRIF: Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer. Exd-Grh-Notch work with different Hox genes through region specific enhancers to pattern respective segments of larval central nervous system.
- Low affinity binding site clusters confer hox specificity and regulatory robustness.
Crocker, Cell 2015 - GeneRIF: Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments.
- Homothorax and Extradenticle alter the transcription factor network in Drosophila ommatidia at the dorsal rim of the retina.
Wernet, Development (Cambridge, England) 2014 - GeneRIF: Hth functions together with its co-factor Extradenticle to repress the R8-specific factor Senseless in dorsal rim area R8 cells, allowing expression of an ultraviolet-sensitive R7 Rhodopsin.
- Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired.
Fujioka, Developmental biology 2012 - GeneRIF: cooperative binding sites for En, with the homeodomain-containing Hox cofactors Extradenticle (Exd) and Homothorax (Hth) was localized, within two CRMs that drive similar expression patterns
- Extradenticle and homothorax control adult muscle fiber identity in Drosophila.
Bryantsev, Developmental cell 2012 - GeneRIF: In the flight muscles, exd and hth are genetically upstream of another muscle identity gene, salm, and are direct transcriptional regulators of the signature flight muscle structural gene, Actin88F.
- Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity.
Saadaoui, Proceedings of the National Academy of Sciences of the United States of America 2011 - GeneRIF: Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity.
- More
- Stability and dynamics of extradenticle modulates its function
Singh, Current research in structural biology 2024 - “...Cloning, mutagenesis, protein expression and purification The minimal homeodomain (residues Ala238Ile300) of Extradenticle (EXD) (UniProtKB P40427) from D. melanogaster was cloned into the pET28a(+) vector. Glycine 290 was mutated to alanine by site-directed mutagenesis using non-overlapping primers ( Boral et al., 2023 ). The methylated template...”
- Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins
Kribelbauer, Molecular cell 2020 - “...2011 ). Briefly, PET-expression vectors containing coding regions for full-length hth (Uniprot-ID: O46339), exd (Uniprot-ID: P40427), dfd (Uniprot-ID: P07548) and Hth HM-domain (amino acids 1242; (Uniprot-ID: O46339) with hexa-histidine tags (except for Exd, which was co-purified with full-length Hth or HM-domain-only Hth) were transformed into Bl21...”
NP_001034501 extradenticle from Tribolium castaneum
100% identity, 20% coverage
PBX2_HUMAN / P40425 Pre-B-cell leukemia transcription factor 2; Homeobox protein PBX2; Protein G17 from Homo sapiens (Human) (see 2 papers)
NP_002577 pre-B-cell leukemia transcription factor 2 from Homo sapiens
93% identity, 17% coverage
- function: Transcriptional activator that binds the sequence 5'- ATCAATCAA-3'. Activates transcription of PF4 in complex with MEIS1.
subunit: Forms heterodimers with MEIS1 and heterotrimers with MEIS1 and HOXA9. Interacts with PBXIP1. - Coexpression of HOXA6 and PBX2 promotes metastasis in gastric cancer.
Lin, Aging 2021 - GeneRIF: Coexpression of HOXA6 and PBX2 promotes metastasis in gastric cancer.
- MicroRNA‑1915‑3p prevents the apoptosis of lung cancer cells by downregulating DRG2 and PBX2.
Xu, Molecular medicine reports 2016 (PubMed)- GeneRIF: miR19153p functions as a silencer of apoptosis, which regulates lung cancer apoptosis via targeting DRG2/PBX2.
- Variant of PBX2 gene in the 6p21.3 asthma susceptibility locus is associated with allergic rhinitis in Chinese subjects.
Zhao, International forum of allergy & rhinology 2016 (PubMed)- GeneRIF: The findings from the present study that a SNP of the PBX2 gene in the MHC region (at 6p21.3) was associated with allergic rhinitis (AR) in allele and genotypic analysis suggests a new susceptibility gene for AR in the MHC region and another gene associated with both asthma and AR in Chinese subjects.
- The abrogation of the HOXB7/PBX2 complex induces apoptosis in melanoma through the miR-221&222-c-FOS pathway.
Errico, International journal of cancer 2013 - GeneRIF: findings suggest the disruption of the HOXB7/PBX2 complexes, miR-221&222 inhibition or even better their combination, as innovative therapeutic approaches
- Expression level of pre-B-cell leukemia transcription factor 2 (PBX2) as a prognostic marker for gingival squamous cell carcinoma.
Qiu, Journal of Zhejiang University. Science. B 2012 - GeneRIF: a high level of PBX2 is a poor prognosticator for disease-free survival and overall survival in gingival squamous cell carcinoma
- Expression level of Pre B cell leukemia homeobox 2 correlates with poor prognosis of gastric adenocarcinoma and esophageal squamous cell carcinoma.
Qiu, International journal of oncology 2010 (PubMed)- GeneRIF: Pre B cell leukemia homeobox 2 has a role in poor prognosis of gastric adenocarcinoma and esophageal squamous cell carcinoma
- Identification of type 2 diabetes-associated combination of SNPs using support vector machine.
Ban, BMC genetics 2010 - GeneRIF: Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
- Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.
Ucisik-Akkaya, Molecular human reproduction 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- More
- Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities.
Miyake, American journal of human genetics 2020 - Computational analysis of multimorbidity between asthma, eczema and rhinitis.
Aguilar, PloS one 2017 - “...beta 2q14.1 P05113 IL5 interleukin 5 5q31.1 P13501 CCL5 chemokine (C-C motif) ligand 5 17q12 P40425 PBX2 pre-B-cell leukemia homeobox 2 6p21.32 P51671 CCL11 chemokine (C-C motif) ligand 11 17q12 P51677 CCR3 chemokine (C-C motif) receptor 3 3p21.31 Q8IZI9 IFNL3 interferon, lambda 3 19q13.2 Q99466 NOTCH4...”
- Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9)
Sun, International journal of molecular sciences 2015 - “...1 RNPS1 34,208.24 11.85 7.11 1 O96019 Actin-like protein 6A ACL6A 47,460.97 5.39 3.03 1 P40425 Pre-B-cell leukemia transcription factor 1 PBX2 45,881.29 7.18 10.79 1 Q5UIP0 Telomere-associated protein RIF1 RIF1 274,465.6 5.39 0.57 1 P49006 MARCKS-related protein MRP 19,528.8 4.65 7.69 1 P25788 Proteasome subunit...”
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...domain; blue, the PBC-B domain; green, the HD domain Accession numbers are: Pbx1: AAG30941; Pbx2: P40425; Pbx3: P40426; Pbx4: CAC28212; Exd: AAC37182.1 An important feature of TALE proteins is the formation of dimers between MEINOX and PBC proteins, even in the absence of DNA. The domains...”
NP_059491 pre-B-cell leukemia transcription factor 2 from Mus musculus
93% identity, 17% coverage
- A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
Losa, Nature communications 2023 - GeneRIF: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
- TBX1 is required for normal stria vascularis and semicircular canal development
Tian, Developmental biology 2020 - “...1 NP_032742 2318 aa 15002318 OTOG Moderate 1 NP_038652 2911 aa 421540 PBX2 Moderate 1 NP_059491 430 aa 110385 * PIAS2 Moderate 1 NP_032628 621 aa 1258 RNF138 Moderate 1 NP_997506 245 aa 1188 STAB1 Moderate 1 NP_619613 2571 aa 212571 THBS4 Moderate 1 NP_035712 963...”
- PBX transcription factors drive pulmonary vascular adaptation to birth.
McCulley, The Journal of clinical investigation 2018 - GeneRIF: mouse PBX1 and PBX2 have roles in pulmonary vascular adaptation to birth
- Characterization of TALE genes expression during the first lineage segregation in mammalian embryos.
Sonnet, Developmental dynamics : an official publication of the American Association of Anatomists 2012 (PubMed)- GeneRIF: Data have demonstrated the presence of Meis, Pbx, and Prep proteins during early lineage segregation in mammals: Meis1, Meis3, Pbx1, Pbx2, Pbx3, and Prep1 in the mouse.
- Control of pelvic girdle development by genes of the Pbx family and Emx2.
Capellini, Developmental dynamics : an official publication of the American Association of Anatomists 2011 - GeneRIF: In compound Pbx1;Pbx2 and Pbx1;Emx2 mutants, pelvic mesenchymal condensation is markedly perturbed, indicative of an upstream control by these homeoproteins.
- Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and Hox in mesoderm and Pax1/Pax9 in sclerotome.
Capellini, Developmental biology 2008 - GeneRIF: Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and Hox in mesoderm and Pax1/Pax9 in sclerotome.
- Pbx/Meis deficiencies demonstrate multigenetic origins of congenital heart disease.
Stankunas, Circulation research 2008 - GeneRIF: Reduction or absence of Pbx2 or Pbx3 leads to Pbx1 haploinsufficiency and specific malformations that resemble tetralogy of Fallot, overriding aorta with ventricular septal defect, and bicuspid aortic valves.
- Meis1 is an essential and rate-limiting regulator of MLL leukemia stem cell potential.
Wong, Genes & development 2007 - GeneRIF: TALE proteins are critical downstream effectors within an essential homeoprotein network that serves a rate-limiting regulatory role in MLL leukemogenesis.
- More
PBX1_HUMAN / P40424 Pre-B-cell leukemia transcription factor 1; Homeobox protein PBX1; Homeobox protein PRL from Homo sapiens (Human) (see 16 papers)
PBX1_MOUSE / P41778 Pre-B-cell leukemia transcription factor 1; Homeobox protein PBX1 from Mus musculus (Mouse) (see 13 papers)
93% identity, 17% coverage
- function: Transcription factor which binds the DNA sequence 5'- TGATTGAT-3' as part of a heterodimer with HOX proteins such as HOXA1, HOXA5, HOXB7 and HOXB8 (PubMed:9191052). Binds to the DNA sequence 5'- TGATTGAC-3' in complex with a nuclear factor which is not a class I HOX protein (PubMed:9191052). Has also been shown to bind the DNA sequence 5'-ATCAATCAA-3' cooperatively with HOXA5, HOXB7, HOXB8, HOXC8 and HOXD4 (PubMed:7791786, PubMed:8327485). Acts as a transcriptional activator of PF4 in complex with MEIS1 (PubMed:12609849). Also activates transcription of SOX3 in complex with MEIS1 by binding to the 5'- TGATTGAC-3' consensus sequence (By similarity). In natural killer cells, binds to the NFIL3 promoter and acts as a transcriptional activator of NFIL3, promoting natural killer cell development (By similarity). Plays a role in the cAMP-dependent regulation of CYP17A1 gene expression via its cAMP-regulatory sequence (CRS1) (By similarity). Probably in complex with MEIS2, involved in transcriptional regulation by KLF4 (PubMed:21746878). Acts as a transcriptional activator of NKX2-5 and a transcriptional repressor of CDKN2B (By similarity). Together with NKX2-5, required for spleen development through a mechanism that involves CDKN2B repression (By similarity).
function: [Isoform PBX1b]: As part of a PDX1:PBX1b:MEIS2B complex in pancreatic acinar cells, is involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element.
subunit: Forms a heterodimer with MEIS1 which binds DNA (PubMed:19799567). The PBX1-MEIS1 heterodimer binds a cAMP-responsive sequence in CYP17 (By similarity). It also binds a consensus region in the SOX3 promoter (PubMed:19799567). PBX1 forms heterotrimers with MEIS1 and a number of HOX proteins including HOXA9, HOXD4, HOXD9 and HOXD10 (By similarity). Forms heterodimers with HOXA1, HOXA5, HOXB7 and HOXB8 which bind the 5'-TGATTGAT-3' consensus sequence (PubMed:9191052). Also forms heterodimers with HOXA5, HOXB7, HOXB8, HOXC8 and HOXD4 which bind the 5'-ATCAATCAA-3' consensus sequence (PubMed:7791786). Interacts with PBXIP1 (PubMed:10825160). Interacts with TLX1 (PubMed:19559479). Interacts with FOXC1 (PubMed:15684392). Interacts with MN1 (PubMed:31839203).
subunit: [Isoform PBX1a]: Interacts with MEIS2 isoform 4, SP1, SP3 and KLF4.
subunit: [Isoform PBX1b]: Part of a PDX1:PBX1b:MEIS2B complex; PBX1b recruits MEIS2B to the complex. - function: Transcription factor which binds the DNA sequence 5'- TGATTGAT-3' as part of a heterodimer with HOX proteins such as HOXA1, HOXA5, HOXB7 and HOXB8 (By similarity). Binds the DNA sequence 5'- TGATTGAC-3' in complex with a nuclear factor which is not a class I HOX protein (By similarity). Has also been shown to bind the DNA sequence 5'-ATCAATCAA-3' cooperatively with HOXA5, HOXB7, HOXB8, HOXC8 and HOXD4 (PubMed:7791786). Acts as a transcriptional activator of PF4 in complex with MEIS1 (By similarity). Also activates transcription of SOX3 in complex with MEIS1 by binding to the 5'-TGATTGAC-3' consensus sequence (PubMed:19799567). In natural killer cells, binds to the NFIL3 promoter and acts as a transcriptional activator of NFIL3, promoting natural killer cell development (PubMed:32190943). Plays a role in the cAMP- dependent regulation of CYP17A1 gene expression via its cAMP-regulatory sequence (CRS1) (PubMed:7913464). Probably in complex with MEIS2, is involved in transcriptional regulation by KLF4 (By similarity). Acts as a transcriptional activator of NKX2-5 and a transcriptional repressor of CDKN2B (PubMed:22560297). Together with NKX2-5, required for spleen development through a mechanism that involves CDKN2B repression (PubMed:22560297).
function: [Isoform PBX1b]: As part of a PDX1:PBX1b:MEIS2B complex in pancreatic acinar cells, is involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element.
function: (Microbial infection) In complex with PREP1, binds to the 5'- TGATTGAC-3' consensus sequence in the U5 region of Moloney murine leukemia virus and promotes viral transcription.
subunit: Forms a heterodimer with MEIS1 which binds DNA (PubMed:19799567, PubMed:9525891). The PBX1-MEIS1 heterodimer binds a cAMP-responsive sequence in CYP17 (PubMed:9525891). It also binds a consensus region in the SOX3 promoter (PubMed:19799567). PBX1 forms heterotrimers with MEIS1 and a number of HOX proteins including HOXA9, HOXD4, HOXD9 and HOXD10 (PubMed:10082572, PubMed:10523646, PubMed:12409300, PubMed:9315626). Forms heterodimers with HOXA1, HOXA5, HOXB7 and HOXB8 which bind the 5'-TGATTGAT-3' consensus sequence (By similarity). Also forms heterodimers with HOXA5, HOXB7, HOXB8, HOXC8 and HOXD4 which bind the 5'-ATCAATCAA-3' consensus sequence (PubMed:7791786). Interacts with PBXIP1 (By similarity). Interacts with TLX1 (By similarity). Interacts with FOXC1 (By similarity). Interacts with MN1 (By similarity).
subunit: [Isoform PBX1a]: Interacts with MEIS2 isoform Meis2D, SP1, SP3 and KLF4.
subunit: [Isoform PBX1b]: Part of a PDX1:PBX1b:MEIS2B complex; PBX1b recruits MEIS2B to the complex.
disruption phenotype: Conditional knockout in hematopoietic cells leads to a reduction in the number of natural killer cell-committed progenitors in bone marrow, decreases the number of natural killer cells in bone marrow and spleen and reduces NFIL3 expression in bone marrow and splenic natural killer cells. - Comprehensive summary: the role of PBX1 in development and cancers.
Liu, Frontiers in cell and developmental biology 2024 - “...in different species to is conserved. We downloaded the PBX1 protein sequences of human (ID: P40424), rat (ID: A0A8I5ZR45), mouse (ID: P41778), and zebrafish (ID: H1A3Y0) from UniProt ( https://www.uniprot.org/ ) and analyzed these sequences using the NCBI Multiple Sequence Alignment Viewer 1.25.1 on the NCBI...”
- Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers
Ershov, International journal of molecular sciences 2023 - “...JUN (P05412), KPNA1 (P52294), MDM2 (Q00987), MEIS2 (O14770), NDFIP2 (Q9NV92), NUP214 (P35658), OPTN (Q96CV9), PBX1 (P40424), PPP2R1A (P30153), PRKACA (P17612), PRKAR1A (P10644), PTPRJ (Q12913), RNF123 (Q5XPI4), SMARCAD1 (Q9H4L7), SPAG5 (Q96R06) and WWP2 (O00308). ijms-24-10190-t004_Table 4 Table 4 Relevant literature data on the known functional characterization of...”
- Identification of potential therapeutic intervening targets by in-silico analysis of nsSNPs in preterm birth-related genes
Azmi, PloS one 2023 - “...NP_001340059 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 4 347 P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 49 PBX homeobox 1PBX1^ NP_001340060, XP_016856885 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 2 347...”
- “...NP_001191892 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 3 420 P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 51 PBX homeobox 1PBX1^ NP_001191890 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 2 347 P40424...”
- The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17.
Chaves-Moreira, Science signaling 2022 - “...+1.27 P53999 SUB1 Activated RNA polymerase II transcriptional coactivator p15 14.4 3 18.9 6.4 +1.90 P40424 PBX1 Pre-B-cell leukemia transcription factor 1 46.6 1 10.3 5.8 +0.78 P18846 ATF1 Cyclic AMP-dependent transcription factor ATF-1 57.6 23 5.8 2.1 +0.03 RNA PROCESSING Q9BQ02 NCL Nucleolin 76.6 11...”
- Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities.
Miyake, American journal of human genetics 2020 - Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis
Tacheny, Nucleic acids research 2012 - “...0 0 0 77.45 3 0 0 75.17 1 Pre-B-cell leukemia transcription factor 1 (PBX1) P40424 N 69.16 6 0 0 70.86 1 179.78 11 0 0 137.86 3 Steroid hormone receptor ERR1 P11474 N 346.44 19 81.45 10 0 0 342.18 35 79.16 8 166.95...”
- Anterior segment alterations and comparative aqueous humor proteomics in the buphthalmic rabbit (an American Ophthalmological Society thesis).
Edward, Transactions of the American Ophthalmological Society 2011 - Comprehensive summary: the role of PBX1 in development and cancers.
Liu, Frontiers in cell and developmental biology 2024 - “...We downloaded the PBX1 protein sequences of human (ID: P40424), rat (ID: A0A8I5ZR45), mouse (ID: P41778), and zebrafish (ID: H1A3Y0) from UniProt ( https://www.uniprot.org/ ) and analyzed these sequences using the NCBI Multiple Sequence Alignment Viewer 1.25.1 on the NCBI website. The analysis results showed that...”
- Transcription factor Sp2 potentiates binding of the TALE homeoproteins Pbx1:Prep1 and the histone-fold domain protein Nf-y to composite genomic sites
Völkel, The Journal of biological chemistry 2018 (secret)
XP_038946720 pre-B-cell leukemia transcription factor 1 isoform X1 from Rattus norvegicus
93% identity, 18% coverage
XP_011507892 pre-B-cell leukemia transcription factor 1 isoform X2 from Homo sapiens
93% identity, 16% coverage
- Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-κB activation.
Jia, Biochimica et biophysica acta. Molecular cell research 2024 (PubMed)- GeneRIF: Mesenchymal stem cells overexpressing PBX1 alleviates haemorrhagic shock-induced kidney damage by inhibiting NF-kappaB activation.
- Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis.
Wang, Molecular cancer research : MCR 2024 (PubMed)- GeneRIF: Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis.
- Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
Roach, Molecular immunology 2024 (PubMed)- GeneRIF: Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
- Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
Wen, Hereditas 2024 - GeneRIF: Extracellular vesicle-derived TP53BP1, CD34, and PBX1 from human peripheral blood serve as potential biomarkers for the assessment and prediction of vascular aging.
- Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression.
Zhang, Functional & integrative genomics 2024 - GeneRIF: Small nucleolar RNA Snora73 promotes psoriasis progression by sponging miR-3074-5p and regulating PBX1 expression.
- PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications.
Kao, Biochimica et biophysica acta. Reviews on cancer 2024 (PubMed)- GeneRIF: PBX1 as a novel master regulator in cancer: Its regulation, molecular biology, and therapeutic applications.
- Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
Choi, Science advances 2024 - GeneRIF: Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
- Whole Exome Sequencing Revealing a Novel PBX1 Gene Variant in a Chinese Family Causing Recurrent Neonatal Death.
Huang, Birth defects research 2024 (PubMed)- GeneRIF: Whole Exome Sequencing Revealing a Novel PBX1 Gene Variant in a Chinese Family Causing Recurrent Neonatal Death.
- More
NP_571522 pre-B-cell leukemia transcription factor 4 from Danio rerio
93% identity, 22% coverage
NP_001340059 pre-B-cell leukemia transcription factor 1 isoform 4 from Homo sapiens
93% identity, 21% coverage
NP_001191892 pre-B-cell leukemia transcription factor 1 isoform 3 from Homo sapiens
93% identity, 18% coverage
NP_032809 pre-B-cell leukemia transcription factor 1 isoform b from Mus musculus
NP_001191890 pre-B-cell leukemia transcription factor 1 isoform 2 from Homo sapiens
NP_001340060 pre-B-cell leukemia transcription factor 1 isoform 2 from Homo sapiens
93% identity, 21% coverage
- Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
Roach, Molecular immunology 2024 (PubMed)- GeneRIF: Regulation of the STAT3 pathway by lupus susceptibility gene Pbx1 in T cells.
- Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
Choi, Science advances 2024 - GeneRIF: Lupus susceptibility gene Pbx1 controls the development, stability, and function of regulatory T cells via Rtkn2 expression.
- Loss of PBX1 function in Leydig cells causes testicular dysgenesis and male sterility.
Wang, Cellular and molecular life sciences : CMLS 2024 - GeneRIF: Loss of PBX1 function in Leydig cells causes testicular dysgenesis and male sterility.
- Overexpression of lipocalin 2 in PBX1-deficient decidual NK cells promotes inflammation at the maternal-fetal interface.
An, American journal of reproductive immunology (New York, N.Y. : 1989) 2023 (PubMed)- GeneRIF: Overexpression of lipocalin 2 in PBX1-deficient decidual NK cells promotes inflammation at the maternal-fetal interface.
- Involvement of Transcriptional Factor Pbx1 in Peripheral B Cell Homeostasis to Constrain Lupus Autoimmunity.
Gu, Arthritis & rheumatology (Hoboken, N.J.) 2023 (PubMed)- GeneRIF: Involvement of Transcriptional Factor Pbx1 in Peripheral B Cell Homeostasis to Constrain Lupus Autoimmunity.
- A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
Losa, Nature communications 2023 - GeneRIF: A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2.
- PBX1-directed stem cell transcriptional program drives tumor progression in myeloproliferative neoplasm.
Muggeo, Stem cell reports 2021 - GeneRIF: PBX1-directed stem cell transcriptional program drives tumor progression in myeloproliferative neoplasm.
- Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells.
Hau, Scientific reports 2021 - GeneRIF: Transcriptional cooperation of PBX1 and PAX6 in adult neural progenitor cells.
- More
- Identification of potential therapeutic intervening targets by in-silico analysis of nsSNPs in preterm birth-related genes
Azmi, PloS one 2023 - “...P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 51 PBX homeobox 1PBX1^ NP_001191890 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 2 347 P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 52 autophagy related 16 like...”
- Identification of potential therapeutic intervening targets by in-silico analysis of nsSNPs in preterm birth-related genes
Azmi, PloS one 2023 - “...P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 49 PBX homeobox 1PBX1^ NP_001340060, XP_016856885 1:164,555,584164,899,296 forward strand 22/11 79,096 4,272 preBcell leukemia transcription factor 1 isoform 2 347 P40424 Ubiquitous expression in endometrium, gall bladder and 22 other tissues 50 PBX homeobox 1PBX1^...”
NP_001277505 pre-B-cell leukemia transcription factor 3 isoform PBX3b from Mus musculus
95% identity, 21% coverage
- Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
Li, Clinical epigenetics 2024 - GeneRIF: Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
- Parallel Pbx-Dependent Pathways Govern the Coalescence and Fate of Motor Columns.
Hanley, Neuron 2016 - GeneRIF: results indicate Pbx genes act in parallel genetic pathways to orchestrate neuronal subtype differentiation, connectivity, and organization. I
- Pbx3 and Meis1 cooperate through multiple mechanisms to support Hox-induced murine leukemia.
Garcia-Cuellar, Haematologica 2015 - GeneRIF: Pbx3 contributes to Hoxa9 leukemogenesis through stabilization of the Meis1 protein.
- PBX3 is an important cofactor of HOXA9 in leukemogenesis.
Li, Blood 2013 - GeneRIF: Collectively, our data suggest that PBX3 is a critical cofactor of HOXA9 in leukemogenesis.
- Characterization of TALE genes expression during the first lineage segregation in mammalian embryos.
Sonnet, Developmental dynamics : an official publication of the American Association of Anatomists 2012 (PubMed)- GeneRIF: Data have demonstrated the presence of Meis, Pbx, and Prep proteins during early lineage segregation in mammals: Meis1, Meis3, Pbx1, Pbx2, Pbx3, and Prep1 in the mouse.
- Pbx3 is required for normal locomotion and dorsal horn development.
Rottkamp, Developmental biology 2008 (PubMed)- GeneRIF: Loss of Pbx3 function thus leads to the incorrect specification of some glutamatergic neurons in the dorsal horn and alters the integration of peripheral sensation into the spinal circuitry regulating locomotion.
- Pbx/Meis deficiencies demonstrate multigenetic origins of congenital heart disease.
Stankunas, Circulation research 2008 - GeneRIF: Reduction or absence of Pbx2 or Pbx3 leads to Pbx1 haploinsufficiency and specific malformations that resemble tetralogy of Fallot, overriding aorta with ventricular septal defect, and bicuspid aortic valves.
- Meis1 is an essential and rate-limiting regulator of MLL leukemia stem cell potential.
Wong, Genes & development 2007 - GeneRIF: TALE proteins are critical downstream effectors within an essential homeoprotein network that serves a rate-limiting regulatory role in MLL leukemogenesis.
- More
XP_038961188 pre-B-cell leukemia transcription factor 3 isoform X2 from Rattus norvegicus
95% identity, 29% coverage
XP_017206849 pre-B-cell leukemia transcription factor 2 isoform X1 from Danio rerio
92% identity, 18% coverage
PBX1_XENLA / Q8QGC4 Pre-B-cell leukemia transcription factor 1; Xpbx1; Homeobox protein pbx1; Pre-B-cell leukemia transcription factor 1b; Xpbx1b from Xenopus laevis (African clawed frog) (see 2 papers)
92% identity, 21% coverage
- function: Acts as a transcriptional activator in complex with isoform 2 of meis1, to induce posterior neural and neural crest gene expression, and thereby specify hindbrain and neural crest cell fate. Binds to a highly conserved region in the promoter of the neural crest gene zic3. Required for the nuclear transport or retention of isoform 2 of meis1.
subunit: Forms a heterodimer with isoform 2 of meis1; the interaction is necessary for neural fate induction.
PBX3_HUMAN / P40426 Pre-B-cell leukemia transcription factor 3; Homeobox protein PBX3 from Homo sapiens (Human) (see paper)
NP_006186 pre-B-cell leukemia transcription factor 3 isoform 1 from Homo sapiens
95% identity, 17% coverage
- function: Transcriptional activator that binds the sequence 5'- ATCAATCAA-3'
subunit: Interacts with PBXIP1. - Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...the PBC-B domain; green, the HD domain Accession numbers are: Pbx1: AAG30941; Pbx2: P40425; Pbx3: P40426; Pbx4: CAC28212; Exd: AAC37182.1 An important feature of TALE proteins is the formation of dimers between MEINOX and PBC proteins, even in the absence of DNA. The domains participating in...”
- Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals
Bürglin, Nucleic acids research 1997 - “...(prl) (M86546); Hs PBX2 (G17) (X59842); Hs PBX3 (X59841, P40426); Mm Pbx1 (L27453); Hs TGIF (X89750); Mm mTGIF (X89749); Mm Meis1 (U33629, U33630); Mm Meis2...”
- Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
Zheng, Biochemical genetics 2024 (PubMed)- GeneRIF: Exosomal circKIAA1797 Regulates Cell Progression and Glycolysis by Targeting miR-4429/PBX3 Pathway in Gastric Cancer.
- PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
Pan, PloS one 2024 - GeneRIF: PBX3 as a biomarker for the early diagnosis and prediction of prognosis of glioma.
- Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
Li, Clinical epigenetics 2024 - GeneRIF: Low expression of miR-182 caused by DNA hypermethylation accelerates acute lymphocyte leukemia development by targeting PBX3 and BCL2: miR-182 promoter methylation is a predictive marker for hypomethylation agents + BCL2 inhibitor venetoclax.
- LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
Xia, Cellular and molecular biology (Noisy-le-Grand, France) 2023 (PubMed)- GeneRIF: LncRNA LINC00885 promotes bladder cancer progression by targeting the miR-98-5p/PBX3 axis.
- Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
Huang, Bioengineered 2022 - GeneRIF: Long non-coding RNA DSCAM-AS1 promotes pancreatic cancer progression via regulating the miR-136-5p/PBX3 axis.
- USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
Wang, International journal of biological sciences 2022 - GeneRIF: USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
- SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
Zhang, Digestive diseases and sciences 2021 (PubMed)- GeneRIF: SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth.
- The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
Li, Acta pharmacologica Sinica 2021 - GeneRIF: The transcription factor PBX3 promotes tumor cell growth through transcriptional suppression of the tumor suppressor p53.
- More
H1A3Y0 PBX homeobox 1 from Taeniopygia guttata
93% identity, 17% coverage
- Comprehensive summary: the role of PBX1 in development and cancers.
Liu, Frontiers in cell and developmental biology 2024 - “...protein sequences of human (ID: P40424), rat (ID: A0A8I5ZR45), mouse (ID: P41778), and zebrafish (ID: H1A3Y0) from UniProt ( https://www.uniprot.org/ ) and analyzed these sequences using the NCBI Multiple Sequence Alignment Viewer 1.25.1 on the NCBI website. The analysis results showed that in humans, rats, mice,...”
1lfuP / P41778 Nmr solution structure of the extended pbx homeodomain bound to DNA (see paper)
92% identity, 89% coverage
XP_017214451 pre-B-cell leukemia homeobox 1a isoform X1 from Danio rerio
91% identity, 16% coverage
NP_079521 pre-B-cell leukemia transcription factor 4 from Homo sapiens
Q9BYU1 Pre-B-cell leukemia transcription factor 4 from Homo sapiens
86% identity, 20% coverage
- Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis.
Song, Biomolecules 2022 - GeneRIF: Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis.
- MEIS1, PREP1, and PBX4 are differentially expressed in acute lymphoblastic leukemia: association of MEIS1 expression with higher proliferation and chemotherapy resistance.
Rosales-Aviña, Journal of experimental & clinical cancer research : CR 2011 - GeneRIF: up-regulation of PREP1 and PBX genes could be implicated in the modulation of the cellular response to chemotherapeutic-induced apoptosis.
- Sex-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels in the Mulao and Han populations.
Yan, Lipids in health and disease 2011 - GeneRIF: Sex (male)-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels is observed both the Mulao and Han ethnic groups.
- Pharmacogenetic analysis of lipid responses to rosuvastatin in Chinese patients.
Hu, Pharmacogenetics and genomics 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Polymorphisms at newly identified lipid-associated loci are associated with blood lipids and cardiovascular disease in an Asian Malay population.
Tai, Journal of lipid research 2009 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
Kathiresan, Nature genetics 2008 - GeneRIF: Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
- MeMo: a web tool for prediction of protein methylation modifications.
Chen, Nucleic acids research 2006 - “...To mimic queries from biologist users, we have randomly submitted to MeMo three proteins, PBX4 (Q9BYU1), Syntaxin 10 (O60499) and Sorting nexin (SNX)-17 (Q15036) from a large-scale experiment to identify the potential methylated proteins ( 20 ), as examples to demonstrate the simplicity and accuracy of...”
- “...radial basis function, exp(gamma*|uv| 2 ). Table 2 The predicted arginine methylation sites of PBX4 (Q9BYU1), Syntaxin 10 (O60499) and Sorting nexin-17 (Q15036) with the methyl-specific antibody epitopes in these protein sequences Methylated proteins Methyl-specific antibody epitope Predicted arginine methylation site PBX4 52-PEKRGRGG-59 55, 57, 63...”
PBX4_MOUSE / Q99NE9 Pre-B-cell leukemia transcription factor 4; Homeobox protein PBX4 from Mus musculus (Mouse) (see paper)
88% identity, 20% coverage
HM20_CAEEL / P41779 Homeobox protein ceh-20 from Caenorhabditis elegans (see 5 papers)
NP_001022555 Homeobox protein ceh-20 from Caenorhabditis elegans
86% identity, 22% coverage
- function: Transcription factor that binds to the 5'-TGATNNAT(G/T)(G/A)- 3' PBC/Hox lineage enhancer region of sem-2 to promote cell fate specification in the postembryonic mesoderm (also known as the M lineage) (PubMed:21307099). Required for the M lineage-specific expression of the transcription factor, mls-2 (PubMed:18316179). Required for asymmetric division of the T hypodermal cell, probably acting via the regulation of asymmetric expression of Meis protein psa- 3 in concert with homeobox protein nob-1 and the Wnt-MAPK pathway (PubMed:16824957). Has a role in the mig-13 pathway to promote the guidance, migration and positioning of Q neuroblasts and their descendants along the anteroposterior body axis and the anterior migration of BDU interneurons (PubMed:15750187). Also required for normal vulval formation (PubMed:15750187). Plays a role in regulating gene expression in dopaminergic neurons, acting in midbody PDE neurons, and acting redundantly with ceh-40 in head neurons (PubMed:23788625). May activate dopamine pathway genes in concert with ETS domain- containing protein ast-1, and homeobox proteins ceh-43 and ceh-40 (PubMed:23788625).
subunit: Interacts with Meis protein psa-3 (PubMed:16824957). Interacts with homeobox protein nob-1 (PubMed:16824957).
disruption phenotype: RNAi-mediated knockdown results in egg laying defects, abnormal migration of QR neuroblast lineage cells and vulval protrusions due to ectopic induction and defective morphogenesis of vulval precursors cells (PubMed:15750187). RNAi-mediated knockdown results in the absence of the transcription factor, mls-2, in the M lineage (PubMed:18316179). - Two Hox cofactors, the Meis/Hth homolog UNC-62 and the Pbx/Exd homolog CEH-20, function together during C. elegans postembryonic mesodermal development.
Jiang, Developmental biology 2009 - GeneRIF: Ceh-20 is genetically required for the promoter activity of unc-62. Unc-62 & ceh-20 have overlapping expression patterns within and outside of the M lineage, & they share physical and regulatory interactions.
- Transcriptional control of Notch signaling by a HOX and a PBX/EXD protein during vulval development in C. elegans.
Takács-Vellai, Developmental biology 2007 (PubMed)- GeneRIF: Transcription factors LIN-39 and CEH-20, which function at the bottom of the RTK/Ras and Wnt pathways in vulval induction, serve as major integration sites in coordinating and transmitting signals to the LIN-12/Notch cascade to regulate vulval cell fates.
- Direct regulation of egl-1 and of programmed cell death by the Hox protein MAB-5 and by CEH-20, a C. elegans homolog of Pbx1.
Liu, Development (Cambridge, England) 2006 (PubMed)- GeneRIF: In the P11 lineage, a complex between MAB-5 and the Pbx homolog CEH-20 directly regulates transcription of the BH3 domain gene egl-1 to initiate programmed cell death.
- Mesodermal expression of the C. elegans HMX homolog mls-2 requires the PBC homolog CEH-20.
Jiang, Mechanisms of development - GeneRIF: mls-2 might be a direct target of CEH-20 in the M lineage and the regulation of CEH-20 on mls-2 is likely Hox-independent
XP_018115010 pre-B-cell leukemia transcription factor 1 isoform X3 from Xenopus laevis
90% identity, 17% coverage
HM40_CAEEL / Q19503 Homeobox protein ceh-40 from Caenorhabditis elegans (see 2 papers)
67% identity, 21% coverage
- function: Plays a role in regulating gene expression in dopaminergic neurons, acting redundantly with homeobox protein ceh-20 in head neurons (PubMed:23788625). May activate dopamine pathway genes in concert with ETS domain-containing protein ast-1, and homeobox proteins ceh-43 and ceh-20 (PubMed:23788625).
disruption phenotype: Worms show no phenotype but, when also lacking ceh-20, incompletely penetrant embryonic lethality is observed.
CBG05292 Protein CBG05292 from Caenorhabditis briggsae
66% identity, 22% coverage
- Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes
Beadell, Genome biology and evolution 2014 - “...Cbr-puf-8 Few germ cells 12 CBG22317 Cbr-nos-2 13 CBG08921 CBG04207 Slow growth of progeny 14 CBG05292 CBG01393 15 CBG16726 CBG05879 16 CBG08527 CBG11569 17 CBG05095 CBG09653 18 CBG10091 CBG13227 19 CBG04372 CBG04373 20 CBG03080 CBG09925 21 CBG20875 CBG14962 22 Cbr-egg-4 Cbr-tpa-1 Injected worms lay only shell-less...”
XP_006509863 pre-B-cell leukemia transcription factor 4 isoform X1 from Mus musculus
88% identity, 14% coverage
CEH60_CAEEL / Q45EK2 Homeobox protein ceh-60 from Caenorhabditis elegans (see 2 papers)
NP_509101 Homeobox protein ceh-60 from Caenorhabditis elegans
54% identity, 19% coverage
- function: Probable transcription regulator which binds to DNA, repressing genes involved in longevity and stress, while activating genes involved in reproduction, such as the vitellogenins (PubMed:30956009, PubMed:31675356). Associates with homeobox unc-62 to regulate gene expression, including repression of genes involved in innate immunity (PubMed:30956009, PubMed:31675356). Required for intestinal expression of vitellogenin genes (PubMed:30956009, PubMed:31675356). Negatively modulates longevity, probably independently of effects on vitellogenesis (PubMed:30956009). Involved in lipid homeostasis, contributing to the reallocation of intestinal lipids to the germline and to the formation of the cuticle (PubMed:30956009, PubMed:31675356). Associates with transcriptional regulator pqm-1 at the daf-16 associated element within the promoters of stress-responsive genes to regulate expression (PubMed:30956009).
subunit: Forms a heterodimer with homeobox unc-62 (PubMed:30956009, PubMed:31675356). Interacts with pqm-1 (PubMed:30956009).
disruption phenotype: RNAi mediated knockdown targeted to the intestine represses expression of vitellogenin genes. - DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans.
Van, PloS one 2020 - GeneRIF: DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans.
XP_018084194 homeobox protein meis3-A isoform X2 from Xenopus laevis
50% identity, 15% coverage
- A hindbrain-repressive Wnt3a/Meis3/Tsh1 circuit promotes neuronal differentiation and coordinates tissue maturation.
Elkouby, Development (Cambridge, England) 2012 (PubMed)- GeneRIF: hindbrain-repressive Wnt3a/Meis3/Tsh1 circuit promotes neuronal differentiation and coordinates tissue maturation
- XMeis3 is necessary for mesodermal Hox gene expression and function.
In, PloS one 2011 - GeneRIF: Synergy between XMeis3 and Hoxd1 in Hoxd1 autoregulation in mesoderm during gastrulation, is shown.
- Xenopus Meis3 protein lies at a nexus downstream to Zic1 and Pax3 proteins, regulating multiple cell-fates during early nervous system development.
Gutkovich, Developmental biology 2010 (PubMed)- GeneRIF: XMeis3 protein knock down also causes a loss of primary neuron and neural crest cell lineages, without altering expression of Zic, Sox or Pax3 genes.
- Xenopus Meis3 protein forms a hindbrain-inducing center by activating FGF/MAP kinase and PCP pathways.
Aamar, Development (Cambridge, England) 2004 (PubMed)- GeneRIF: XMeis3 activates FGF/MAP-kinase signaling, which then modulates the PCP pathway.
- The Meis3 protein and retinoid signaling interact to pattern the Xenopus hindbrain.
Dibner, Developmental biology 2004 (PubMed)- GeneRIF: XMeis3 protein appears crucial for initial hindbrain induction, whereas Retinoic Acid signaling defines the spatial limits of hindbrain gene expression by modifying XMeis3 protein activity
MEI3A_XENLA / Q5U4X3 Homeobox protein meis3-A; XMeis3 from Xenopus laevis (African clawed frog) (see 5 papers)
50% identity, 12% coverage
- function: Caudalizing protein which is required to pattern the anterior/posterior (A/P) axis during central nervous system (CNS) formation. Inhibits anterior neural expression and acts as a transcriptional activator to induce posterior neural gene expression. Maintains a proper A/P balance required for hindbrain formation by activating the FGF/MAPK pathway, which modulates the planar cell polarity (PCP) pathway. Interacts with retinoid signaling during hindbrain patterning.
Q99687 Homeobox protein Meis3 from Homo sapiens
50% identity, 15% coverage
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...P160, and 4EHP are highlighted in green. Accession numbers are: hMeis1: O00470; hMeis2: O14770; hMeis3: Q99687; Hth: NP_476578; hPrep1: NP_004562; hPrep2: CAD01142. Mammalian cells contain four PBX genes (14) that code for six proteins, because of two alternatively spliced isoforms of PBX1 and PBX3. The gene...”
NP_001009813 homeobox protein Meis3 isoform 2 from Homo sapiens
50% identity, 16% coverage
NP_571853 homeobox protein Meis3 from Danio rerio
45% identity, 14% coverage
XP_008196218 homothorax isoform X4 from Tribolium castaneum
47% identity, 13% coverage
MEIS3_MOUSE / P97368 Homeobox protein Meis3; Meis1-related protein 2 from Mus musculus (Mouse) (see paper)
50% identity, 15% coverage
- function: Transcriptional regulator which directly modulates PDPK1 expression, thus promoting survival of pancreatic beta-cells. Also regulates expression of NDFIP1, BNIP3, and CCNG1.
ATEG_00728 uncharacterized protein from Aspergillus terreus NIH2624
47% identity, 18% coverage
- Genome-Wide Identification and Characterization of Homeobox Transcription Factors in Phoma sorghina var. saccharum Causing Sugarcane Twisted Leaf Disease
Bao, International journal of molecular sciences 2024 - “..., Fusarium graminearum FGSG_07097 , Neurospora crassa NCU09556 , Aspergillus nidulans AN2009 , Aspergillus terreus ATEG_00728 , and Aspergillus flavus AFLA_03039 . The amino acid sequences of the homeodomains in these proteins were similar and had identical amino acid residues at the L, P, W, N,...”
NP_476578 homothorax, isoform A from Drosophila melanogaster
47% identity, 12% coverage
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...4EHP are highlighted in green. Accession numbers are: hMeis1: O00470; hMeis2: O14770; hMeis3: Q99687; Hth: NP_476578; hPrep1: NP_004562; hPrep2: CAD01142. Mammalian cells contain four PBX genes (14) that code for six proteins, because of two alternatively spliced isoforms of PBX1 and PBX3. The gene products are...”
HTH_DROME / O46339 Homeobox protein homothorax; Homeobox protein dorsotonals from Drosophila melanogaster (Fruit fly) (see 5 papers)
NP_476576 homothorax, isoform C from Drosophila melanogaster
47% identity, 12% coverage
- function: All isoforms are required for patterning of the embryonic cuticle. Acts with exd to delimit the eye field and prevent inappropriate eye development. Isoforms that carry the homeodomain are required for proper localization of chordotonal organs within the peripheral nervous system and antennal identity; required to activate antennal-specific genes, such as sal and to repress the leg-like expression of dac. Necessary for the nuclear localization of the essential HOX cofactor, extradenticle (exd). Both necessary and sufficient for inner photoreceptors to adopt the polarization-sensitive 'dorsal rim area' (DRA) of the eye fate instead of the color-sensitive default state. This occurs by increasing rhabdomere size and uncoupling R7-R8 communication to allow both cells to express the same opsin rather than different ones as required for color vision.
subunit: Interacts with exd; required for nuclear translocation of exd.
disruption phenotype: Severe head defects, including a failure of head involution and transformation of the thoracic and abdominal segments into a more posterior identity. - Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins
Kribelbauer, Molecular cell 2020 - “...in ( Slattery, 2011 ). Briefly, PET-expression vectors containing coding regions for full-length hth (Uniprot-ID: O46339), exd (Uniprot-ID: P40427), dfd (Uniprot-ID: P07548) and Hth HM-domain (amino acids 1242; (Uniprot-ID: O46339) with hexa-histidine tags (except for Exd, which was co-purified with full-length Hth or HM-domain-only Hth) were...”
- Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax.
Rader, Developmental cell 2023 - GeneRIF: Combined inactivation of RB and Hippo converts differentiating Drosophila photoreceptors into eye progenitor cells through derepression of homothorax.
- Homothorax controls a binary Rhodopsin switch in Drosophila ocelli.
Mishra, PLoS genetics 2021 - GeneRIF: Homothorax controls a binary Rhodopsin switch in Drosophila ocelli.
- Nuclear receptors connect progenitor transcription factors to cell cycle control.
Neto, Scientific reports 2017 - GeneRIF: Rather than directly regulating cell cycle genes, hth and tsh control cell proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway.
- Nuclear microenvironments modulate transcription from low-affinity enhancers.
Tsai, eLife 2017 - GeneRIF: The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency.
- Increased avidity for Dpp/BMP2 maintains the proliferation of progenitors-like cells in the Drosophila eye.
Neto, Developmental biology 2016 (PubMed)- GeneRIF: Hth+Tsh-induced tissue overgrowth requires the BMP2 Dpp and the abnormal hyperactivation of its pathway. Rather than using autocrine Dpp expression, Hth+Tsh cells increase their avidity for Dpp, produced locally, by upregulating extracellular matrix components.
- The retinal determination gene Dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex.
Brás-Pereira, Development (Cambridge, England) 2015 (PubMed)- GeneRIF: The retinal determination gene Dachshund restricts cell proliferation by limiting the activity of the Homothorax-Yorkie complex
- The TALE transcription factor homothorax functions to assemble heterochromatin during Drosophila embryogenesis.
Zaballos, PloS one 2015 - GeneRIF: the satellite repeats get transcribed in wild type embryos and that this transcription depends on the presence of Hth, which binds to them as well as to the ribosomal DNA region.
- Homothorax and Extradenticle alter the transcription factor network in Drosophila ommatidia at the dorsal rim of the retina.
Wernet, Development (Cambridge, England) 2014 - GeneRIF: Hth functions together with its co-factor Extradenticle to repress the R8-specific factor Senseless in dorsal rim area R8 cells, allowing expression of an ultraviolet-sensitive R7 Rhodopsin.
- More
NP_571968 homeobox protein Meis1b from Danio rerio
48% identity, 14% coverage
- Hoxa9/meis1-transgenic zebrafish develops acute myeloid leukaemia-like disease with rapid onset and high penetrance.
Wang, Open biology 2022 - GeneRIF: Hoxa9/meis1-transgenic zebrafish develops acute myeloid leukaemia-like disease with rapid onset and high penetrance.
- Meis1, Hi1α, and GATA1 are integrated into a hierarchical regulatory network to mediate primitive erythropoiesis.
Chung, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021 (PubMed)- GeneRIF: Meis1, Hi1alpha, and GATA1 are integrated into a hierarchical regulatory network to mediate primitive erythropoiesis.
- MiR-144 regulates hematopoiesis and vascular development by targeting meis1 during zebrafish development.
Su, The international journal of biochemistry & cell biology 2014 (PubMed)- GeneRIF: Data indicate that MiR-144 regulates primitive hematopoiesis through repression of meis1 during embryogenesis.
- The role of meis1 in primitive and definitive hematopoiesis during zebrafish development.
Cvejic, Haematologica 2011 - GeneRIF: Loss of meis1 is associated with impaired hematopoiesis as well as vascular development.
- The Hox cofactors Meis1 and Pbx act upstream of gata1 to regulate primitive hematopoiesis.
Pillay, Developmental biology 2010 (PubMed)- GeneRIF: The Hox cofactor Meis1 acts upstream of gata1 to regulate primitive hematopoiesis.
- Meis1 specifies positional information in the retina and tectum to organize the zebrafish visual system.
Erickson, Neural development 2010 - GeneRIF: This study demonistrated that Meis1 plays an important role in establishing the retinotectal map and organizing the visual system in zebrafish.
- A functional interaction between Irx and Meis patterns the anterior hindbrain and activates krox20 expression in rhombomere 3.
Stedman, Developmental biology 2009 (PubMed)- GeneRIF: Data show that Irx7 and Irx1b are required for the proper formation and specification of rhombomeres 1 to 4, and that Irx7 functionally interacts with Meis1.1 to activate the expression of anterior hindbrain markers, such as krox20.
- meis1 regulates cyclin D1 and c-myc expression, and controls the proliferation of the multipotent cells in the early developing zebrafish eye.
Bessa, Development (Cambridge, England) 2008 (PubMed)- GeneRIF: Results implicate meis1 as a positive cell cycle regulator in early retinal cells, and provide evidence of an evolutionary conserved function for Hth/Meis genes in the maintenance of the proliferative, multipotent cell state during early eye development.
- More
AFUA_4G10110, Afu4g10110 homeobox transcription factor, putative from Aspergillus fumigatus Af293
47% identity, 21% coverage
- The Influence of Aspergillus fumigatus Fatty Acid Oxygenases PpoA and PpoC on Caspofungin Susceptibility
Delbaje, Journal of fungi (Basel, Switzerland) 2024 - “...proteins), such as with AFUA_3G08010 (encoding a C 2 H 2 transcription factor Ace1) and AFUA_4G10110 (encoding HtfA, a homeobox domain-containing protein); and (v) iron metabolism, such as with AFUA_3G03390, AFUA_3G03400, and AFUA_1G17190 (encoding SidJ, SidF, and SidI, respectively, which are important for siderophore biosynthesis) (...”
- “...concentrations of 0.25 g/mL and 8.0 g/mL ( Figure 4 a,b). In contrast, AFUA_2G05310 and AFUA_4G10110 were more resistant to only 0.25 g/mL of CAS, and AFUA_4G09710 was only more resistant to CAS 8.0 g/mL ( Figure 4 a,b). We have identified that ppsA ( ppsA...”
- Potential Antifungal Targets for Aspergillus sp. from the Calcineurin and Heat Shock Protein Pathways
Ancuceanu, International journal of molecular sciences 2022 - “...H 2 transcription factor encoded by Afu8g05010 ), htfA (a C6 transcription factor encoded by Afu4g10110 ), nosA (encoded by Afu4g09710 ), and ctfA (a C6 transcriptor factor encoded by Afu1g17460 ) [ 92 ]. A fumigatus strains with deletions of the genes encoding these transcription...”
- The Aspergillus fumigatus CrzA Transcription Factor Activates Chitin Synthase Gene Expression during the Caspofungin Paradoxical Effect
Ries, mBio 2017 - “...the chitin synthase-encoding genes upon caspofungin exposure. Previously, four TFs encoded by the genes htfA (Afu4g10110), zfpA (Afu8g05010), zfpB (Afu1g10230), and zipD (Afu2g03280) were found to be upregulated in the presence of calcium ( 27 , 28 ). Deletion of only zipD resulted in a reduced...”
- A Plastic Vegetative Growth Threshold Governs Reproductive Capacity in Aspergillus nidulans
Noble, Genetics 2016 - “...al. 2012). The A. fumigatus ahpA ortholog, htfA (Afu4g10110), is expressed at higher levels, particularly during early growth, in a calAD (Afu5g09360)...”
- RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus
O'Keeffe, BMC genomics 2014 - “...0.990 2.982 0.001 AFUA_4G02930 - 0.450 0.796 1.971 0.001 AFUA_3G10120 - 0.819 0.488 1.669 0.003 AFUA_4G10110 htfA 0.105 0.986 1.565 0.012 AFUA_1G10080 zafA 0.434 0.843 1.535 0.001 AFUA_1G01240 - 0.561 0.770 1.702 0.025 AFUA_1G14945 - 0.839 0.505 1.754 0.026 AFUA_2G04262 - 1.644 0.012 0.759 0.171 AFUA_2G11180...”
- The predicted G-protein-coupled receptor GPR-1 is required for female sexual development in the multicellular fungus Neurospora crassa
Krystofova, Eukaryotic cell 2006 - “...F. graminearum (FG; FG05475.1), A. fumigatus (AF; Afu4g10110), A. nidulans (AN; AN2020.2), and C. albicans (CA; CaJ7.0235) and previously characterized...”
NP_034919 homeobox protein Meis1 isoform A from Mus musculus
49% identity, 11% coverage
- A patient-enriched MEIS1 coding variant causes a restless legs syndrome-like phenotype in mice.
Leu, Sleep 2024 - GeneRIF: A patient-enriched MEIS1 coding variant causes a restless legs syndrome-like phenotype in mice.
- Meis1 Targets Protein Tyrosine Phosphatase Receptor J in Fibroblast to Retard Chronic Kidney Disease Progression.
Bai, Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2024 - GeneRIF: Meis1 Targets Protein Tyrosine Phosphatase Receptor J in Fibroblast to Retard Chronic Kidney Disease Progression.
- Npm1 haploinsufficiency in collaboration with MEIS1 is sufficient to induce AML in mice.
Muranyi, Blood advances 2023 - GeneRIF: Npm1 haploinsufficiency in collaboration with MEIS1 is sufficient to induce AML in mice.
- A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML.
Lieske, Leukemia 2023 - GeneRIF: A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML.
- Meis1 plays roles in cortical development through regulation of cellular proliferative capacity in the embryonic cerebrum.
Isogai, Biomedical research (Tokyo, Japan) 2022 (PubMed)- GeneRIF: Meis1 plays roles in cortical development through regulation of cellular proliferative capacity in the embryonic cerebrum.
- Transcription factor Meis1 act as a new regulator of ischemic arrhythmias in mice.
Liu, Journal of advanced research 2022 - GeneRIF: Transcription factor Meis1 act as a new regulator of ischemic arrhythmias in mice.
- Homeobox transcription factor Meis1 is crucial to Sertoli cell mediated regulation of male fertility.
Sarkar, Andrology 2021 (PubMed)- GeneRIF: Homeobox transcription factor Meis1 is crucial to Sertoli cell mediated regulation of male fertility.
- Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid.
López-Delgado, Development (Cambridge, England) 2021 (PubMed)- GeneRIF: Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid.
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Q3TYM2 Meis homeobox 2 from Mus musculus
49% identity, 13% coverage
- The neuronal transcription factor MEIS2 is a calpain-2 protease target.
Müller, Journal of cell science 2024 - “...sites Computer-based prediction of the calpain cleavage sites in murine MEIS2 (isoform 2; UniProt identifier: Q3TYM2) was performed using the open-source software GPS-CCD (group-based prediction system-calpain cleavage detector; http://ccd.biocuckoo.org/ ; Liu et al., 2011 ). Prediction of the PEST-sequence in MEIS2 was done with the PESTfind...”
XP_015133525 homeobox protein Meis1 isoform X1 from Gallus gallus
49% identity, 11% coverage
MEIS2_MOUSE / P97367 Homeobox protein Meis2; Meis1-related protein 1 from Mus musculus (Mouse) (see 7 papers)
49% identity, 11% coverage
- function: Involved in transcriptional regulation. Binds to HOX or PBX proteins to form dimers, or to a DNA-bound dimer of PBX and HOX proteins and thought to have a role in stabilization of the homeoprotein-DNA complex. Isoform Meis2B is required for the activity of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element; MEIS2 is not involved in complex DNA-binding. Probably in complex with PBX1, is involved in transcriptional regulation by KLF4. Isoforms Meis2B and Meis2D can bind to a EPHA8 promoter sequence containing the DNA motif 5'-CGGTCA-3'; in cooperation with a PBX protein (such as PBX2) is proposed to be involved in the transcriptional activation of EPHA8 in the developing midbrain. May be involved in regulation of myeloid differentiation. Can bind to the DNA sequence 5'-TGACAG-3'in the activator ACT sequence of the D(1A) dopamine receptor (DRD1) promoter and activate DRD1 transcription.
subunit: Monomer and homodimer. Heterodimer with HOXB13 (By similarity). Isoform Meis2A interacts with TLX1. Isoform Meis2B interacts with HOXA13 and PBX1 isoform PBX1b. Isoform Meis2D interacts with SP1, SP3 and KLF4. Isoform Meis2D interacts with PBX1 isoform PBX1a; the interaction partially relieves MEIS2 autoinhibition. Isoform Meis2B is part of a PDX1:PBX1b:MEIS2b complex; Meis2B is recruited by PBX1b and can be replaced by isoform Meis2D in a small fraction of complexes. Can form trimeric complexes including HOXB8 and PBX2 or PBX3.
XP_063129699 homeobox protein Meis1 isoform X3 from Rattus norvegicus
49% identity, 11% coverage
XP_042101912 homeobox protein Meis1 isoform X2 from Ovis aries
49% identity, 11% coverage
- Down-regulation of MEIS1 promotes the maturation of oxidative phosphorylation in perinatal cardiomyocytes.
Lindgren, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019 - GeneRIF: Cardiomyocyte respiratory capacity increased with age along with decreased expression of MEIS1. MEIS1 suppression with siRNA increased maximal O2 consumption in fetal cells, not postnatal ones. Mitochondrial activity increased and glycolytic genes expression decreased when MEIS1 expression was suppressed. MEIS1 is a key regulator of cardiomyocyte metabolism. Downregulation underlies switching to oxidative metabolism.
XP_005662564 homeobox protein Meis1 isoform X4 from Sus scrofa
49% identity, 11% coverage
NP_034955 homeobox protein Meis2 isoform 2 from Mus musculus
49% identity, 11% coverage
- The neuronal transcription factor MEIS2 is a calpain-2 protease target.
Müller, Journal of cell science 2024 - GeneRIF: The neuronal transcription factor MEIS2 is a calpain-2 protease target.
- Touch receptor end-organ innervation and function require sensory neuron expression of the transcription factor Meis2.
Desiderio, eLife 2024 - GeneRIF: Touch receptor end-organ innervation and function require sensory neuron expression of the transcription factor Meis2.
- Dlx1/2-dependent expression of Meis2 promotes neuronal fate determination in the mammalian striatum.
Su, Development (Cambridge, England) 2022 - GeneRIF: Dlx1/2-dependent expression of Meis2 promotes neuronal fate determination in the mammalian striatum.
- The autism-associated Meis2 gene is necessary for cardiac baroreflex regulation in mice.
Roussel, Scientific reports 2022 - GeneRIF: The autism-associated Meis2 gene is necessary for cardiac baroreflex regulation in mice.
- Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid.
López-Delgado, Development (Cambridge, England) 2021 (PubMed)- GeneRIF: Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid.
- Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors.
Delgado, Nature communications 2021 - GeneRIF: Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors.
- The transcriptional regulator MEIS2 sets up the ground state for palatal osteogenesis in mice.
Wang, The Journal of biological chemistry 2020 - GeneRIF: The transcriptional regulator MEIS2 sets up the ground state for palatal osteogenesis in mice.
- Neural crest cells require Meis2 for patterning the mandibular arch via the Sonic hedgehog pathway.
Fabik, Biology open 2020 - GeneRIF: Neural crest cells require Meis2 for patterning the mandibular arch via the Sonic hedgehog pathway.
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MEIS2_HUMAN / O14770 Homeobox protein Meis2; Meis1-related protein 1 from Homo sapiens (Human) (see 10 papers)
49% identity, 11% coverage
- function: Involved in transcriptional regulation. Binds to HOX or PBX proteins to form dimers, or to a DNA-bound dimer of PBX and HOX proteins and thought to have a role in stabilization of the homeoprotein-DNA complex. Isoform 3 is required for the activity of a PDX1:PBX1b:MEIS2b complex in pancreatic acinar cells involved in the transcriptional activation of the ELA1 enhancer; the complex binds to the enhancer B element and cooperates with the transcription factor 1 complex (PTF1) bound to the enhancer A element; MEIS2 is not involved in complex DNA-binding. Probably in complex with PBX1, is involved in transcriptional regulation by KLF4. Isoform 3 and isoform 4 can bind to a EPHA8 promoter sequence containing the DNA motif 5'-CGGTCA-3'; in cooperation with a PBX protein (such as PBX2) is proposed to be involved in the transcriptional activation of EPHA8 in the developing midbrain. May be involved in regulation of myeloid differentiation. Can bind to the DNA sequence 5'-TGACAG-3'in the activator ACT sequence of the D(1A) dopamine receptor (DRD1) promoter and activate DRD1 transcription; isoform 5 cannot activate DRD1 transcription.
subunit: Monomer and homodimer (PubMed:26550823). Heterodimer with HOXB13 (Ref.16). Isoform 2 interacts with TLX1. Isoform 3 interacts with HOXA13 and PBX1 isoform PBX1b. Isoform 4 interacts with SP1, SP3 and KLF4. Isoform 4 and isoform 5 interact with PBX1 isoform PBX1a; the interaction partially relieves MEIS2 autoinhibition. Isoform 3 also known as MEIS2b is part of a PDX1:PBX1b:Meis2B complex; Meis2B is recruited by PBX1b and can be replaced by isoform 4 in a small fraction of complexes. Can form trimeric complexes including HOXB8 and PBX2 or PBX3. - Uncharacterized Proteins CxORFx: Subinteractome Analysis and Prognostic Significance in Cancers
Ershov, International journal of molecular sciences 2023 - “...EZR (P15311), FBXW8 (Q8N3Y1), GAPDHS (O14556), GPR161 (Q8N6U8), JUN (P05412), KPNA1 (P52294), MDM2 (Q00987), MEIS2 (O14770), NDFIP2 (Q9NV92), NUP214 (P35658), OPTN (Q96CV9), PBX1 (P40424), PPP2R1A (P30153), PRKACA (P17612), PRKAR1A (P10644), PTPRJ (Q12913), RNF123 (Q5XPI4), SMARCAD1 (Q9H4L7), SPAG5 (Q96R06) and WWP2 (O00308). ijms-24-10190-t004_Table 4 Table 4 Relevant...”
- The perinuclear region concentrates disordered proteins with predicted phase separation distributed in a 3D network of cytoskeletal filaments and organelles.
do, Biochimica et biophysica acta. Molecular cell research 2022 - “...O75112-6 Isoform 6 of LIM domain-binding protein 3 65.72 70.30 (protein binding) 0.1 2.53 58 O14770 Homeobox protein Meis2 65.62 0.8 3.58 59 Q13137 Calcium-binding and coiled-coil domain-containing protein 2 65.47 0.3 1.86 60 O94972 E3 ubiquitin-protein ligase TRIM37 65.46 0.5 1.65 61 Q9Y605 MORF4 family-associated...”
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...for Pbx1, P160, and 4EHP are highlighted in green. Accession numbers are: hMeis1: O00470; hMeis2: O14770; hMeis3: Q99687; Hth: NP_476578; hPrep1: NP_004562; hPrep2: CAD01142. Mammalian cells contain four PBX genes (14) that code for six proteins, because of two alternatively spliced isoforms of PBX1 and PBX3....”
NP_002390 homeobox protein Meis2 isoform f from Homo sapiens
49% identity, 13% coverage
- LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-κB pathway by sponging miR-576-5p.
Li, The American journal of the medical sciences 2024 (PubMed)- GeneRIF: LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-kappaB pathway by sponging miR-576-5p.
- Cellular Ligand-Receptor Perturbations Unravel MEIS2 as a Key Factor for the Aggressive Progression and Prognosis in Stage II/III Colorectal Cancer.
Xu, Journal of proteome research 2024 (PubMed)- GeneRIF: Cellular Ligand-Receptor Perturbations Unravel MEIS2 as a Key Factor for the Aggressive Progression and Prognosis in Stage II/III Colorectal Cancer.
- Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study.
Arunachalam, Genome medicine 2024 - GeneRIF: Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study.
- MEIS2 suppresses breast cancer development by downregulating IL10.
Xiao, Cancer reports (Hoboken, N.J.) 2024 - GeneRIF: MEIS2 suppresses breast cancer development by downregulating IL10.
- CircDHRS3 inhibits prostate cancer cell proliferation and metastasis through the circDHRS3/miR-421/MEIS2 axis.
Dai, Epigenetics 2023 - GeneRIF: CircDHRS3 inhibits prostate cancer cell proliferation and metastasis through the circDHRS3/miR-421/MEIS2 axis.
- IGF2BP2 promotes the progression of ovarian endometriosis by regulating m6A-modified MEIS2 and GATA6.
Zhao, The international journal of biochemistry & cell biology 2022 (PubMed)- GeneRIF: IGF2BP2 promotes the progression of ovarian endometriosis by regulating m6A-modified MEIS2 and GATA6.
- MEIS2 sequence variant in a child with intellectual disability and cardiac defects: Expansion of the phenotypic spectrum and documentation of low-level mosaicism in an unaffected parent.
Su, American journal of medical genetics. Part A 2021 (PubMed)- GeneRIF: MEIS2 sequence variant in a child with intellectual disability and cardiac defects: Expansion of the phenotypic spectrum and documentation of low-level mosaicism in an unaffected parent.
- Intellectual disability associated with craniofacial dysmorphism, cleft palate, and congenital heart defect due to a de novo MEIS2 mutation: A clinical longitudinal study.
Gangfuß, American journal of medical genetics. Part A 2021 (PubMed)- GeneRIF: Intellectual disability associated with craniofacial dysmorphism, cleft palate, and congenital heart defect due to a de novo MEIS2 mutation: A clinical longitudinal study.
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4xrmB / O14770 Homodimer of tale type homeobox transcription factor meis1 complexes with specific DNA (see paper)
49% identity, 69% coverage
MEIS1_XENLA / P79937 Homeobox protein Meis1; XMeis1 from Xenopus laevis (African clawed frog) (see 3 papers)
48% identity, 15% coverage
- function: Induces expression of a number of neural crest marker genes as part of a heterodimer with isoform b of pbx1, to specify neural crest cell fate. Binds to a highly conserved region in the promoter of the neural crest marker gene zic3.
subunit: Interacts with pbx1 isoform b.
MEIS1_MOUSE / Q60954 Homeobox protein Meis1; Myeloid ecotropic viral integration site 1 from Mus musculus (Mouse) (see 8 papers)
49% identity, 13% coverage
- function: Acts as a transcriptional regulator of PAX6. Also acts as a transcriptional activator of PF4 in complex with PBX1 or PBX2. Required for hematopoiesis, megakaryocyte lineage development and vascular patterning. May function as a cofactor for HOXA7 and HOXA9 in the induction of myeloid leukemias.
subunit: Interacts with the N-terminal region of PBX1 to form a heterodimer which binds DNA including a cAMP-responsive sequence in CYP17. Also forms heterodimers with PBX2. Forms heterotrimers with PBX1 or PBX2 and a number of HOX proteins including HOXA9, HOXD4 and HOXD9 where it acts as a non-DNA-binding partner. Also forms heterotrimers with PBX1 and HOX proteins including HOXD9 and HOXD10 where PBX1 is the non-DNA-binding partner. Heterodimer with DLX3. Heterodimer with HOXB13 (By similarity).
disruption phenotype: Mice die between embryonic days 11.5 and 14.5, showing internal hemorrhage, liver hypoplasia and anemia.
MEIS1_HUMAN / O00470 Homeobox protein Meis1 from Homo sapiens (Human) (see 4 papers)
49% identity, 13% coverage
- function: Acts as a transcriptional regulator of PAX6. Acts as a transcriptional activator of PF4 in complex with PBX1 or PBX2. Required for hematopoiesis, megakaryocyte lineage development and vascular patterning. May function as a cofactor for HOXA7 and HOXA9 in the induction of myeloid leukemias.
subunit: Interacts with the N-terminal region of PBX1 to form a heterodimer which binds DNA including a cAMP-responsive sequence in CYP17. Also forms heterodimers with PBX2. Forms heterotrimers with PBX1 or PBX2 and a number of HOX proteins including HOXA9, HOXD4 and HOXD9 where it acts as a non-DNA-binding partner. Also forms heterotrimers with PBX1 and HOX proteins including HOXD9 and HOXD10 where PBX1 is the non-DNA-binding partner. Heterodimer with DLX3 (PubMed:26550823). Heterodimer with HOXB13 (PubMed:28473536). - Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities.
Miyake, American journal of human genetics 2020 - Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders
Tahira, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2019 - “...4088 SMAD3 N Y P84022, Q9P0T0 MH1 hsa_V$SMAD3_Q6 Cell cycle 4211 MEIS1 Y N F5GYS8, O00470 Homeobox hsa_TGACAGNY_V$MEIS1_01, hsa_V$MEIS1_01, hsa_V$MEIS1AHOXA9_01 Crucial for normal development 4609 MYC N Y P01106 bHLH hsa_V$MYCMAX_01, hsa_V$MYCMAX_02, has_V$MYCMAX_03 Cell cycle 5080 PAX6 Y N F1T0F8, P26367, Q66SS1 PAX hsa_V$PAX6_01 Neural development,...”
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...binding sequences for Pbx1, P160, and 4EHP are highlighted in green. Accession numbers are: hMeis1: O00470; hMeis2: O14770; hMeis3: Q99687; Hth: NP_476578; hPrep1: NP_004562; hPrep2: CAD01142. Mammalian cells contain four PBX genes (14) that code for six proteins, because of two alternatively spliced isoforms of PBX1...”
- Unbiased proteomic analysis of proteins interacting with the HIV-1 5'LTR sequence: role of the transcription factor Meis
Tacheny, Nucleic acids research 2012 - “...238.31 12 25.7 1 0 0 265.99 22 72.73 5 256.22 8 Homeobox protein Meis O00470 N 0 0 0 0 0 0 77.45 3 0 0 75.17 1 Pre-B-cell leukemia transcription factor 1 (PBX1) P40424 N 69.16 6 0 0 70.86 1 179.78 11 0...”
F2DV82 Predicted protein from Hordeum vulgare subsp. vulgare
46% identity, 9% coverage
- Identification of the Genetic Basis of Response to De-Acclimation in Winter Barley
Wójcik-Jagła, International journal of molecular sciences 2021 - “...A0A287PXC8 N/A Unknown function protein anthranilate phosphoribosyltransferase, chloroplastic [ Aegilops tauschii subsp. tauschii ] HORVU4HR1G084590 F2DV82 N/A Predicted protein homeobox protein BEL1 homolog [ Aegilops tauschii subsp. tauschii ] HORVU4HR1G085250 A0A287PY55 N/A Unknown function protein tonoplast intrinsic protein [ Hordeum vulgare subsp. vulgare ] HORVU5HR1G000640 A0A287Q624...”
YGL096W Homeodomain-containing transcription factor; SBF regulated target gene that in turn regulates expression of genes involved in G1/S phase events such as bud site selection, bud emergence and cell cycle progression; similarity to Cup9p from Saccharomyces cerevisiae
42% identity, 26% coverage
- A New Method, "Reverse Yeast Two-Hybrid Array" (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5
Lev, Genetics 2017 - “...YLR405W YOR076C Stress response YNR074C YIL111W YBR159W YER118C YGL096W YDR346C Others YLR023C YDR393W RNH70 DUS4 SKI7 AIF1 COX5B IFA38 SHO1 TOS8 Description...”
- “...YJR135W-A YGR276C YLR023C YBR157C YKR056W YOR357C YPR062W YGL096W YDR532C YBR101C YIL111W YBR223C YBR010W YLR361C YDR503C YMR284W YDR346C YDR219C YHR134W...”
- Dynamic large-scale chromosomal rearrangements fuel rapid adaptation in yeast populations
Chang, PLoS genetics 2013 - “...the novel 650-kb chromosome is a fusion product of a small chromosome 7 fragment (between YGL096W and YGL200C ), a large chromosome 8 fragment (between YHL050C and YHR145C ) and the telomere of chromosome 8 (between YHR210C to YHR217C ) ( Figure 2 ). We also...”
- “...and YHL008C to YHR219W ) while the 650-kb chromosome contained a chromosome 7 fragment (between YGL096W and YGL200C ) and a chromosome 8 fragment (between YHL050C and YHR144C ). The 550-kb fragment is a wild type copy of chromosome 8. The shaded areas are the fragments...”
- A highly redundant gene network controls assembly of the outer spore wall in S. cerevisiae
Lin, PLoS genetics 2013 - “...protein YER182w FMP10 mitochondrial protein YFR023w PES4 RNA binding motif YFR039c OSW7 Fly signal peptide YGL096w TOS8 putative transcription factor YGL144c ROG1 putative lipase YHR153c SPO16 synaptonemal complex assembly YIR013c GAT4 putative transcription factor YJL037w YJL037w IRC18 / OSW6 Fly paralog of OSW4 YJL038c LOH1 /...”
- The checkpoint transcriptional response: make sure to turn it off once you are satisfied
Smolka, Cell cycle (Georgetown, Tex.) 2012 - “...YER112W LSM4 RNA processing - not observed 15 YGL096W TOS8 Putative transcription factor - vegetative growth: decreased rate 16 YGL179C TOS3 Kinase: activates...”
- Information processing in the transcriptional regulatory network of yeast: functional robustness
Emmert-Streib, BMC systems biology 2009 - “...other genes. gene d out d in D k essential YML027W 314 2 26.8 N YGL096W 248 0 97.4 N YDL056W 129 0 149.8 Y YHR206W 128 0 27.8 N First column: gene name. Second column: out-degree. Third column: in-degree. Fourth column: D k . Fifth...”
- The predicted G-protein-coupled receptor GPR-1 is required for female sexual development in the multicellular fungus Neurospora crassa
Krystofova, Eukaryotic cell 2006 - “...Pth12p (MG; DQ060925.1), S. cerevisiae Tos8p (SCTos8; YGL096W) and Cup9p (SCCup9; YPL177C), and human PKNOX1 (HS; accession number AAC51243). Boxshade was...”
- SUT1-promoted sterol uptake involves the ABC transporter Aus1 and the mannoprotein Dan1 whose synergistic action is sufficient for this process
Alimardani, The Biochemical journal 2004 - “...YBR238c Transcription and translation YOR032c * YJR066w YGL096w YKL043w YJR047c * Stress response YKL026c YML058w-a Metabolism YHR033w YGR286c YJL088w YGR180c *...”
- Disruption and phenotypic analysis of six open reading frames from the left arm of Saccharomyces cerevisiae chromosome VII
Lillo, Yeast (Chichester, England) 2000 (PubMed)- “...The other four ORFs (YGL101w, YGL099w, YGL098w and YGL096w) code for proteins of unknown function, although the protein encoded by YGL101w has a strong...”
- “...arm of chromosome VII (YGL101w, YGL100w, YGL099w, YGL098w, YGL096w and YGL094c). These ORFs were previously sequenced as part of the cosmid pEGH427 (Rieger et...”
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IRX_CAEEL / Q93348 Putative iroquois-class homeodomain protein irx-1 from Caenorhabditis elegans (see 3 papers)
NP_492533 Putative iroquois-class homeodomain protein irx-1 from Caenorhabditis elegans
47% identity, 15% coverage
- function: Transcription factor (By similarity). Required for D-type inhibitory GABAergic motor neuron synaptic remodeling, acting via degenerin unc-8-dependent and -independent mechanisms (PubMed:22031882, PubMed:34045310). Regulates expression of genes involved in synaptic remodeling, including negative modulation of immunoglobulin domain- containing protein oig-1 and positive modulation of unc-8 (PubMed:22031882, PubMed:26387713, PubMed:34045310).
disruption phenotype: RNAi-mediated knockdown delays the first appearance of synaptobrevin snb-1 at puncta, probably corresponding to neuromuscular junctions, in dorsal D (DD) motor neurons in L1 stage larvae by about 4 hours (PubMed:22031882). Causes ectopic expression of immunoglobulin domain-containing protein oig-1 in late larval and adult DD motor neurons (PubMed:26387713). Causes a significant increase in expression of snb-1 at puncta in the ventral nerve cord on an unc-55 mutant background (PubMed:22031882). Ectopically expressed in ventral D (VD) motor neurons on an unc-55 mutant background (PubMed:22031882). Restores normal backward locomotion on an unc-55 mutant background (PubMed:22031882). Knockdown targeted to GABAergic neurons restores normal synaptic function in the ventral muscles on an unc-55 mutant background (PubMed:22031882). Restores expression of oig-1 to VD motor neurons on an unc-55 mutant background (PubMed:26387713). Targeted RNAi-mediated knockdown abolishes expression of unc-8 in DD neurons (PubMed:34045310). - A transcriptional program promotes remodeling of GABAergic synapses in Caenorhabditis elegans.
Petersen, The Journal of neuroscience : the official journal of the Society for Neuroscience 2011 - GeneRIF: This study demonistrated that irx-1 as an unc-55-regulated target defines a transcriptional pathway that orchestrates an intricate synaptic remodeling program.
UV8b_06464 uncharacterized protein from Ustilaginoidea virens
44% identity, 14% coverage
A9UP33 Homeobox domain-containing protein from Monosiga brevicollis
46% identity, 9% coverage
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...I QV WF S NRR A KW RR 5/1/0.94 Monosiga brevicollis (Choanoflagellate) Mb_hbx2 homeobox-domain protein/ A9UP33 Q QI NN WF I N A R RRLLN R 4/0/0.76 Capsaspora owczarzaki amoebae (Filasterea clade) CAOG_004648 Homeobox domain-containing protein/ A0A0D2VSA1 R V I R IWFQNRR A K QRR RRQKARRNQFWIRIVRR...”
GLRG_00169 homeobox domain-containing protein from Colletotrichum graminicola M1.001
44% identity, 14% coverage
- The C2H2 Transcription Factor Con7 Regulates Vegetative Growth, Cell Wall Integrity, Oxidative Stress, Asexual Sporulation, Appressorium and Hyphopodium Formation, and Pathogenicity in Colletotrichum graminicola and Colletotrichum siamense
Zhou, Journal of fungi (Basel, Switzerland) 2024 - “...]. From the RNA-Seq result of Cgrcon7 , we noticed that a homeobox transcription factor (GLRG_00169), an ortholog of MoHox7 (Pth12) in M. oryzae , was downregulated in Cgrcon7 [ 35 ]. The mutant Mohox7 could not produce appressoria (hyphopodia) at the tips of germ tubes...”
- “...loss of pathogenicity [ 35 ]. CgrCon7 may be involved in regulating the expression of GLRG_00169 and further driving the appressorium formation of C. graminicola . In the pathogenicity assay, both Cgrcon7 and Cscon7 exhibited complete loss of virulence on maize and rubber tree leaves, respectively....”
CUP9_YEAST / P41817 Homeobox protein CUP9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
NP_015148 Cup9p from Saccharomyces cerevisiae S288C
YPL177C Cup9p from Saccharomyces cerevisiae
47% identity, 18% coverage
- function: Probable DNA-binding protein which plays a role in protecting yeast cells against copper toxicity. May regulate the expression of important copper homeostatic genes
- Heat stress-induced Cup9-dependent transcriptional regulation of SIR2.
Laskar, Molecular and cellular biology 2015 - GeneRIF: Cup9 overexpression represses SIR2 transcription and leads to a failure in the establishment of heterochromatin
- Amino acids induce peptide uptake via accelerated degradation of CUP9, the transcriptional repressor of the PTR2 peptide transporter.
Xia, The Journal of biological chemistry 2008 - GeneRIF: analysis of functional links between the amino acids-sensing SPS system, the CUP9-TUP1-SSN6 repressor complex, the PTR2 peptide transporter, and the UBR1-dependent N-end rule pathway
- Harnessing natural diversity to probe metabolic pathways
Homann, PLoS genetics 2005 - “...numbers for the genes and gene products discussed in this paper are ASP3 (P11163), Cup9p (P41817), DAL5 (P15365), Ptr2p (P32901), and Ubr1p (P19812). We thank John McCusker, Barbara Garvik, Gerald Fink, and Rodney Rothstein for providing the strains utilized in this study. We are also grateful...”
- Cucurbitacin B Exerts Antiaging Effects in Yeast by Regulating Autophagy and Oxidative Stress
Lin, Oxidative medicine and cellular longevity 2019 - “...ends part II YOL071W SDH5 Succinate dehydrogenase YOR311C DGK1 Diacylglycerol kinase YPR111W DBF20 Dumbbell forming YPL177C CUP9 Homeodomain-containing transcriptional repressor YBR054W YRO2 Protein with a putative role in response to acid stress YBR238C YBR238C Mitochondrial membrane protein YIL089W YIL089W Protein of unknown function found in the...”
- Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae
Dahlquist, Bulletin of mathematical biology 2015 - “...AFT1 YGL071W RCS1 AFT1, RAP1 AFT1 CIN5 YOR028C HAL6, YAP4 YAP6 MSN1, ROX1, YAP6 CUP9 YPL177C MAC1, PHD1 YAP6 FHL1 YPR104C SPP42 ABF1, MSN4 GTS1 YGL181W FHT1, LSR1 REB1 HAL9 YOL089C MSN4 HSF1 YGL073W EXA3, MAS3 RAP1 REB1 MAC1 YMR021C CUA1 CUP9 MSN1 YOL116W FUP1, HRB382,...”
- Transcription factor regulation and chromosome dynamics during pseudohyphal growth
Mayhew, Molecular biology of the cell 2014 - “...DNA sequence corresponding to bases 1 to 1217 from the transcription start site of CUP9 (YPL177C) was amplified by PCR from 1278b genomic DNA and cloned to drive expression of DsRed on a yeast centromere vector pRS314 to create plasmid pRM1145. The Flo8-binding site at 617...”
- Information processing in the transcriptional regulatory network of yeast: functional robustness
Emmert-Streib, BMC systems biology 2009 - “...YFR034C 73 2 14.0 N YER040W 44 1 17.8 Y YBR112C 26 1 13.6 Y YPL177C 23 2 13.3 N YOL148C 13 1 20.4 N YGL207W 12 2 18.1 N YLR399C 9 3 12.2 Y YDR138W 5 1 15.6 Y YPR072W 4 1 16.1 Y The...”
- “...response to starvation, YER040W positive regulation of transcription YBR112C negative regulation of transcription, chromatin remodeling YPL177C cellular copper ion homeostasis YOL148C chromatin modification, mitotic cell cycle YGL207W DNA repair, chromatin modification YLR399C DNA repair, chromatin remodeling YDR138W response to DNA damage stimulus YPR072W protein ubiquitination In...”
- On cycles in the transcription network of Saccharomyces cerevisiae
Jeong, BMC systems biology 2008 - “...YJR060W CBF1 21 YOR028C CIN5 9 YKL043W PHD1 22 YOR372C NDD1 10 YKL062W MSN4 23 YPL177C CUP9 11 YKL112W ABF1 24 YPR065W ROX1 12 YLR131C ACE2 25 YPR104C FHL1 13 YLR182W SWI6 Conclusion We inspected graph-theoretic properties of the cycles in the transcription network of Saccharomyces...”
- Dosage rescue by UBC4 restores cell wall integrity in Saccharomyces cerevisiae lacking the myosin type II gene MYO1
Díaz-Blanco, Yeast (Chichester, England) 2007 - “...Systematic name Gene Redundancy (No. of clones) YPL177C CUP9 1 84.2 Homeodomain-containing transcriptional repressor of PTR2, which encodes a major peptide...”
- The predicted G-protein-coupled receptor GPR-1 is required for female sexual development in the multicellular fungus Neurospora crassa
Krystofova, Eukaryotic cell 2006 - “...S. cerevisiae Tos8p (SCTos8; YGL096W) and Cup9p (SCCup9; YPL177C), and human PKNOX1 (HS; accession number AAC51243). Boxshade was used to indicate identical...”
- Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals
Bürglin, Nucleic acids research 1997 - “...fUm bE6 (X54071); fUm bE7 (X54070); fy CUP9 (YPL177c) (L36815, Z73533); fy MAT2 (P01367, L00059); fy YGL096w (Z72168); Hs IRX2a (U90304, U90309); Hs PBX1...”
CCM_07504 homeobox transcription factor, putative from Cordyceps militaris CM01
42% identity, 15% coverage
- Expanded Gene Regulatory Network Reveals Potential Light-Responsive Transcription Factors and Target Genes in Cordyceps militaris
Buradam, International journal of molecular sciences 2024 - “...for comparing transcriptomic responses between light-exposure and dark conditions, we identified five key TFshomeobox TF (CCM_07504), FlbC (CCM_04849), FlbB (CCM_01128), C6 zinc finger TF (CCM_05172), and mcrA (CCM_06477)along with ten regulated genes within the light-responsive subnetwork. These TFs and regulated genes are likely crucial for the...”
- “...five TFs with the highest number of regulated genes and highest normalized betweenness scores are CCM_07504, CCM_04849, CCM_01128, CCM_05172, and CCM_06477. The normalized betweenness scores further imply that the homeobox TF is central to the regulatory network, potentially serving as a key hub that integrates various...”
- Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris
In-On, Biology 2022 - “...the network, five TFs, Snf21 (CCM_04586), an AT-hook DNA-binding motif TF (CCM_08536), a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and a heat shock factor Hsf1 (CCM_05142), were identified as key regulators that co-regulate a large group of growth and developmental genes. The identified...”
- “...forming several network motifs, as shown in Figure 4 . Snf21 regulates a homeobox TF (CCM_07504), a forkhead box protein L2 (CCM_02646) and Heat shock factor 1 (Hsf1) (CCM_05142) in multiple feed-forward loops (FFLs). The AT-hook DNA-binding motif TF (CCM_08536) co-regulates the homeobox TF (CCM_07504) with...”
- Metabolic comparison of aerial and submerged mycelia formed in the liquid surface culture of Cordyceps militaris
Suparmin, MicrobiologyOpen 2019 - “...mycelia to assemble the pieces of the small cakelike mycelia. Interestingly, the homeobox transcription factor (CCM_07504) was found to be upregulated in both types of mycelia. The disruption of the homeobox gene AFLA_069100 of A. flavus resulted in the loss of the conidia and aflatoxin production...”
NP_001087637 TGFB induced factor homeobox 2 L homeolog from Xenopus laevis
47% identity, 23% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different species were not high, three conserved helixes and one...”
B6SXN6 Homeodomain protein JUBEL1 from Zea mays
40% identity, 8% coverage
- Quantitative analysis of changes in the phosphoproteome of maize induced by the plant hormone salicylic acid
Wu, Scientific reports 2015 - “...transcription factor Y subunit B-3 S(3): 99.9 57.63 2.55 2.67E-02 4.4 1.05E-04 0.8 3.78E-01 GGASSSGAAAQSPSSAPNKEPPQLSPADR B6SXN6 100281671 Homeodomain protein JUBEL1 S(5): 95.5; S(12): 99.9 43.8 0.93 6.15E-01 0.68 5.79E-02 0.78 1.11E-01 VDFDEFGSMDATK B6TPK0 100284050 CAK1AT S(8): 100.0 20.65 0.92 7.32E-01 1.53 3.11E-04 1.34 4.89E-03 QIAGGDDSMDEQEDETQENVWGR C0HIQ2...”
- Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress.
Hu, Frontiers in plant science 2015 - “...ii gFVAPQLDPSTPSPIFGGStGGLLR 0.63 (Y) 0.80 (N) 0.55 (N) atAGEAVTEEAPk 1.35 (N) 1.69 (N) 2.01 (Y) B6SXN6 Bel1-type homeodomain protein gAsASNPNNNPGNk 1.11 (N) 0.37 (Y) 0.37 (Y) gGASSsGAAAQsPSSAPNkEPPQLSPADR 2.18 (Y) 0.74 (N) 0.78 (N) B7ZYS1 tpa: phototropic-responsive nph4 family protein eAPTSSFYGGEsPTPAPSLQGR 0.68 (Y) 0.41 (Y) 0.49 (Y)...”
- “...5.17 H 1 xxxxxxx R xx S xxxxxxxxxx BF4F7Z5; BF4F976; B4FI93; B4FRF2; B4FRV0; B4FUV7; B6SRZ6; B6SXN6; B6T1H0; B6T2A6; B6TDN3; B6TQS9; B6TWH2; B6U787; B8A0K2; C0HIM6; C0P3W9; C0P4D8; C0P9L7; C0PCR0; C0PDN0; C0PD30; K7TRK2; K7U573; K7V0H0; K7VBI0; K7VBA5; K7W2Z7; K7WC16; Q41729; Q9ATN2 11.33 31 132 55507 1013205 4.29 2...”
AFUA_1G15550 homeobox and C2H2 transcription factor, putative from Aspergillus fumigatus Af293
42% identity, 7% coverage
- Transcriptome analysis of cyclic AMP-dependent protein kinase A-regulated genes reveals the production of the novel natural compound fumipyrrole by Aspergillus fumigatus
Macheleidt, Molecular microbiology 2015 - “...transcription factor (Azf1) 1.64 AFUA_2G10850 C6 finger domain protein 1.67 AFUA_4G01010 C6 transcription factor 1.69 AFUA_1G15550 Homeobox and C2H2 transcription factor 1.76 AFUA_2G12330 Zn cluster transcription factor AcuM 1.81 AFUA_6G01840 C6 transcription factor 1.82 AFUA_2G03020 MYB DNA-binding domain protein 1.83 AFUA_4G11480 C2H2 finger domain protein 2.02...”
- Regulation of sulphur assimilation is essential for virulence and affects iron homeostasis of the human-pathogenic mould Aspergillus fumigatus
Amich, PLoS pathogens 2013 - “...2.169 8,6E-08 AFUA_8G01090 thioredoxin, putative 2.241 0,00037 AFUA_1G02270 ARS binding protein Abp2, putative 2.696 2,0E-07 AFUA_1G15550 homeobox and C2H2 transcription factor, putative 2.697 1,7E-10 Resistance proteins and transporters (p-value=0.00036) AFUA_2G15130 ABC multidrug transporter, putative 1.569 0,00294 AFUA_1G10370 MFS multidrug transporter, putative 1.620 0,00121 AFUA_3G08530 MFS drug...”
NP_571966 homeobox protein PKNOX1.1 from Danio rerio
39% identity, 13% coverage
UNC62_CAEEL / Q9N5D6 Homeobox protein unc-62; Uncoordinated protein 62 from Caenorhabditis elegans (see 5 papers)
44% identity, 10% coverage
- function: Acts redundantly with ceh-20 and ceh-40 to perform overlapping roles during embryogenesis (PubMed:12399316). Required for postembryonic development of the ectoderm, including the Q, V and P cell lineages, playing a crucial role in ensuring that these cells and their descendants undergo their invariant patterns of cell division, migration, fusion and morphogenesis (PubMed:15750187). Has a role in the mig-13 pathway to promote anterior migration of neuroblasts in the Q lineage (PubMed:15750187). Required for multiple roles in regulating vulva development (PubMed:15750187). Associates with homeobox ceh-60 to regulate gene expression, including repression of genes involved in innate immunity and activation of genes involved in vitellogenesis (PubMed:30956009, PubMed:31675356). Involved in lipid homeostasis, contributing to the formation of the cuticle (PubMed:30956009, PubMed:31675356).
subunit: Forms a heterodimer with homeobox ceh-60.
disruption phenotype: Worms exhibit severe posterior disorganization during embryogenesis (Nob phenotype) (PubMed:12399316). Mutants exhibit Q cell migration defects, affecting cell position along the anterior posterior axis (PubMed:12399316). RNAi mediated knockdown abolishes nuclear localization of ceh-60 (PubMed:30956009). RNAi mediated knockdown targeted to the intestine represses expression of vitellogenin genes; further repressed on ceh-60 mutant background (PubMed:30956009).
XP_015138071 homeobox protein AKR isoform X1 from Gallus gallus
44% identity, 21% coverage
XP_005538457 unknown homeobox protein from Cyanidioschyzon merolae strain 10D
42% identity, 16% coverage
- A unique life cycle transition in the red seaweed Pyropia yezoensis depends on apospory
Mikami, Communications biology 2019 - “...crispus , CcBELL1 XP_005711328; Cyanidioschyzon merolae , CmKNOX (CMR153C) XP_005538442, CmBELL1 (CMH049C) XP_005536034, CmBELL2 (CMR176C) XP_005538457. PopKNOX (esisotig02479) and PouKNOX (esisotig04347) are KNOX homologs of Porphyra purpurea and Porphyra umbilicalis , respectively, which were derived from NoriBLAST ( http://dbdata.rutgers.edu/nori/ ). Gene IDs derived from our transcriptome...”
Smp_063520 irx-related from Schistosoma mansoni
44% identity, 10% coverage
- A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture
Attenborough, eLife 2024 - “...levels) are the germline-specific regulatory genes eled (Smp_041540) ( Figure 6G ), onecut1 (Smp_196950), irx (Smp_063520), akkn (Smp_131630), and boule (Smp_144860) (expressed in the female Kappa cells and Stem E, Figure 6figure supplement 5 ; Wang et al., 2018 ; Li et al., 2021 ), as...”
- A single-cell atlas of the miracidium larva of the human blood flukeSchistosoma mansoni: cell types, developmental pathways and tissue architecture
Attenborough, 2023 - Single-cell analysis of Schistosoma mansoni identifies a conserved genetic program controlling germline stem cell fate
Li, Nature communications 2021 - “...nr only in S1 cells, and a homolog of iroquois homeobox TF ( irx , Smp_063520) in GSCs. Whole-mount in situ hybridization (WISH) confirmed their expression (Fig. 2a ). oc-1 is expressed in both primordial testes and vitellaria, nr is specific to primordial vitellaria, and irx...”
XP_001455625 uncharacterized protein from Paramecium tetraurelia
39% identity, 12% coverage
- Homeodomain proteins: an update
Bürglin, Chromosoma 2016 - “...Saccoglossus kowalevskii (acorn worm; hemichordate); Ce: Caenorhabditis elegans ; Pt: Paramecium tetraurelia (sequence accession number: XP_001455625). (PDF 3.03 MB) Sup. Fig. S2 Multiple sequence alignment of fungal MAT2 proteins. Default color code from SeaView (Gouy et al. 2010 ). Species abbreviations: Scer: Saccharomyces cerevisiae ; Vpol:...”
BLH4_ARATH / Q94KL5 BEL1-like homeodomain protein 4; BEL1-like protein 4; Protein SAWTOOTH 2 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
NP_850044 BEL1-like homeodomain 4 from Arabidopsis thaliana
AT2G23760 BLH4 (BEL1-LIKE HOMEODOMAIN 4); DNA binding / transcription factor from Arabidopsis thaliana
42% identity, 10% coverage
- function: Transcription factor that establishes leaf shape by repressing growth in specific subdomains of the leaf. Negatively regulates knox homeobox gene KNAT1/BP expression.
subunit: May form heterodimeric complexes with TALE/KNOX proteins (By similarity). Interacts with OFP1, OFP2 and OFP5 (PubMed:15781858). Interacts with KNATM, isoform KNATM-B (PubMed:18398054). - SAW homeodomain transcription factors regulate initiation of leaf margin serrations.
Jeon, Journal of experimental botany 2021 (PubMed)- GeneRIF: SAW homeodomain transcription factors regulate initiation of leaf margin serrations.
- The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2 act redundantly to regulate KNOX expression spatially in leaf margins.
Kumar, The Plant cell 2007 - GeneRIF: These data suggest that BLH2/SAW1 and BLH4/SAW2 establish leaf shape by repressing growth in specific subdomains of the leaf at least in part by repressing expression of one or more of the KNOX genes. [SAW2]
- The Quantitative Biotinylproteomics Studies Reveal a WInd-Related Kinase 1 (Raf-Like Kinase 36) Functioning as an Early Signaling Component in Wind-Induced Thigmomorphogenesis and Gravitropism
Yang, Molecular & cellular proteomics : MCP 2024 - “...domain-containing protein (RPS10B) Y shoot system morphogenesis; RNA binding; regulation of developmental process; meristem development AT2G23760 BEL1-like homeodomain 4 (BLH4) Y shoot system morphogenesis AT1G73030 SNF7 family protein (VPS46.2) Y embryo development AT2G22475 GRAM domain family protein (GEM) Y AT1G10200 A member of the Arabidopsis LIM...”
- RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines
Arro, BMC plant biology 2019 - “...transcription factor YABBY family protein GSVIVG01019399001 AT5G41410 BEL1 0.811*** POX (plant homeobox) family protein GSVIVG01019043001 AT2G23760 BLH4 0.781*** 0.715*** BEL1-like homeodomain 4 GSVIVG01009589001 AT5G42630 KAN4 0.73*** 0.916*** 0.868*** Homeodomain-like superfamily protein GSVIVG01035391001 AT3G13810 AtIDD11 0.8*** 0.889*** Indeterminate(ID)-domain 11 GSVIVG01010283001 AT2G02070 AtIDD5 0.93*** Indeterminate(ID)-domain 5 GSVIVG01010284001 AT2G02070...”
- Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression
Archacki, Nucleic acids research 2017 - “...the respective genomic regions, we have selected and amplified: At1g18700 (+440; 1941), At1g70300 (+1747; 1273), At2g23760 (+3019; 413), At2g29090 (+3122; 364), At3g16785 (+2334; 391), At1g18690 (+793; 1245), At2g29080 (+506; 821), At5g21326 (+493; 1236) from Arabidopsis Col-0 genomic DNA and cloned into pGWB635 ( 40 ). As...”
- A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function
Zhai, Frontiers in plant science 2016 - “...addition, through a literature review, we found that nine of the top 20 candidates (AT2G25170, AT2G23760, AT1G21700, AT1G19220, AT4G36870, AT4G38130, AT1G28420, AT5G18620, and AT1G48410) have been recently demonstrated to have roles in the control of flowering time with phenotype experiments (Table S7 ). From these results,...”
- cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica
Xiao, Horticulture research 2016 - “...24 AB474685 258 AT5G42870 PAH2 Bra027461 BcPAH2 _A09 D x x x 25 AB474659 100 AT2G23760 BLH4 Bra032147 BcBLH4 _A04 D x x x 26 AB474677 100 AT1G25540 MED25 Bra038087 BcMED25 _A08 D x x 27 AB474686 67 AT3G14210 ESM1 Bra027359 BcESM1 _A05 D x X...”
- Genome-wide identification of KANADI1 target genes
Merelo, PloS one 2013 - “...5964 UP 12,8 6,1 3,27E-49 1,04E-29 AT1G78240 TSD2 3094 7048 UP 6,7 2,6 1,98E-19 1,28E-02 AT2G23760 SAW2 1267 436 UP 7,2 3,8 9,78E-36 5,35E-25 - yes AT2G23760 SAW2 1145 2496 DOWN 6,0 3,2 7,38E-38 5,57E-27 AT2G31070 TCP10 344 76 UP 8,0 4,3 6,40E-73 1,79E-54 yes yes...”
- Leaf development
Tsukaya, The arabidopsis book 2013 - “...SAWTOOTH1 (BEL1-LIKE HOMEODOMAIN (BHL)2/SAW1; AT4G36870), BHL4/SAW2 (AT2G23760), JAGGED (JAG; AT1G68480), JAGGED LATERAL ORGANS 8 of 21 The Arabidopsis...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...[ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 14 ] AT2G23760 BLH5 [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] AT2G27220 BLH6 [ 16 ] [ 16 ] [ 16 ] [ 16 ]...”
- More
LOC100257488 BEL1-like homeodomain protein 7 from Vitis vinifera
35% identity, 11% coverage
EIN_475530 homeobox protein knotted-1, putative from Entamoeba invadens IP1
43% identity, 21% coverage
ECU06_0740 MEI2-RELATED PROTEIN from Encephalitozoon cuniculi GB-M1
44% identity, 28% coverage
BLH5_ARATH / Q8S897 BEL1-like homeodomain protein 5; BEL1-like protein 5 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G27220 BLH5 (BELL1-like homeodomain 5); DNA binding / transcription factor from Arabidopsis thaliana
39% identity, 15% coverage
- subunit: May form heterodimeric complexes with TALE/KNOX proteins (By similarity). Interacts with OFP1.
- Global gene regulatory network underlying miR165a in Arabidopsis shoot apical meristem
Sinha, Scientific reports 2023 - “...transition 1.07 1.03 1.03 AT1G20700 WUSCHEL related homeobox 14 (WOX14) Regulate plant vascular proliferation 1.34 AT2G27220 BEL1-like homeodomain 5 (BLH5) 1.27 5.36 1.85 Among these genes, Beta-Galactosidase 5 was down-regulated at all time-points and was also found to be down-regulated in miR165a cell-types, compared with other...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...[ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] AT2G27220 BLH6 [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] AT4G34610 BLH7 [ 16 , 19 ] [...”
NP_001157546 homeobox protein TGIF1 isoform c from Mus musculus
42% identity, 23% coverage
Q941S9 Os01g0848400 protein from Oryza sativa subsp. japonica
39% identity, 10% coverage
- Prospects for the accelerated improvement of the resilient crop quinoa
López-Marqués, Journal of experimental botany 2020 - “...as follows: AtDA2, Q93YV5; OsGIF1, Q6AVI1; OsGW2, B9F4Q9; AtMFT, Q6XFK7; AtHSFA1A, P41151; AtPIE1, Q7X9V2; OsqSH1, Q941S9; TaRHT1, Q9ST59; OsSHAT1, A0A0N7KJT8; AtSHP1, P29381; AtSHP2, P29385; AtSOC1, O64645; HvMKK3, A0A140JZ28; AtCKX5, Q67YU0; and AtCKX3, A0A1P8BER3. The basic local alignment search tool (BLAST) was used to search for genes...”
HBX3_DICDI / Q54F11 Homeobox protein 3; DdHbx-3 from Dictyostelium discoideum (Social amoeba) (see paper)
43% identity, 9% coverage
- function: Putative transcription factor.
Pc06g01320 uncharacterized protein from Penicillium rubens
40% identity, 7% coverage
XP_005536034 unknown homeobox protein from Cyanidioschyzon merolae strain 10D
50% identity, 13% coverage
- A unique life cycle transition in the red seaweed Pyropia yezoensis depends on apospory
Mikami, Communications biology 2019 - “...AtKNAT3 X92392; Chondrus crispus , CcBELL1 XP_005711328; Cyanidioschyzon merolae , CmKNOX (CMR153C) XP_005538442, CmBELL1 (CMH049C) XP_005536034, CmBELL2 (CMR176C) XP_005538457. PopKNOX (esisotig02479) and PouKNOX (esisotig04347) are KNOX homologs of Porphyra purpurea and Porphyra umbilicalis , respectively, which were derived from NoriBLAST ( http://dbdata.rutgers.edu/nori/ ). Gene IDs derived...”
NP_777480 homeobox protein TGIF1 isoform d from Homo sapiens
42% identity, 23% coverage
TGIF1_HUMAN / Q15583 Homeobox protein TGIF1; 5'-TG-3'-interacting factor 1 from Homo sapiens (Human) (see 2 papers)
42% identity, 14% coverage
- function: Binds to a retinoid X receptor (RXR) responsive element from the cellular retinol-binding protein II promoter (CRBPII-RXRE). Inhibits the 9-cis-retinoic acid-dependent RXR alpha transcription activation of the retinoic acid responsive element. Active transcriptional corepressor of SMAD2. Links the nodal signaling pathway to the bifurcation of the forebrain and the establishment of ventral midline structures. May participate in the transmission of nuclear signals during development and in the adult, as illustrated by the down-modulation of the RXR alpha activities
subunit: Interacts with SMAD2 (PubMed:10835638). Interacts with CTBP, SMAD3 and HDAC1. - TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-β signaling.
Guca, Nucleic acids research 2018 - “...Cloning, expression and purification The cDNA encoding the human TGIF1 protein (Isoform 2, Uniprot entry Q15583) was used as a template for cloning all domain constructs (pCMV5 Flag-TGIF1, Addgene Plasmid #14047, provided by the laboratory of Dr J. Massagu). All constructs were amplified by PCR. HD...”
NP_001015020 homeobox protein TGIF1 from Rattus norvegicus
42% identity, 20% coverage
BLH1_ARATH / Q9SJ56 BEL1-like homeodomain protein 1; BEL1-like protein 1; Protein EMBRYO SAC DEVELOPMENT ARREST 29 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_181138 BEL1-like homeodomain 1 from Arabidopsis thaliana
AT2G35940 BLH1 (BEL1-LIKE HOMEODOMAIN 1); DNA binding / protein heterodimerization/ protein homodimerization/ transcription factor from Arabidopsis thaliana
40% identity, 9% coverage
- subunit: May form heterodimeric complexes with TALE/KNOX proteins KNAT2 and KNAT 5. Interacts with OFP1, OFP2, OFP3, OFP4, OFP5 and OFP15.
- Transcriptional regulation of Lonicera japonica Thunb. during flower development as revealed by comprehensive analysis of transcription factors
Wang, BMC plant biology 2019 - “...C2H2 IDD1 Q9LVQ7 Ath 1.7E-93 94.48 14.36 13.96 19.01 24.23 31.01 PCD 89 TALE BLH1 Q9SJ56 Ath 3.2E-52 94.29 14.36 13.96 19.01 24.23 31.01 PCD 90 NAC NAC100 Q9FLJ2 Ath 2.6E-79 79.88 17.04 10.57 32.60 62.18 82.40 PCD - means no corresponding annotation in Swiss-Prot database....”
- QTL Analyses in Multiple Populations Employed for the Fine Mapping and Identification of Candidate Genes at a Locus Affecting Sugar Accumulation in Melon (Cucumis melo L.)
Argyris, Frontiers in plant science 2017 - “...3,147,173 1,746,367 1,750,303 3,936 Similar to BEL1-like homeodomain protein 1 ( Arabidopsis thaliana ) (uniprot_sprot:sp| Q9SJ56 |BLH1_ARATH) MELO3C014520 + 3,156,700 3,157,969 1,735,571 1,736,840 1,269 Similar to E3 ubiquitin-protein ligase PUB22 ( Arabidopsis thaliana ) (uniprot_sprot:sp| Q9SVC6 |PUB22_ARATH) MELO3C014521 3,170,295 3,172,387 1,721,153 1,723,245 2,092 Similar to Protein...”
- BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis.
Kim, The Plant journal : for cell and molecular biology 2013 (PubMed)- GeneRIF: BLH1 and KNAT3 together modulate seed germination and early seedling development by directly regulating ABI3 expression.
- Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A.
Staneloni, Proceedings of the National Academy of Sciences of the United States of America 2009 - GeneRIF: BLH1 specifically regulates high-irradiance response and not very-low-fluence response of phytochrome A.
- Cell-fate switch of synergid to egg cell in Arabidopsis eostre mutant embryo sacs arises from misexpression of the BEL1-like homeodomain gene BLH1.
Pagnussat, The Plant cell 2007 - GeneRIF: The eostre phenotype is caused by misexpression of the homeodomain gene BEL1-like homeodomain 1 (BLH1) in the embryo sac.
- Floral Homeotic Factors: A Question of Specificity
Goslin, Plants (Basel, Switzerland) 2023 - “...Basic pentacysteine AP1 Two-hybrid [ 43 ] AT2G17950 WUS Homeodomain SEP3 Two-hybrid [ 44 ] AT2G35940 BLH1 Homeodomain AP1 IP-MS [ 19 ] AT2G37630 AS1 MYB AG Two-hybrid [ 44 ] AT3G11100 VFP3 SANT and trihelix SEP4 Two-hybrid [ 42 ] AT3G15030 TCP4 TCP AP1, SEP4...”
- Transcriptome analysis of Rafflesia cantleyi flower stages reveals insights into the regulation of senescence
Mohd-Elias, Scientific reports 2021 - “...UN015470 RING/U-box family protein AT5G41350 Unclear UN016492 AUX/IAA transcription factor AT3G23050 Unclear UN017419 Homeobox protein AT2G35940 Unclear UN021998 C3H zinc-finger domain AT5G58620 Unclear UN005311 C2H2 zinc-finger domain AT2G28200 Unclear Nutrient remobilization UN020537 ATG4 AT2G44140 Delay UN046014 ATG6 AT3G61710 Delay UN027071 ATG7 AT5G45900 Delay UN051413 ATG8 AT4G21980...”
- Stimulation of adventitious root formation by the oligosaccharin OSRG at the transcriptome level
Larskaya, Plant signaling & behavior 2020 (secret) - Circular and Micro RNAs from Arabidopsis thaliana Flowers Are Simultaneously Isolated from AGO-IP Libraries
Frydrych, Plants (Basel, Switzerland) 2019 - “...intronic 1 224 3 DDH-IP At2g02410 circ_At2g02410 K06962uncharacterized protein (K06962) exonic 1 71 4 DDH-IP At2g35940 ** circ_At2g35940 BEL1-like homeodomain 1 exonic 1 930 4 DDH-IP At2g42170 ** circ_At2g42170 Actin family protein exonic 4 1063 5 DDH-IP At5g16880 circ_At5g16880 Target of Myb protein 1 exonic *...”
- Crassulacean Acid Metabolism Abiotic Stress-Responsive Transcription Factors: a Potential Genetic Engineering Approach for Improving Crop Tolerance to Abiotic Stress
Amin, Frontiers in plant science 2019 - “...fruit ripening, leaf senescence, multicellular organism development, multidimensional cell growth, regulation of transcription McBLH1 HB/Homeodomain AT2G35940 Polar nuclei fusion, response to abscisic acid, response to continuous far red-light stimulus by the high-irradiance response system, response to symbiotic fungus McbZIP2 bZIP AT2G18160 Positive regulation of transcription McAGL8...”
- A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs
Vargas-Asencio, Frontiers in plant science 2019 - “...Allen etal. (2005) Chr2 15090887 15091257 + gene + AT2G35945 Natural antisense transcript overlaps with AT2G35940 370 Chr2 16011479 16012261 + gene + AT2G38230 Pyridoxine biosynthesis 1.1 782 Chr2 16537499 16538006 - gene - AT2G39675 Trans-acting siRNA1c primary transcript (TAS1c) 507 Allen etal. (2005) Chr2 16539685...”
- Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size
Pathak, Scientific reports 2016 - “...on a model ovule developmental pathway. Higher expression of NGATHA (AT2G46870; c41974_g2_i1 & c41974_g4_i2), BEL1-like (AT2G35940; c45509_g1_i1, c45509_g1_i2, c45509_g1_i3, c39557_g3_i1 & c39557_g3_i2), HB-5 like (AT4G36740; c35680_g1_i1), LOB domain containing protein (AT2G28500; c36314_g1_i1) and HB-7 like gene (AT2G46680; c44555_g1_i1 & c44555_g1_i2) was noticed in the small-seeded litchi...”
- Pre-symptomatic transcriptome changes during cold storage of chilling sensitive and resistant peach cultivars to elucidate chilling injury mechanisms
Pons, BMC genomics 2015 - “...VN establishment, maintenance, cell number and pattern HB - family PPN069A12 BEL1-like homeodomain transcription factor AT2G35940 BLH1 Signal transduction pathway AUX signaling/ AUX receptor E3 ubiquitin ligase SFC - TIR PPN078E01 Transport inhibitor response 1 protein AT3G62980 TIR1 AUX nuclear signaling AUX signaling/ Nuclear signaling pathway...”
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Pc22g06630 uncharacterized protein from Penicillium rubens
33% identity, 11% coverage
XP_006362847 BEL1-like homeodomain protein 3 from Solanum tuberosum
34% identity, 10% coverage
Sb05g003750 No description from Sorghum bicolor
41% identity, 9% coverage
PITG_01080 uncharacterized protein from Phytophthora infestans T30-4
47% identity, 31% coverage
Q8LLD9 BEL1-related homeotic protein 29 (Fragment) from Solanum tuberosum
40% identity, 11% coverage
XP_006348467 BEL1-like homeodomain protein 1 from Solanum tuberosum
40% identity, 9% coverage
XP_038954473 homeobox protein PKNOX1 isoform X1 from Rattus norvegicus
34% identity, 13% coverage
PKNX1_MOUSE / O70477 Homeobox protein PKNOX1; PBX/knotted homeobox 1 from Mus musculus (Mouse) (see 2 papers)
34% identity, 13% coverage
Q7Y0Z9 Bell-like homeodomain protein 3 (Fragment) from Solanum lycopersicum
41% identity, 11% coverage
F2DUL1 Predicted protein from Hordeum vulgare subsp. vulgare
34% identity, 12% coverage
- Identification of the Genetic Basis of Response to De-Acclimation in Winter Barley
Wójcik-Jagła, International journal of molecular sciences 2021 - “...] HORVU4HR1G072880 A0A287PM62 N/A Phosphoserine aminotransferase phosphoserine aminotransferase 1, chloroplastic [ Brachypodium distachyon ] HORVU4HR1G074250 F2DUL1 N/A Unknown function protein BEL1-like homeodomain protein 7 [ Aegilops tauschii subsp. tauschii ] HORVU4HR1G082710 A0A287PVS7 MLO MLO-like protein MLO [ Triticum aestivum ] HORVU4HR1G083210 A0A287PXC8 N/A Unknown function protein...”
NP_683752 homeobox protein PKNOX2 isoform 1 from Mus musculus
Q8BG99 Homeobox protein PKNOX2 from Mus musculus
38% identity, 12% coverage
- PBX/Knotted 1 homeobox-2 (PKNOX2) is a novel regulator of myocardial fibrosis.
Chen, Signal transduction and targeted therapy 2024 - GeneRIF: PBX/Knotted 1 homeobox-2 (PKNOX2) is a novel regulator of myocardial fibrosis.
- Accelerated Evolution Analysis Uncovers PKNOX2 as a Key Transcription Factor in the Mammalian Cochlea.
Trigila, Molecular biology and evolution 2023 - GeneRIF: Accelerated Evolution Analysis Uncovers PKNOX2 as a Key Transcription Factor in the Mammalian Cochlea.
- PKNOX2 regulates myofibroblast functions and tubular cell survival during kidney fibrosis.
Miyake, Biochemical and biophysical research communications 2021 (PubMed)- GeneRIF: PKNOX2 regulates myofibroblast functions and tubular cell survival during kidney fibrosis.
- Misexpression of Pknox2 in mouse limb bud mesenchyme perturbs zeugopod development and deltoid crest formation.
Zhou, PloS one 2013 - GeneRIF: results indicated that Pknox2 misexpression affected mesenchymal condensation and early chondrogenic differentiation in the zeugopod skeletons of transgenic embryos
- Subcellular localization of multiple PREP2 isoforms is regulated by actin, tubulin, and nuclear export.
Haller, The Journal of biological chemistry 2004 (PubMed)- GeneRIF: transcriptional regulation by PREP2 is modulated through the subcellular distribution of multiple isoforms and by interaction with two distinct cytoskeletal systems
- Prep2: cloning and expression of a new prep family member.
Haller, Developmental dynamics : an official publication of the American Association of Anatomists 2002 (PubMed)- GeneRIF: Prep2 functions to varying degrees in a broad array of tissues and developmental processes.
- The nonpolymorphic MHC Qa-1b mediates CD8+ T cell surveillance of antigen-processing defects.
Oliveira, The Journal of experimental medicine 2010 - “...factor 6, mitochondrial 5 PTEEESPV 486-493 493 P53986 Monocarboxylate transporter 1 6 QAIPQGAIQ 246-254 461 Q8BG99 Homeobox protein PKNOX2 7 QLQPQQPLPQPQ 125-136 672 Q9WVH4 Forkhead protein FKHR2 TAP-negative 1 AAIENIEHL 1193-1201 1392 Q6PB66 Leucine-rich PPR motif-containing protein, mitochondrial 2 AALKLGQEL 799-807 1271 Q9JJ28 Protein flightless-1 homologue...”
PKNX2_HUMAN / Q96KN3 Homeobox protein PKNOX2; Homeobox protein PREP-2; PBX/knotted homeobox 2 from Homo sapiens (Human) (see paper)
38% identity, 12% coverage
PKNX1_HUMAN / P55347 Homeobox protein PKNOX1; Homeobox protein PREP-1; PBX/knotted homeobox 1 from Homo sapiens (Human) (see 3 papers)
NP_004562 homeobox protein PKNOX1 isoform 1 from Homo sapiens
34% identity, 13% coverage
- function: Activates transcription in the presence of PBX1A and HOXA1.
subunit: Interacts with MN1. - Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis.
Liu, Nutrition (Burbank, Los Angeles County, Calif.) 2023 (PubMed)- GeneRIF: Polyunsaturated fatty acids ameliorate renal stone-induced renal tubular damage via miR-93-5p/Pknox1 axis.
- Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis.
Bruckmann, Scientific reports 2020 - GeneRIF: Mapping the native interaction surfaces of PREP1 with PBX1 by cross-linking mass-spectrometry and mutagenesis.
- PREP1 tumor suppressor protects the late-replicating DNA by controlling its replication timing and symmetry.
Palmigiano, Scientific reports 2018 - GeneRIF: the replication timing of a specific fraction of the human genome is affected by PREP1 tumor suppressor
- MiR-17 family-mediated regulation of Pknox1 influences hepatic steatosis and insulin signaling.
Ye, Journal of cellular and molecular medicine 2018 - GeneRIF: These data implicate the upregulated hepatic expression of Pknox1 in type 2 diabetes mellitus (T2DM) complicated with nonalcoholic fatty liver disease (NAFLD) may be caused by the reduced expression of miR-17 family, indicating that developing miRNA-mediated regulation strategies on Pknox1 may provide new therapeutic options for metabolic disease
- Biochemistry of the tale transcription factors PREP, MEIS, and PBX in vertebrates
Longobardi, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - “...highlighted in green. Accession numbers are: hMeis1: O00470; hMeis2: O14770; hMeis3: Q99687; Hth: NP_476578; hPrep1: NP_004562; hPrep2: CAD01142. Mammalian cells contain four PBX genes (14) that code for six proteins, because of two alternatively spliced isoforms of PBX1 and PBX3. The gene products are extremely well...”
- Transcription factor PREP1 induces EMT and metastasis by controlling the TGF-β-SMAD3 pathway in non-small cell lung adenocarcinoma.
Risolino, Proceedings of the National Academy of Sciences of the United States of America 2014 - GeneRIF: PREP1 modulates the cellular sensitivity to TGF-beta by inducing the small mothers against decapentaplegic homolog 3 (SMAD3) nuclear translocation.
- Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia.
Bol, PloS one 2012 - GeneRIF: Single nucleotide polymorphism in gene encoding transcription factor Prep1 is associated with HIV-1-associated dementia
- Homeodomain transcription factor and tumor suppressor Prep1 is required to maintain genomic stability.
Iotti, Proceedings of the National Academy of Sciences of the United States of America 2011 - GeneRIF: The tumor suppressor role of Prep1 is associated with the maintenance of genomic stability.
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- Gain-of-Function MN1 Truncation Variants Cause a Recognizable Syndrome with Craniofacial and Brain Abnormalities.
Miyake, American journal of human genetics 2020 - Complementary quantitative proteomics reveals that transcription factor AP-4 mediates E-box-dependent complex formation for transcriptional repression of HDM2
Ku, Molecular & cellular proteomics : MCP 2009 - “...N/A 1.63 0.36 1.73 0.19 1.94 0.49 1.78 N/A 1.75 0.05 N/A P55347 P08047 Q12857 P38398 PKNOX1 SP1 NFIA BRCA1 47577 80644 55909 207592 37 92 75 38 1 1 2 1 3.69 N/A...”
XP_644890 homeodomain containing protein from Dictyostelium discoideum AX4
41% identity, 8% coverage
TRIATDRAFT_288678 uncharacterized protein from Trichoderma atroviride
42% identity, 6% coverage
- A comprehensive transcription factor and DNA-binding motif resource for the construction of gene regulatory networks in Botrytis cinerea and Trichoderma atroviride
Olivares-Yañez, Computational and structural biotechnology journal 2021 - “...& TF domain Fungi TRIATDRAFT_31689; 1323 Zinc Cluster and fungal specific TF domain Bcin12g03330; 3295 TRIATDRAFT_288678; 4128 Bcin13g00670; 1934 Zn_Cluster & TF domain Fungi TRIATDRAFT_42504; 1305 Zn_Cluster domain TF Bcin13g05200; 3033 TRIATDRAFT_163506; 4099 Bcin02g08650; 1892 Bcskn7 Response regulator TF TRIATDRAFT_22050; 1301 Zn_Cluster & TF domain Fungi...”
- “...1300 C2H2 domain TF Bcin11g02190; 3048 TRIATDRAFT_295974; 3917 Bcin12g01230; 1801 Zn_Cluster & TF domain Fungi TRIATDRAFT_288678; 1293 Homeobox domain and Zinc finger C2H2-type To characterize the topology of the reference GRNs, their properties were analyzed. Both reference networks comprised a single connected component, indicating that there...”
PITG_01135 uncharacterized protein from Phytophthora infestans T30-4
41% identity, 24% coverage
TRIATDRAFT_161626 uncharacterized protein from Trichoderma atroviride
42% identity, 5% coverage
NP_001274921 BEL1-related homeotic protein 5 from Solanum tuberosum
40% identity, 9% coverage
XP_308755 uncharacterized protein LOC1270088 isoform X2 from Anopheles gambiae
41% identity, 12% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...33.3 and 32.5% similarity with TGIF of Aedes aegypti (XP_001653660), Culex quinquefasciatus (XP_001849992), Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus...”
TGIF2_HUMAN / Q9GZN2 Homeobox protein TGIF2; 5'-TG-3'-interacting factor 2; TGF-beta-induced transcription factor 2; TGFB-induced factor 2 from Homo sapiens (Human) (see paper)
NP_068581 homeobox protein TGIF2 from Homo sapiens
NP_001186443 homeobox protein TGIF2 from Homo sapiens
40% identity, 24% coverage
- function: Transcriptional repressor, which probably repress transcription by binding directly the 5'-CTGTCAA-3' DNA sequence or by interacting with TGF-beta activated SMAD proteins. Probably represses transcription via the recruitment of histone deacetylase proteins.
subunit: Interacts with the transcriptional modulator SMAD3 and the histone deacetylase HDAC1. - BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...(XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different species were not high, three conserved helixes and one adjacent C-domain were prominent ( Fig....”
- Phosphorylation of TGIF2 represents a therapeutic target that drives EMT and metastasis of lung adenocarcinoma.
Du, BMC cancer 2023 - GeneRIF: Phosphorylation of TGIF2 represents a therapeutic target that drives EMT and metastasis of lung adenocarcinoma.
- Circular RNA circMMP1 Contributes to the Progression of Glioma Through Regulating TGIF2 Expression by Sponging miR-195-5p.
Zhang, Biochemical genetics 2022 (PubMed)- GeneRIF: Circular RNA circMMP1 Contributes to the Progression of Glioma Through Regulating TGIF2 Expression by Sponging miR-195-5p.
- Circ-RNF13, as an oncogene, regulates malignant progression of HBV-associated hepatocellular carcinoma cells and HBV infection through ceRNA pathway of circ-RNF13/miR-424-5p/TGIF2.
Chen, Bosnian journal of basic medical sciences 2021 - GeneRIF: Circ-RNF13, as an oncogene, regulates malignant progression of HBV-associated hepatocellular carcinoma cells and HBV infection through ceRNA pathway of circ-RNF13/miR-424-5p/TGIF2.
- Circular RNA circCPA4 promotes tumorigenesis by regulating miR-214-3p/TGIF2 in lung cancer.
Tao, Thoracic cancer 2021 - GeneRIF: Circular RNA circCPA4 promotes tumorigenesis by regulating miR-214-3p/TGIF2 in lung cancer.
- TGIF2 promotes cervical cancer metastasis by negatively regulating FCMR.
Jiang, European review for medical and pharmacological sciences 2020 (PubMed)- GeneRIF: TGIF2 promotes cervical cancer metastasis by negatively regulating FCMR.
- miR-541 serves as a prognostic biomarker of osteosarcoma and its regulatory effect on tumor cell proliferation, migration and invasion by targeting TGIF2.
Liu, Diagnostic pathology 2020 - GeneRIF: miR-541 serves as a prognostic biomarker of osteosarcoma and its regulatory effect on tumor cell proliferation, migration and invasion by targeting TGIF2.
- Three inflammation-related genes could predict risk in prognosis and metastasis of patients with breast cancer.
Zhao, Cancer medicine 2019 - GeneRIF: our study identified three mRNAs (TBX21, TGIF2, and CYCS) that were significantly altered between high- and low-risk patients with breast cancer. The three-mRNA model was independent and predicted the prognosis of patients robustly. Furthermore, this model could predict survival probability precisely in patients with or without metastasis.
- Effects on hepatic lipid metabolism in human hepatoma cells following overexpression of TGFβ induced factor homeobox 1 or 2.
Härdfeldt, Biochimica et biophysica acta. Molecular and cell biology of lipids 2019 (PubMed)- GeneRIF: Overexpression of TGIF1 lowers levels of cholesterol, triglycerides, and apoB. Overexpression of TGIF2 has more limited effects on lipid metabolism.
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- The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02.
Mukherjee, Frontiers in immunology 2021 - “...9 Q8WYB5 Histone acetyltransferase KAT6B Nucleus HLA-B*07:02 70 17581766 ( 26 ) 16 LPRGSSPSVL 10 Q9GZN2 Homeobox protein TGIF2 Nucleus HLA-B*07:02 5 105-114 CS 17 APTgSAAAL 8 Q86Z02 Homeodomain-interacting protein kinase 1 Nucleus, Cytoplasm HLA-B*07:02 90 11161123 CS, ( 26 ) 18 APVgSSKSSL a 9 Q86Z02...”
LOC105059537 homeobox protein BEL1 homolog from Elaeis guineensis
42% identity, 10% coverage
BLH2_ARATH / Q9SW80 BEL1-like homeodomain protein 2; BEL1-like protein 2; Protein SAWTOOTH 1 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT4G36870 BLH2 (BEL1-LIKE HOMEODOMAIN 2); DNA binding / transcription factor from Arabidopsis thaliana
NP_001031797 BEL1-like homeodomain 2 from Arabidopsis thaliana
40% identity, 8% coverage
- function: Transcription factor that establishes leaf shape by repressing growth in specific subdomains of the leaf. Negatively regulates knox homeobox gene KNAT1/BP expression
subunit: May form heterodimeric complexes with TALE/KNOX proteins STM, KNAT1/BP, KNAT2 and KNAT5 (PubMed:17873098). Interacts with OFP1, OFP2, OFP4 and OFP5 (PubMed:15781858). Interacts with KNATM, isoform KNATM-B (PubMed:18398054). - LsBLH2-LsOFP6-LsKANT3 module regulates bolting by orchestrating the gibberellin biosynthesis and metabolism in lettuce
Chen, Plant biotechnology journal 2025 (no snippet) - A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress
Karami, PloS one 2023 - “..., ATERF2 , ERF2 AP2-EREBP At4g24020 NLP7 NLP At4g32010 HSI2-L1 , HSL1 , VAL2 ABI3VP1 At4g36870 BLH2 , SAW1 Homeobox At4g38960 - C2C2-CO-like At3g54990 SMZ AP2-EREBP At1g50600 SCL5 GRAS At1g64625 - bHLH At1g80840 ATWRKY40 , WRKY40 WRKY At2g20570 GLK1 , GPRI1 G2-like 10.1371/journal.pone.0287761.t002 Table 2 List...”
- “...to target five genes encoding TFs in C3 plants. These genes included C2C2-CO-like (AT3G38960), Homeobox (AT4G36870), AP2/EREBP (At5g47220 and AT3G54990), and bHLH (AT3G64625). Additionally, the gene encoding C2H2 TF (AT3G18290), which was identified in both C3 and C4 groups, was targeted by three miRNAs, namely ath-miR5021,...”
- Multi-Omics Analysis Reveals Synergistic Enhancement of Nitrogen Assimilation Efficiency via Coordinated Regulation of Nitrogen and Carbon Metabolism by Co-Application of Brassinolide and Pyraclostrobin in Arabidopsis thaliana
An, International journal of molecular sciences 2023 - “...AT5G43270 SPL2 0.26 DBB AT1G06040 BBX24 0.15 SRS AT4G36260 SRS2 0.90 AT4G38960 - 0.41 TALE AT4G36870 BLH2 0.31 Dof AT1G51700 DOF1.7 0.30 TCP AT1G72010 TCP22 0.23 AT3G47500 CDF3 0.20 AT3G15030 TCP4 0.50 AT5G60200 DOF5.3 0.47 AT3G47620 TCP14 0.28 ERF AT1G33760 ERF022 0.87 AT4G18390 TCP2 0.26 AT1G64380...”
- Gene regulation network analyses of pistil development in papaya
Liao, BMC genomics 2022 - “...development sunup.03G0015290 EXP NO CpSCL32 AT3G49950 FS4 Regulate growth and flowering sunup.04G0013610 EXP NO CpBLH4 AT4G36870 FS2-3/FS4 Ovule morphogenesis sunup.03G0020730 NO EXP CpMUTE AT3G06120 MS2-3 Stomatal development sunup.06G0008830 NO EXP CpAMS AT2G16910 MS2-3 Tapetal cell development sunup.01G0006170 NO EXP CpBZIP43L AT5G38800 MS1/MS4 NA sunup.08G0003710 NO EXP...”
- Population genomics of the eastern cottonwood (Populus deltoides)
Fahrenkrog, Ecology and evolution 2017 - “...P.trichocarpa by four scans performed in that species. This gene is orthologous to the gene AT4G36870 that encodes the BEL1LIKE HOMEODOMAIN 2 (BLH2) transcription factor also known as SAWTOOTH 1 (SAW1), a negative regulator of growth involved in leaf margin development in A.thaliana (Kumar etal., 2007...”
- A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function
Zhai, Frontiers in plant science 2016 - “...literature review, we found that nine of the top 20 candidates (AT2G25170, AT2G23760, AT1G21700, AT1G19220, AT4G36870, AT4G38130, AT1G28420, AT5G18620, and AT1G48410) have been recently demonstrated to have roles in the control of flowering time with phenotype experiments (Table S7 ). From these results, we conclude that...”
- Leaf development
Tsukaya, The arabidopsis book 2013 - “...BOP2 (AT2G41370), SAWTOOTH1 (BEL1-LIKE HOMEODOMAIN (BHL)2/SAW1; AT4G36870), BHL4/SAW2 (AT2G23760), JAGGED (JAG; AT1G68480), JAGGED LATERAL ORGANS 8 of 21...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...[ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 14 ] AT4G36870 BLH3 [ 8 ] [ 8 ] [ 16 ] [ 16 ] [ 16 ] AT1G75410 BLH4/ SAW2 [ 16 ] [ 16 ] [ 16 ] [ 16...”
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- SAW homeodomain transcription factors regulate initiation of leaf margin serrations.
Jeon, Journal of experimental botany 2021 (PubMed)- GeneRIF: SAW homeodomain transcription factors regulate initiation of leaf margin serrations.
- The Arabidopsis BEL1-LIKE HOMEODOMAIN proteins SAW1 and SAW2 act redundantly to regulate KNOX expression spatially in leaf margins.
Kumar, The Plant cell 2007 - GeneRIF: These data suggest that BLH2/SAW1 and BLH4/SAW2 establish leaf shape by repressing growth in specific subdomains of the leaf at least in part by repressing expression of one or more of the KNOX genes. [SAW1]
FGSG_07909 hypothetical protein from Fusarium graminearum PH-1
41% identity, 7% coverage
- A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi
Sperschneider, BMC genomics 2013 - “...PF00168) Endocytosis, exocytosis, synaptotagmin-1 (100%/54%) 52.1 No 41% Metazoan, 29% Viridiplantae, 22% Ascomycota, 8% others FGSG_07909 0.62 Homeobox KN domain (2.3e-15, PF05920) Homeobox domain (99.7%/11%) 84.6 Yes 56% Metazoan, 29% Viridiplantae, 12% Ascomycota, 3% others FGSG_07846 0.61 FMO-like (5.8e-16, PF00734) Monooxygenase (100%/75%) 62.6 No 37% Bacteria,...”
- “...domain (3.5e-05, PF04082) Centromere DNA-binding protein complex cbf3 (98.2%/72%) 62.6 No 94% Ascomycota, 6% Basidiomycota FGSG_07909 0.48 Homeobox KN domain (2.3e-15, PF05920) Homeobox domain (99.7%/11%) 84.6 Yes 56% Metazoan, 29% Viridiplantae, 12% Ascomycota, 3% others For each protein, its Pfam annotation, Phyre2 structure prediction, molecular weight...”
NP_955861 homeobox protein TGIF1 from Danio rerio
40% identity, 21% coverage
- Retinal regeneration in adult zebrafish requires regulation of TGFβ signaling.
Lenkowski, Glia 2013 - GeneRIF: Tgif1 expression and regulation of TGFbeta signaling are implicated in the function of several types of stem cells, but this is the first demonstration that this regulatory network is necessary for regeneration of neurons.
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different species were not high, three conserved helixes and one adjacent C-domain were...”
- Zebrafish model of holoprosencephaly demonstrates a key role for TGIF in regulating retinoic acid metabolism.
Gongal, Human molecular genetics 2008 (PubMed)- GeneRIF: Tgif is necessary for normal initiation of genes that control RA synthesis and degradation, resulting in defects in RA-dependent central nervous system patterning in Tgif-depleted embryos.
XP_006499416 homeobox protein TGIF2 isoform X1 from Mus musculus
NP_775572 homeobox protein TGIF2 isoform a from Mus musculus
40% identity, 24% coverage
- Downregulation of TGIF2 is possibly correlated with neuronal apoptosis and autism-like symptoms in mice.
Lei, Brain and behavior 2022 - GeneRIF: Downregulation of TGIF2 is possibly correlated with neuronal apoptosis and autism-like symptoms in mice.
- Circular RNA circCPA4 promotes tumorigenesis by regulating miR-214-3p/TGIF2 in lung cancer.
Tao, Thoracic cancer 2021 - GeneRIF: Circular RNA circCPA4 promotes tumorigenesis by regulating miR-214-3p/TGIF2 in lung cancer.
- TGIF transcription factors repress acetyl CoA metabolic gene expression and promote intestinal tumor growth.
Shah, Genes & development 2019 - GeneRIF: Tgifs play an important role in regulating basic energy metabolism in normal cells, and that this function of Tgifs is amplified in some cancers.
- The juvenility-associated long noncoding RNA Gm14230 maintains cellular juvenescence.
Tano, Journal of cell science 2019 (PubMed)- GeneRIF: Gm14230 safeguards cellular juvenescence through recruiting the histone methyltransferase Ezh2 to Tgif2, thereby repressing the functional role of Tgif2 in cellular senescence.
- TGFβ-induced factor homeobox 2 blocks osteoblastic differentiation through targeting pSmad3/HDAC4/H4ac/Runx2 axis.
Yu, Journal of cellular physiology 2019 (PubMed)- GeneRIF: Tgif2 plays an important role in the regulation of osteoblastic differentiation in vitro
- Tgif1 and Tgif2 Repress Expression of the RabGAP Evi5l.
Anderson, Molecular and cellular biology 2017 - GeneRIF: Tgifs regulate ciliogenesis and suggests that Evi5l mediates at least part of this effect.
- Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2.
Cerdá-Esteban, Nature communications 2017 - GeneRIF: Studies indicate the reprogramming activity of TG-interacting factor 2 (TGIF2) and suggest a stepwise reprogramming paradigm.
- Tgif1 and Tgif2 Regulate Axial Patterning in Mouse.
Melhuish, PloS one 2016 - GeneRIF: loss of Tgif1 causes axial patterning defects that are enhanced by mutations in Tgif2
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- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different species were not high, three conserved helixes and one adjacent C-domain were prominent ( Fig. 2A ). Based on...”
BEL1_ARATH / Q38897 Homeobox protein BEL1 homolog from Arabidopsis thaliana (Mouse-ear cress) (see 8 papers)
NP_198957 POX (plant homeobox) family protein from Arabidopsis thaliana
AT5G41410 BEL1 (BELL 1); DNA binding / protein binding / transcription factor from Arabidopsis thaliana
42% identity, 10% coverage
- function: Plays a major role in ovule patterning and in determination of integument identity via its interaction with MADS-box factors. Formation of complex with AG-SEP dimers negatively regulates the carpel identity process and favors the maintenance of ovule identity. BEL1-STM complex maintains the indeterminacy of the inflorescence meristem. Required, with SPL, for cytokinin-induced PIN1 expression in ovules (PubMed:22786869).
subunit: May form heterodimeric complexes with TALE/KNOX proteins STM, KNAT1/BP, KNAT2 and KNAT5 (PubMed:17873098). Interacts with AG-SEP1 and AG-SEP3 dimers (PubMed:17693535). Interacts with KNATM, isoform KNATM-B (PubMed:18398054). Interacts with BZIP30 (PubMed:27402171). - CORONA, PHABULOSA and PHAVOLUTA collaborate with BELL1 to confine WUSCHEL expression to the nucellus in Arabidopsis ovules.
Yamada, Development (Cambridge, England) 2016 (PubMed)- GeneRIF: The branching ovules of the mutant resemble those of some fossil gymnosperms, implicating BEL1 and HD-ZIPIII genes as players in the evolution of the unbranched ovule form in extant angiosperms.
- The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis.
Bencivenga, The Plant cell 2012 - GeneRIF: The transcription factors BEL1 and SPL/NZZ, previously described as key regulators of ovule development, are needed for the auxin and cytokinin signaling pathways for the correct patterning of the ovule.
- Genetic and molecular interactions between BELL1 and MADS box factors support ovule development in Arabidopsis.
Brambilla, The Plant cell 2007 - GeneRIF: BEL1 interacts with the ovule identity MADS box factors when they dimerize with SEPALLATA proteins.
- PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference
Zhang, Plant direct 2020 - “...panel. 2.4 Functionalities 2.4.1 Searching phylogenes Users can search PhyloGenes using a UniProt ID (e.g. Q38897), gene ID (e.g. AT5G41410), gene symbol (e.g. BEL1), or a keyword that occurs within a gene family name (e.g. homeodomain). The allowable types of gene IDs are described in the...”
- Systematic identification of novel protein domain families associated with nuclear functions
Doerks, Genome research 2002 - “...70 / Unknown 15 ZnF_C2HC d P46995 (63-119) Q38897 (199-337) O44939 (546-616) First column, domain name; second column, domain description (e.g., associated...”
- Genome-wide characterization and expression analysis of GATA transcription factors under combination of light wavelengths and drought stress in potato
Aksoy, Plant direct 2024 - “...this group for the expression analysis. IV had two proteins, AT3G45620 (CUL4associated factor 8) and AT5G41410 (BEL1), respectively, which were highly upregulated under drought conditions and downregulated under light stress (DaszkowskaGolec et al., 2018 ; Rossel et al., 2002 ). StGATA24 from IV was chosen to...”
- Single-cell RNA-seq reveals a link of ovule abortion and sugar transport in Camellia oleifera
Zhao, Frontiers in plant science 2024 - “...experimental markers ( AT2G17950 / AtWUS , AT1G23420 / AtYAB4 , AT4G27330 / AtSPL , AT5G41410 / AtBEL1 , and AT5G42630 / AtKAN4 ) in PCMDB ( Jin etal., 2022 ), were utilized to determine that clusters 2, 5, 9, and 12 were OV cells. AtYAB4,...”
- Floral Homeotic Factors: A Question of Specificity
Goslin, Plants (Basel, Switzerland) 2023 - “...PI Two-hybrid [ 42 ] AT5G38480 GRF3 Growth regulating factor PI IP-MS [ 46 ] AT5G41410 BEL1 Homeodomain AG, SEP3 Reconstituted Complex [ 47 ] AT5G41920 SCL23 GRAS SEP4 Two-hybrid [ 48 ] AT5G61850 LFY FLO/LFY SEP3 Reconstituted Complex [ 49 ] Identifiers of the corresponding...”
- Arabidopsis TCP4 transcription factor inhibits high temperature-induced homeotic conversion of ovules
Lan, Nature communications 2023 - “...TCP10 (AT2G31070), TCP12 (AT1G68800), TCP13 (AT3G02150), TCP16 (AT3G45150), TCP17 (AT5G08070), TCP18 (AT3G18550), TCP24 (AT1G30210), BEL1 (AT5G41410), CRC (AT1G69180), HEC1 (AT5G67060), HEC2 (AT3G50330), HEC3 (AT5G09750), INO (AT1G23420), SEP3 (AT1G24260), SHP1 (AT3G58780), SHP2 (AT2G42830), SPT (AT4G36930), STK (AT4G09960) and WUS (AT2G17950). The amino acid, CDS, and genomic sequences...”
- Molecular Network for Regulation of Ovule Number in Plants
Qadir, International journal of molecular sciences 2021 - “...LUG AT4G32551 Gynoecium, ON carpel development [ 3 , 7 , 65 ] Arabidopsis BEL1 AT5G41410 SPL for CK-induced PIN1 expression in ovules [ 14 , 31 , 60 ] Arabidopsis , Brassica AG AT4G18960 Transcription regulation by RNA polymerase II [ 14 , 31 ,...”
- Molecular Control of Sporophyte-Gametophyte Ontogeny and Transition in Plants
Pandey, Frontiers in plant science 2021 - “...Arabidopsis eFP Browser, Winter et al., 2007 ). TABLE 2 Tissue-specific expression levels of BELL1 (At5g41410) in Arabidopsis. Tissue AtBELL1 expression level (Absolute) Cauline leaf 222.3 Cotyledon 109.3 Flower stage 9 33 Flower stage 10/11 70 Mature pollen 24.7 Haploid-to-Diploid Switch Genetic control for the haploid-to-diploid...”
- Deciphering the evolution of the ovule genetic network through expression analyses in Gnetum gnemon
Zumajo-Cardona, Annals of botany 2021 - “...BLAST search using arabidopsis sequences as query (BEL1 = At5g41410; KAN1 = At5g16560; KAN2 = At1g32240; KAN3 = At4g17695; KAN4 = At5g42630; UCN = At1g51170)....”
- Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi
Moseley, Cells 2021 - “...Gene Desc. Arth Phase Call Kafe Shift 1 (hrs) Spear Shift 2 Kaladp0748s0043 (CTF1) 6 AT5G41410 BEL1 POX (plant homeobox) family protein 12 6 0.97 Kaladp0007s0017 (CTF2) 14 AT2G46510 JAM1 ABA-inducible BHLH-type transcription factor 12 +2 0.91 Kaladp0007s0017 (CTF2) 14 AT1G01260 JAM2 basic helix-loop-helix (bHLH) DNA-binding...”
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VDAG_00465 uncharacterized protein from Verticillium dahliae VdLs.17
42% identity, 4% coverage
- Transcription factors containing both C2H2 and homeobox domains play different roles in Verticillium dahliae
Tang, mSphere 2024 - “...seven C 2 H 2 -homeobox transcription f actors in the genome of VdLs.17 are VDAG_00465, VDAG_02532, VDAG_02889, VDAG_04660, VDAG_04837, VDAG_04891, and VDAG_07897, named VdChtf1 to VdChtf7, respectively (Fig. S1A and B). To further investigate their functions, we knocked them out using Agrobacterium-mediated genetic transformation (...”
FGSG_07914 hypothetical protein from Fusarium graminearum PH-1
45% identity, 9% coverage
vaamana / CAD58040.1 homeodomain protein vaamana from Arabidopsis thaliana (see paper)
37% identity, 10% coverage
BLH9_ARATH / Q9LZM8 BEL1-like homeodomain protein 9; BEL1-like protein 9; Protein BELLRINGER; Protein LARSON; Protein PENNYWISE; Protein REPLUMLESS; Protein VAAMANA from Arabidopsis thaliana (Mouse-ear cress) (see 9 papers)
NP_195823 POX (plant homeobox) family protein from Arabidopsis thaliana
AT5G02030 RPL (REPLUMLESS); DNA binding / sequence-specific DNA binding / transcription factor from Arabidopsis thaliana
37% identity, 10% coverage
- function: Transcription factor that is involved in the preservation of the spiral phyllotactic arrangement leading to a regular pattern of organ initiation. Required for maintenance of stem cell fate in the shoot apical meristem, and is essential for specifying floral primordia and establishing early internode patterning events during inflorescence development. Acts as a transcription repressor of AG expression in floral and inflorescence meristems. Is also responsive of the nuclear import of SHOOT MERISTEMLESS (STM). In the fruit, plays a central role in patterning by negatively regulating SHP expression in order to prevent replum cells from adopting a valve margin cell fate.
subunit: May form heterodimeric complex with the TALE/KNOX proteins STM, KNAT1/BP and KNAT6 (PubMed:12897247, PubMed:16513846, PubMed:16741748). Interacts with KNATM, isoform KNATM-B (PubMed:18398054). - The REPLUMLESS Transcription Factor Controls the Expression of the RECEPTOR-LIKE CYTOPLASMIC KINASE VI_A2 Gene Involved in Shoot and Fruit Patterning of Arabidopsis thaliana.
Kenesi, International journal of molecular sciences 2024 - GeneRIF: The REPLUMLESS Transcription Factor Controls the Expression of the RECEPTOR-LIKE CYTOPLASMIC KINASE VI_A2 Gene Involved in Shoot and Fruit Patterning of Arabidopsis thaliana.
- Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
Khan, Plant physiology 2015 - GeneRIF: The data reveal a potential mechanism by which repression of lateral organ boundary genes by PNY-PNF is essential for flowering.
- The NTT transcription factor promotes replum development in Arabidopsis fruits.
Marsch-Martínez, The Plant journal : for cell and molecular biology 2014 (PubMed)- GeneRIF: NTT loss of function leads to reduced replum width and cell number, whereas increased expression promotes replum enlargement. NTT activates the homeobox gene BP, which, together with RPL, is important for replum development.
- A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes.
Etchells, BMC plant biology 2012 - GeneRIF: These data support a role for BLR in ordering the shoot apex.
- The role of PENNYWISE and POUND-FOOLISH in the maintenance of the shoot apical meristem in Arabidopsis.
Ung, Plant physiology 2011 - GeneRIF: PNY and PNF act to restrict organogenesis to the peripheral zone by maintaining a boundary between the central zone and peripheral zone.
- Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA156 module by the homeodomain proteins PENNYWISE and POUND-FOOLISH in Arabidopsis.
Lal, Molecular plant 2011 (PubMed)- GeneRIF: SPL3, SPL4, and SPL5 function is dependent upon PNY and PNF
- The same regulatory point mutation changed seed-dispersal structures in evolution and domestication.
Arnaud, Current biology : CB 2011 (PubMed)- GeneRIF: Reduced repla resembling Arabidopsis rpl mutant correlated across the Brassicaceae with a point mutation in a conserved cis-element of RPL. When introduced in Arabidopsis, this nucleotide change specifically reduced RPL expression + function in the fruit.
- Regulation of shoot meristem integrity during Arabidopsis vegetative development.
Ung, Plant signaling & behavior 2011 - GeneRIF: Regulation of meristem central zone integrity by PNY and PNF is crucial for vegetative and reproductive development.
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- Elucidating the callus-to-shoot-forming mechanism in Capsicum annuum 'Dempsey' through comparative transcriptome analyses
Han, BMC plant biology 2024 - “...five GO terms, two key hub genes were observed within the ternary GO network. The AT5G02030 homologue, BEL1-like homeodomain RPL ( CaDEM09G08050 ), was the hub among GO terms phloem or xylem histogenesis, post-embryonic plant morphogenesis, and pattern specification process. The AT1G73590 homologue, auxin efflux carrier...”
- “...of budding organs by directing auxin flow [ 14 ]. The BEL1-like homeodomain RPL ( AT5G02030 homologue CaDEM09G08050 ) interacts to regulate inflorescence growth positively, and the paralogous protein interacts positively with STM to regulate meristem function [ 85 ]. Ankyrin repeat and BTB/POZ domain-containing AT2G41370...”
- Floral Homeotic Factors: A Question of Specificity
Goslin, Plants (Basel, Switzerland) 2023 - “...AG Two-hybrid [ 42 ] AT4G37740 GRF2 Growth regulating factor PI Two-hybrid [ 42 ] AT5G02030 RPL Homeodomain AP1 IP-MS [ 19 ] AT5G05120 - Zinc finger PI Two-hybrid [ 42 ] AT5G09750 HEC3 Basic helix-loop-helix PI Two-hybrid [ 42 ] AT5G11270 OCP3 Homeodomain SEP1 Two-hybrid...”
- Differential tolerance to heat stress of young leaves compared to mature leaves of whole plants relate to differential transcriptomes involved in metabolic adaptations to stress
Xiang, AoB PLANTS 2022 - “...important regulatory mechanism ( Peaucelle et al. 2011 ). The gene encoding BLR (such as AT5G02030 ) was not expressed differentially between young and old leaf while PME5 showed significant differential expression especially under 10 h heat stress. Our results showed that three genes AT3G14310 ,...”
- VPB1 Encoding BELL-like Homeodomain Protein Is Involved in Rice Panicle Architecture
Li, International journal of molecular sciences 2021 - “...), OsBOP1 ( LOC_Os01g72020 ), OsBOP2 ( LOC_Os11g04600 ), OsBOP3 ( LOC_Os12g04410 ), PNY ( AT5G02030 ), BOP1 ( AT3G57130 ), and BOP2 ( AT2G41370 ). 5. Conclusions and Future Prospects In conclusion, we show that a BELL-like homeodomain protein, VPB1, is involved in the regulation...”
- Genetic and signalling pathways of dry fruit size: targets for genome editing-based crop improvement
Hussain, Plant biotechnology journal 2020 - “...) STK Arabidopsis AT4G09960 Ovule development Zhang et al. ( 2016 ) Homeobox RPL Arabidopsis AT5G02030 Homeodomain transcription factor Roeder et al. ( 2003 ) WOX14 Arabidopsis AT1G20700 Vasculature development Deveaux et al. ( 2008 ) bHLHfamily AMS Arabidopsis AT2G16910 Regulation of transcription Sorensen et al....”
- The Osmotin-Like Protein Gene PdOLP1 Is Involved in Secondary Cell Wall Biosynthesis during Wood Formation in Poplar
Li, International journal of molecular sciences 2020 - “...in the regulation of secondary cell wall biosynthesis. [ 18 , 73 ] PtrBEL1 Potri.010G197300 AT5G02030 BEL1 interacts with proteins related to wood formation to regulate secondary cell wall formation. [ 21 ] PtrbZIP42 Potri.017G106700 AT3G30530 BZIPs show vascular cell expression patterns and can bind to...”
- Convergent Evolution of the Seed Shattering Trait
Di, Genes 2019 - “...] A. thaliana AT5G60910 5 FRUITFULL, AGL8 Gu et al. [ 4 ] A. thaliana AT5G02030 5 REPLUMLESS Roeder et al. [ 7 ] A. thaliana AT1G32770 1 NST3, SND1 Mitsuda and Ohme-Takagi [ 9 ] A. thaliana AT2G46770 2 NST1 Mitsuda and Ohme-Takagi [ 9...”
- Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra
Wildhagen, Tree physiology 2018 - “...AT4G37750 AINTEGUMENTA (ANT) 0.93 3.75E69 Potri.014G012200 0.47 2.06E02 AT1G32170 Xyloglucan endotransglucosylase/hydrolase 30 Potri.003G097300 0.61 1.51E03 AT5G02030 REPLUMLESS (RPL) 0.86 5.29E51 Potri.010G197300 0.50 1.34E02 AT1G11580 Methylesterase PCR A Potri.011G135000 0.68 2.91E04 AT5G02030 REPLUMLESS (RPL) 0.90 1.69E59 Potri.010G197300 0.50 1.34E02 AT2G42800 Receptor like protein 29 Potri.008G211800 0.48 1.63E02...”
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VDAG_04660 uncharacterized protein from Verticillium dahliae VdLs.17
38% identity, 11% coverage
- Transcription factors containing both C2H2 and homeobox domains play different roles in Verticillium dahliae
Tang, mSphere 2024 - “...H 2 -homeobox transcription f actors in the genome of VdLs.17 are VDAG_00465, VDAG_02532, VDAG_02889, VDAG_04660, VDAG_04837, VDAG_04891, and VDAG_07897, named VdChtf1 to VdChtf7, respectively (Fig. S1A and B). To further investigate their functions, we knocked them out using Agrobacterium-mediated genetic transformation ( 23 ) and...”
XP_018120525 homeobox protein SIX2 isoform X2 from Xenopus laevis
44% identity, 21% coverage
XP_001653660 uncharacterized protein LOC5571407 isoform X2 from Aedes aegypti
42% identity, 12% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...45.4, 38.8, 32.3, 31.5, 30.2, 30.5, 33.3 and 32.5% similarity with TGIF of Aedes aegypti (XP_001653660), Culex quinquefasciatus (XP_001849992), Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio...”
IRX6A_DANRE / Q503Z8 Iroquois homeobox protein 6a from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
40% identity, 12% coverage
- function: Transcription factor (By similarity). Binds to the iroquois binding site (IBS) motif of target genes to regulate gene expression; functions as a transcriptional activator or repressor (By similarity). In concert with irx5a, plays a role in visual performance (PubMed:33891002).
BLH8_ARATH / Q9SJJ3 BEL1-like homeodomain protein 8; BEL1-like protein 8; Protein POUND-FOOLISH from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT2G27990 BLH8 (BEL1-LIKE HOMEODOMAIN 8); DNA binding / transcription factor from Arabidopsis thaliana
NP_180366 BEL1-like homeodomain 8 from Arabidopsis thaliana
37% identity, 10% coverage
- function: Required for specifying floral primordia and establishing early internode patterning events during inflorescence development.
subunit: May form heterodimeric complex with the TALE/KNOX proteins STM and KNAT1/BP - Identification of QTLs for early maturity-related traits based on RIL population of two elite cotton cultivars
Wang, BMC plant biology 2024 - “...for further analysis. GH_D03G1554 , annotated as BEL1-like homeodomain protein 8 , is homologous to AT2G27990 , which plays a key role in the process of plant flowering [ 33 ]. Moreover, this gene was predicted to interact with protein of LFY and AGL8 (AGAMOUS-LIKE 8)...”
- Identification of Genomic Regions Associated with Differences in Flowering Time and Inflorescence Architecture between Melastoma candidum and M. normale
Chen, International journal of molecular sciences 2024 - “...SNP(s) Arabidopsis Orthologs MLD38_040423 12 JAG 5 0.220.30 AT1G13400, AT1G68480 MLD38_004029 2 PNF 1 0.22 AT2G27990 MLD38_023819 7 FIL 1 0.26 AT2G45190 MLD38_035107 10 LAS 2 0.24, 0.24 AT1G55580...”
- Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
Kumar, Frontiers in plant science 2020 - “...redox-controlled regulator of SAR and development PAMP, ROS, P, JA, and BR signaling, BOP1/2 Potri.004G213300 AT2G27990 BLH8 + BEL1-like TF, regulating BOP1 and integrating stress signaling via JA PAMP, ROS, P, JA, and BR signaling, BOP1/2 Potri.001G392200 AT2G42590 GRF9 + GROWTH-REGULATING FACTOR 9, 14-3-3 gene. Binds...”
- Comparative transcriptome analyses define genes and gene modules differing between two Populus genotypes with contrasting stem growth rates
Han, Biotechnology for biofuels 2020 - “...analysis between Populus and Arabidopsis TALE factors showed a close relationship between BLH8 / PNF (At2g27990) and PeuBELL15 (Fig. 4 b). The PeuBELL15 gene showed higher expression levels throughout the growing season in Neva (Fig. 4 c). Tissue-specific expression analysis showed that PeuBELL15 gene mainly expressed...”
- Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship Between Photosynthesis and Leaf Development
Testone, Plants (Basel, Switzerland) 2019 - “...(NAC053) 0.971 6 NAC_1 Ce_contig47321 TF AT5G13180 VND-INTERACTING 2 (VNI2) 0.990 6 NAC_49 Ce_contig85206 TF AT2G27990 BEL1-LIKE HOMEODOMAIN PROTEIN 8 (BLH8) 0.893 6 TALE_22 Ce_contig23430 TF AT4G01250 WRKY22 0.957 6 WRKY_25 Ce_contig27558 TF AT4G23810 WRKY53 0.974 6 WRKY_29 Ce_contig33086 TF AT3G56400 WRKY70 0.963 6 WRKY_34 Ce_contig60019...”
- pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies
Zhang, Heredity 2017 - “...0.15 AT2G22540 2 9588685 1.00E16 0.072 16.74 5.41 AT2G18790 2 8124967 1.98E04 0.019 3.01 0.81 AT2G27990 2 11931686 4.95E14 0.041 12.32 2.25 AT3G47870 3 17653089 9.62E08 0.015 6.18 0.46 AT3G01780 3 286197 1.29E04 0.017 3.18 0.32 AT4G01220 4 518797 1.47E07 0.024 6.00 2.35 AT3G28780 3 10816150...”
- Developmental genetic mechanisms of C4 syndrome based on transcriptome analysis of C3 cotyledons and C4 assimilating shoots in Haloxylon ammodendron
Li, PloS one 2015 - “...ZF-HD family At3g14740 C2H2 family At1g79840 Homeobox family At5g65410 ZF-HD family At3g44750 * C2H2 family At2g27990 Homeobox family Putative negative regulators At1g01030 ABI3VP1 family At5g50915 bHLH family At2g46680 Homeobox family At1g25560 ABI3VP1 family At5g62610 bHLH family At3g01220 Homeobox family At1g03800 AP2-EREBP family At5g67060 bHLH family At3g61890...”
- Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta
Cano, PloS one 2013 - “...KNOTTED-LIKE1 KNAT1 Inhibition of flower differentiation and maturation Down-regulated -1.06 4.54E-02 1708 Cell fate specification At2g27990 POUND-FOOLISH PNF Inhibition of flower differentiation and maturation Down-regulated -1.18 2.93E-02 10076 Maintenance of floral meristem identity At1g65480 FLOWERING LOCUS T FT Inhibition of flower differentiation and maturation Down-regulated -1.28...”
- “...LOCUS T ( FT , At1g65480), KNOTTED-LIKE1 ( KNAT1 , At4g08150), POUND-FOOLISH ( PNF , At2g27990) and SEPATALLA4 ( SEP4 , At2g03710) genes were down-regulated, whereas the QUARTER2 ( QRT2 , At3g07970) gene was up-regulated ( Table 1 and Figure 4B ). FT produces a mobile...”
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- Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
Khan, Plant physiology 2015 - GeneRIF: The data reveal a potential mechanism by which repression of lateral organ boundary genes by PNY-PNF is essential for flowering.
- The role of PENNYWISE and POUND-FOOLISH in the maintenance of the shoot apical meristem in Arabidopsis.
Ung, Plant physiology 2011 - GeneRIF: PNY and PNF act to restrict organogenesis to the peripheral zone by maintaining a boundary between the central zone and peripheral zone.
- Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA156 module by the homeodomain proteins PENNYWISE and POUND-FOOLISH in Arabidopsis.
Lal, Molecular plant 2011 (PubMed)- GeneRIF: SPL3, SPL4, and SPL5 function is dependent upon PNY and PNF
- Regulation of shoot meristem integrity during Arabidopsis vegetative development.
Ung, Plant signaling & behavior 2011 - GeneRIF: Regulation of meristem central zone integrity by PNY and PNF is crucial for vegetative and reproductive development.
- A novel role of BELL1-like homeobox genes, PENNYWISE and POUND-FOOLISH, in floral patterning.
Yu, Planta 2009 (PubMed)- GeneRIF: PNF functions in the inner whorls to regulate flower patterning events. [PNF]
- Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1-like homeodomain proteins.
Rutjens, The Plant journal : for cell and molecular biology 2009 (PubMed)- GeneRIF: combined lesions in ATH1, PNY and PNF result in a full phenocopy of shoot apical meristem loss-of-function mutants.
- Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)
Roberts, BMC genomics 2017 - “...Ap m12 PRMT11 Protein arginine N-methyltransferase 1.1 Q9SU94 El m12 BLH8 BEL1-like homeodomain protein 8 Q9SJJ3 El m12 GDL15 GDSL esterase/lipase at1g29670 Q9C7N4 El m12 GK-2 Guanylate kinase 2 Q9M682 El m12 CUT1 3-ketoacyl-CoA synthase 6 Q9XF43 El m12 AATL1 Lysine histidine transporter-like 8 Q9SX98 El...”
IRX4_MOUSE / Q9QY61 Iroquois-class homeodomain protein IRX-4; Homeodomain protein IRXA3; Iroquois homeobox protein 4 from Mus musculus (Mouse) (see 2 papers)
XP_006517355 iroquois-class homeodomain protein IRX-4 isoform X1 from Mus musculus
37% identity, 12% coverage
- function: Likely to be an important mediator of ventricular differentiation during cardiac development
subunit: Interacts with the vitamin D receptor VDR but doesn't affect its transactivation activity. - Comparative quantitative mass spectrometry analysis of MHC class II-associated peptides reveals a role of GILT in formation of self-peptide repertoire.
Bogunovic, PloS one 2010 - “...cells. Peptide sequence Length (aa) Peptide Source Position * No of Cys ** ASSPAVTAP 9 Q9QY61 Iroquois homeodomain protein IRX-4 (515aa) 408416 10 KLDLGSGGRALGGVGTAPAGGPAS iTRAQ4plex(K)@1 24 BAF64834.1 Apoptosis-associated Tyr kinase 3 (1424aa) 10801103 18 SPRIQLSSCRSLESLR Protein Terminal iTRAQ4plex@N-term, Methylthio(C)@9 16 Q8BKW6 Putative uncharectarized protein (Fragment) [Syde...”
- “...PP 19aa Q9Z1R2 Large proline-rich protein BAT3 (1154 aa) 7.485 21.01% 5. ASSPAVTAP ASSPAVTAP 9aa Q9QY61 Iroquois homeodomain protein IRX-4 (515aa) 7.092 19.90% 6. ATAGSGGVNGG A TAGSGGVNG G 11aa Q00PI9 Heterogeneous nuclear ribonucleoprotein U-like protein 2 (MLF1-associated nuclear protein) [Hnrnpul2] (745aa) 0.756 2.12% 7. AATEGTTAT AATEGTTAT...”
- Irx4 identifies a chamber-specific cell population that contributes to ventricular myocardium development.
Nelson, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - GeneRIF: IRX4+ cells in the cardiac crescent represent the earliest cell population in the cellular hierarchy underlying ventricular myocardium development.
NP_001153689 vismay from Tribolium castaneum
41% identity, 19% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...of Aedes aegypti (XP_001653660), Culex quinquefasciatus (XP_001849992), Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence...”
BLH10_ARATH / Q9FXG8 BEL1-like homeodomain protein 10; BEL1-like protein 10 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G19700 BEL10 (BEL1-LIKE HOMEODOMAIN 10); DNA binding / transcription factor from Arabidopsis thaliana
36% identity, 11% coverage
- subunit: Interacts with TLP1. May form heterodimeric complexes with TALE/KNOX proteins (By similarity). Interacts with OFP1, OFP2, OFP4 and OFP5.
- The Trithorax Group Factor ULTRAPETALA1 Regulates Developmental as Well as Biotic and Abiotic Stress Response Genes in Arabidopsis
Tyler, G3 (Bethesda, Md.) 2019 - “...HIG1 1.54 1.29E-04 At3g50060 MYB77 0.90 6.42E-04 Homeobox HD-Zip I At3g01220 ATHB20 1.09 6.68E-06 BEL At1g19700 BEL10 0.65 0.000809994 AT-hook At4g14465 AHL20 0.89 3.69E-04 bZIP At1g06850 bZIP52 0.88 1.83E-04 bHLH At3g19860 bHLH121 1.01 1.17E-04 C2H2 At1g27730 STZ, ZAT10 1.67 7.16E-04 DOF At1g69570 CDF5 0.86 5.95E-05 HSF...”
- Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development
Laubscher, Scientific reports 2018 - “...AT1G75410 BEL1-LIKE HOMEODOMAIN 3 (BLH3) 3.4 4.4 AT4G34610 BEL1-LIKE HOMEODOMAIN 6 (BLH6) 18.5 12.9 361.7 AT1G19700 BEL1-LIKE HOMEODOMAIN 10 (BEL10) 3.5 5.7 AT1G66810 CCCH ZINC FINGER 14 (C3H14) 5.2 7.5 34.0 AT1G62990 KNOTTED-LIKE HOMEOBOX OF ARABIDOPSIS THALIANA 7 (KNAT7) 162.4 108.8 1139.7 AT2G40470 LATERAL ORGAN BOUNDARIES...”
- Skewing in Arabidopsis roots involves disparate environmental signaling pathways
Schultz, BMC plant biology 2017 - “...NONEXPRESSER OF PATHOGENESIS-RELATED 1 ; At4g16890 and At1g64280, respectively) and BEL1-LIKE HOMEODOMAIN 10 (BEL10 ; At1g19700, where BEL1 is a homeodomain transcription factor controlling ovule patterning; At5g41410). MOS2 is a DNA-binding gene that plays a role in the immune response pathway and in microRNA (miRNA) maturation...”
- An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: application on Arabidopsis thaliana
Santoni, Omics : a journal of integrative biology 2014 - “...3 3 3 3 3 AT2G24550 AT1G76520 AT1G19700 AT1G23390 AT1G32640 AT1G28480 AT2G02810 AT3G02140 AT2G22510 AT1G64150 AT1G31280 AT1G24260 AT2G38300 AT4G22212 AT1G62180...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...] [ 16 ] [ 16 ] [ 14 ] AT5G020309 BLH10 [ 16 ] AT1G19700 BLH11 AT1G75430 Plant KNOX1 proteins have been largely characterized in monocotyledons and dicotyledons as key players in developmental processes where a fine equilibrium between undifferentiated and differentiated cell fate is...”
- Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model
Ingkasuwan, BMC systems biology 2012 - “...p At2g35940 Homeo domain HB Y 0.233 2173 127 12/89 At4g17090 b-AMY3 0.0674 / p At1g19700 HB-ZIP HB Y 0.009 7815 644 41/89 At4g17090 b-AMY3 0.0916 / p At4g39780 AP2 domain AP2-EREBP Y -0.179 18803 1537 110/130 At4g17090 b-AMY3 0.0810 / p At3g58680 ethylene-responsive MBF1 NA...”
- Expression of ROS-responsive genes and transcription factors after metabolic formation of H(2)O(2) in chloroplasts
Balazadeh, Frontiers in plant science 2012 - “...CCAAT-HAP2 0.08 0.43 At3g24120 GARP-G2-like 0.25 0.59 At1g17920 HB 0.71 0.02 At1g20693 HMG 0.09 0.62 At1g19700 HB 0.25 0.60 At1g20696 HMG 0.12 0.51 At1g20700 HB 0.24 0.40 At2g17560 HMG 0.01 0.52 At2g34450 HMG 0.28 0.23 At1g23380 HB 0.88 1.05 At3g28730 HMG 0.80 0.27 At1g26960 HB 0.45...”
- High-diversity genes in the Arabidopsis genome
Cork, Genetics 2005 - “...by our BLAST analysis (AT1G63910, AT5G24300, AT1G19700) (Table 1 and supplementary Tables S2 and S3 at http://www.genetics.org/supplemental/). Primers...”
- “...soluble starch synthase I enzyme; and (iii) AT1G19700, which encodes a member of the homeobox-leucine zipper transcription factor gene family. High-diversity...”
IRX4_HUMAN / P78413 Iroquois-class homeodomain protein IRX-4; Homeodomain protein IRXA3; Iroquois homeobox protein 4 from Homo sapiens (Human) (see paper)
NP_001265561 iroquois-class homeodomain protein IRX-4 isoform b from Homo sapiens
37% identity, 12% coverage
- function: Likely to be an important mediator of ventricular differentiation during cardiac development
subunit: Interacts with the vitamin D receptor VDR but doesn't affect its transactivation activity. - Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
Malik, Proteins 2024 (PubMed)- GeneRIF: Dynamics and recognition of homeodomain containing protein-DNA complex of IRX4.
- Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer.
Fernando, Genes 2021 - GeneRIF: Identification and Characterization of Alternatively Spliced Transcript Isoforms of IRX4 in Prostate Cancer.
- Epigenetic inactivation of IRX4 is responsible for acceleration of cell growth in human pancreatic cancer.
Chakma, Cancer science 2020 - GeneRIF: Epigenetic inactivation of IRX4 is responsible for acceleration of cell growth in human pancreatic cancer.
- Variants at IRX4 as prostate cancer expression quantitative trait loci.
Xu, European journal of human genetics : EJHG 2014 - GeneRIF: We independently validated IRX4 as a potential prostate cancer risk gene through cis-expression quantitative trait loci analysis of prostate cancer risk variants.
- IRX4 at 5p15 suppresses prostate cancer growth through the interaction with vitamin D receptor, conferring prostate cancer susceptibility.
Nguyen, Human molecular genetics 2012 (PubMed)- GeneRIF: the prostate cancer (PC)-susceptibility locus represented by rs12653946 at 5p15 is likely to regulate IRX4 expression in prostate which could suppress PC growth by interacting with the VDR pathway, conferring to PC susceptibility
- Two novel mutations of the IRX4 gene in patients with congenital heart disease.
Cheng, Human genetics 2011 (PubMed)- GeneRIF: IRX4 had a potential causative impact on the development of congenital heart disease, particularly ventricular septal defect.
- Genetic determinants of cardiovascular events among women with migraine: a genome-wide association study.
Schürks, PloS one 2011 - GeneRIF: Among migraineurs with aura rs7698623 in MEPE (OR = 6.37; 95% CI 3.15-12.90; p = 2.7x10(-7)) and rs4975709 in IRX4 (OR = 5.06; 95% CI 2.66-9.62; p = 7.7x10(-7)) appeared to be associated with ischemic stroke.
- Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Bailey, Diabetes care 2010 - GeneRIF: Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
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NP_524047 mirror, isoform A from Drosophila melanogaster
38% identity, 9% coverage
- Spalt-mediated dve repression is a critical regulatory motif and coordinates with Iroquois complex in Drosophila vein formation.
Sugimori, Mechanisms of development 2016 (PubMed)- GeneRIF: The relationship between Sal, Dve, and Iro-C in wing vein specification is quite similar to that in ommatidial cell-type specification. Our results provide information about the conserved function of dve regulatory motifs in cell differentiation.
- Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror.
Peters, Developmental biology 2013 - GeneRIF: indicate that tramtrack69 regulates ovary epithelial tube morphogenesis through Paxillin, Dynamin, and the homeobox protein Mirror.
- The Iroquois complex is required in the dorsal mesoderm to ensure normal heart development in Drosophila.
Mirzoyan, PloS one 2013 - GeneRIF: Iro-C as a new set of transcription factors that are required for normal development of the heart
- Mirror represses pipe expression in follicle cells to initiate dorsoventral axis formation in Drosophila.
Andreu, Development (Cambridge, England) 2012 (PubMed)- GeneRIF: findings show that Mirror (Mirr), a homeodomain transcription factor induced by EGFR signaling in DA follicle cells, directly represses pipe expression by binding to a conserved element in the pipe regulatory region
- Convergent local identity and topographic projection of sensory neurons.
Karim, The Journal of neuroscience : the official journal of the Society for Neuroscience 2011 - GeneRIF: Manipulation of mirror activity in class IV neurons retargets axonal projections and causes concordant changes in larval nociceptive escape behavior.
- Prepatterning the Drosophila notum: the three genes of the iroquois complex play intrinsically distinct roles.
Ikmi, Developmental biology 2008 (PubMed)- GeneRIF: Caupolican and mirror, but not araucan, are required for the neural patterning of the lateral notum and are required for stripe expression and, therefore, to specify the muscular attachment sites prepattern.
- Apposition of iroquois expressing and non-expressing cells leads to cell sorting and fold formation in the Drosophila imaginal wing disc.
Villa-Cuesta, BMC developmental biology 2007 - GeneRIF: Cells that overexpress a member of the Iro-C and that confront non-expressing cells establish contacts between themselves and become organized in a network of thin strings
- Capicua regulates follicle cell fate in the Drosophila ovary through repression of mirror.
Atkey, Development (Cambridge, England) 2006 (PubMed)- GeneRIF: Capicua regulates the pattern of follicle cell fates along the dorsoventral axis by blocking the induction of appendage determinants, such as mirror, by anterior positional cues
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BLH3_ARATH / Q9FWS9 BEL1-like homeodomain protein 3; BEL1-like protein 3 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G75410 BLH3 (BEL1-LIKE HOMEODOMAIN 3); DNA binding / transcription factor from Arabidopsis thaliana
NP_177674 BEL1-like homeodomain 3 from Arabidopsis thaliana
32% identity, 13% coverage
- function: Transcription factor that is responsive of the nuclear import of SHOOT MERISTEMLESS (STM).
subunit: May form heterodimeric complex with the TALE/KNOX protein STM. Interacts with OFP1, OFP2, OFP3, OFP4, OFP5 and OFP15. - Overexpression and cosuppression of xylem-related genes in an early xylem differentiation stage-specific manner by the AtTED4 promoter
Endo, Plant biotechnology journal 2018 - “...7.264 2.244 3 At5g49900 0.194 0.018 20 At5g17600 7.397 3.301 0 At1g70550 0.225 0.023 5 At1g75410 15.512 2.736 3 At2g38480 0.231 0.021 2 At4g28500 18.555 0.095 2 At5g26330 0.263 ( n =2) 1 At5g03170 23.441 3.623 0 At5g08370 0.311 ( n =2) 13 At2g38080 27.376 0.503...”
- “...T3 lines. The data are the meansSD ( n =3). The AtTED4 promoter could overexpress At1g75410, At4g28500, At4g18780, At5g60490 and At3g16920 genes in the nonrepeat type lines, even though their wildtype expression level was much higher than that of wildtype AtTED4 expression level (Figure 4 b;...”
- Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development
Laubscher, Scientific reports 2018 - “...Linear fold change EgrNAC26-OX EgrNAC61-OX 7 hpt 14 hpt 7 hpt 14 hpt Transcription factors AT1G75410 BEL1-LIKE HOMEODOMAIN 3 (BLH3) 3.4 4.4 AT4G34610 BEL1-LIKE HOMEODOMAIN 6 (BLH6) 18.5 12.9 361.7 AT1G19700 BEL1-LIKE HOMEODOMAIN 10 (BEL10) 3.5 5.7 AT1G66810 CCCH ZINC FINGER 14 (C3H14) 5.2 7.5 34.0...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...[ 8 ] [ 8 ] [ 16 ] [ 16 ] [ 16 ] AT1G75410 BLH4/ SAW2 [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 14 ] AT2G23760 BLH5 [ 16 ] [ 16...”
- Expression of ROS-responsive genes and transcription factors after metabolic formation of H(2)O(2) in chloroplasts
Balazadeh, Frontiers in plant science 2012 - “...HB 0.28 1.29 At4g28610 GARP-G2-like 0.50 0.62 At1g73360 HB 0.50 0.20 At4g37180 GARP-G2-like 0.53 1.36 At1g75410 HB 0.09 0.62 At5g05090 GARP-G2-like 0.21 0.30 At5g06800 GARP-G2-like 0.46 0.73 At1g79840 HB 0.06 0.26 At5g16560 GARP-G2-like 0.68 0.18 At2g01430 HB 0.89 0.31 At5g03510 C2H2 0.33 0.01 At3g53340 CCAAT-HAP3 1.44...”
- Towards reliable isoform quantification using RNA-SEQ data
Howard, BMC bioinformatics 2010 - “...Figure 3 Example of several TAIR 8 gene models used in alternative splicing simulation. (A) AT1G75410, (B) AT2G40140, (C) AT2G01260 and (D) AT1G75380. For each of the 500 replications, we also computed approximate confidence intervals about the estimates. To evaluate the performance of our approximation, we...”
- “...confidence interval to see if it included the true value for the parameter. For the AT1G75410 simulation, 97.4% of the 95% C.I.s contained the true parameter; 92.2% of the 90% C.I.s contained the true parameter; and 63.2% of the 65% C.I.s contained the true parameter. This...”
- Ovate family protein1 interaction with BLH3 regulates transition timing from vegetative to reproductive phase in Arabidopsis.
Zhang, Biochemical and biophysical research communications 2016 (PubMed)- GeneRIF: These results support our assumption that, by interacting with OFP1, BLH3 forms a functional protein complex that controls timing of progression from vegetative to reproductive phase.
- Binding properties of the complex formed by the Arabidopsis TALE homeodomain proteins STM and BLH3 to DNA containing single and double target sites.
Viola, Biochimie 2009 (PubMed)- GeneRIF: the DNA-binding properties of the complex formed by the Arabidopsis TALE homeodomain (HD) proteins STM and BLH3
XP_001122713 iroquois-class homeodomain protein IRX-6 isoform X2 from Apis mellifera
41% identity, 18% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...(XP_001653660), Culex quinquefasciatus (XP_001849992), Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the...”
T265_04509 hypothetical protein from Opisthorchis viverrini
47% identity, 22% coverage
ECU10_1480 TRANSCRIPTION FACTOR OF THE TALE/PBX FAMILY from Encephalitozoon cuniculi GB-M1
39% identity, 29% coverage
- Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi
Pombert, Eukaryotic cell 2013 - “...E. romaleae and appears to be a distant paralog of ECU10_1480 found in all four congeners); (ii) in ECI the genes ECU06_0690 and ECU06_0700 are found in two...”
- Evolution of the sex-related locus and genomic features shared in microsporidia and fungi
Lee, PloS one 2010 - “...three homeodomain gene clusters described previously (six HD genes: ECU03_0600, ECU03_0610, ECU04_0970, ECU04_1030, ECU10_1470, and ECU10_1480) [17] , [51] in three E. cuniculi isolates that were previously proposed to represent candidate mating type loci [52] . Once again, however, no evidence for distinct alleles or idiomorphs...”
LOC100862767 uncharacterized protein LOC100862767 from Bombyx mori
40% identity, 16% coverage
SIX1A_DANRE / Q6DHF9 Homeobox protein six1a; Homeobox protein six1b; Sine oculis homeobox homolog 1a; Sine oculis homeobox homolog 1b from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
49% identity, 18% coverage
- function: Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development. Depending on context, functions as a transcriptional repressor or activator. Plays an important role in the development of the inner ear, where it promotes hair cell proliferation and inhibits proliferation of neural progenitor cells (By similarity). Required for normal myogenesis. Plays a role in the development of fast muscle fibers throughout the body, as well as the development of craniofacial muscles.
disruption phenotype: Morpholino knockdown of the protein disrupts both skeletal muscle development in the trunk and cranial muscle development. Disrupts myogenesis by interfering with the proliferation of dermomyotomal cells expressing pax7.
NP_001009904 homeobox protein six1a from Danio rerio
49% identity, 18% coverage
CAUP_DROME / P54269 Homeobox protein caupolican from Drosophila melanogaster (Fruit fly) (see paper)
NP_524046 caupolican from Drosophila melanogaster
35% identity, 10% coverage
- function: Controls proneural and vein forming genes. Positive transcriptional controller of ac-sc (achaete-scute). May act as an activator that interacts with the transcriptional complex assembled on the ac and sc promoters and participates in transcription initiation.
- Complementary expression of optomotor-blind and the Iroquois complex promotes fold formation to separate wing notum and hinge territories.
Wang, Developmental biology 2016 (PubMed)- GeneRIF: complementary expression of omb and Iro-C establishes the wing hinge/notum fold formation
- The Homeodomain Iroquois Proteins Control Cell Cycle Progression and Regulate the Size of Developmental Fields.
Barrios, PLoS genetics 2015 - GeneRIF: physical interaction of the Iroquois protein Caupolican with Cyclin E-containing protein complexes, through its IRO box and Cyclin-binding domains, underlies its activity in cell-cycle control.
- Drosophila araucan and caupolican integrate intrinsic and signalling inputs for the acquisition by muscle progenitors of the lateral transverse fate.
Carrasco-Rando, PLoS genetics 2011 - GeneRIF: Data show that genes araucan and caupolican as novel muscle identity genes that confer lateral transverse muscle identity, and the acquisition of this fate requires that Araucan/Caupolican repress other muscle identity genes such as slouch and vestigial.
- Prepatterning the Drosophila notum: the three genes of the iroquois complex play intrinsically distinct roles.
Ikmi, Developmental biology 2008 (PubMed)- GeneRIF: Caupolican and mirror, but not araucan, are required for the neural patterning of the lateral notum and are required for stripe expression and, therefore, to specify the muscular attachment sites prepattern.
- Antagonistic and cooperative actions of the EGFR and Dpp pathways on the iroquois genes regulate Drosophila mesothorax specification and patterning.
Letizia, Development (Cambridge, England) 2007 (PubMed)- GeneRIF: Antagonistic and cooperative actions of the EGFR and Dpp pathways on the iroquois genes regulate Drosophila mesothorax specification and patterning.
XP_002431193 Homeobox protein SIX1, putative from Pediculus humanus corporis
49% identity, 18% coverage
XP_011244637 homeobox protein SIX2 isoform X2 from Mus musculus
49% identity, 24% coverage
- Microglial SIX2 suppresses lipopolysaccharide (LPS)-induced neuroinflammation by up-regulating FXYD2 expression.
Cao, Brain research bulletin 2024 (PubMed)- GeneRIF: Microglial SIX2 suppresses lipopolysaccharide (LPS)-induced neuroinflammation by up-regulating FXYD2 expression.
- Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment.
Liang, Journal of the American Society of Nephrology : JASN 2023 - GeneRIF: Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment.
- Chromatin Remodelers Interact with Eya1 and Six2 to Target Enhancers to Control Nephron Progenitor Cell Maintenance.
Li, Journal of the American Society of Nephrology : JASN 2021 - GeneRIF: Chromatin Remodelers Interact with Eya1 and Six2 to Target Enhancers to Control Nephron Progenitor Cell Maintenance.
- Generation and characterization of Six2 conditional mice.
Li, Genesis (New York, N.Y. : 2000) 2020 - GeneRIF: Generation and characterization of Six2 conditional mice.
- Comprehensive analysis of chromatin signature and transcriptome uncovers functional lncRNAs expressed in nephron progenitor cells.
Nishikawa, Biochimica et biophysica acta. Gene regulatory mechanisms 2019 (PubMed)- GeneRIF: identified a lncRNA, Gm29418, in nephron progenitor cells that has an enhancer-like function on a key regulatory gene, Six2.
- Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number.
Combes, Kidney international 2018 - GeneRIF: Reveal a unique dose response of nephron progenitors to the level of SIX2 protein in which the role of SIX2 in progenitor proliferation versus self-renewal is separable.
- Gulo regulates the proliferation, apoptosis and mesenchymal-to-epithelial transformation of metanephric mesenchyme cells via inhibiting Six2.
He, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: Six2 expression is regulated by Gulo in the metanephric mesenchyme cells.
- Six2 is involved in GATA1-mediated cell apoptosis in mouse embryonic kidney-derived cell lines.
Xia, In vitro cellular & developmental biology. Animal 2017 (PubMed)- GeneRIF: GATA1 may be a potential regulator of Six2-maintained population of nephron progenitor cells.
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XP_005264157 homeobox protein SIX2 isoform X1 from Homo sapiens
49% identity, 17% coverage
XP_005212711 homeobox protein SIX2 isoform X1 from Bos taurus
49% identity, 17% coverage
SIX2_HUMAN / Q9NPC8 Homeobox protein SIX2; Sine oculis homeobox homolog 2 from Homo sapiens (Human) (see 3 papers)
49% identity, 18% coverage
- function: Transcription factor that plays an important role in the development of several organs, including kidney, skull and stomach. During kidney development, maintains cap mesenchyme multipotent nephron progenitor cells in an undifferentiated state by opposing the inductive signals emanating from the ureteric bud and cooperates with WNT9B to promote renewing progenitor cells proliferation. Acts through its interaction with TCF7L2 and OSR1 in a canonical Wnt signaling independent manner preventing transcription of differentiation genes in cap mesenchyme such as WNT4. Also acts independently of OSR1 to activate expression of many cap mesenchyme genes, including itself, GDNF and OSR1. During craniofacial development plays a role in growth and elongation of the cranial base through regulation of chondrocyte differentiation. During stomach organogenesis, controls pyloric sphincter formation and mucosal growth through regulation of a gene network including NKX2-5, BMPR1B, BMP4, SOX9 and GREM1. During branchial arch development, acts to mediate HOXA2 control over the insulin-like growth factor pathway. May also be involved in limb tendon and ligament development (By similarity). Plays a role in cell proliferation and migration.
subunit: Interacts with TCF7L2; in a canonical Wnt signaling independent manner; prevents transcription of differentiation genes in cap mesenchyme. Interacts with OSR1; form a strong repressor complex with TCF7L2, TLE2 and TLE3 to prevent the activation of Wnt/beta- catenin target genes in the cap mesenchyme. Interacts with HOXA11, EYA1 and EYA3. - Autoantibody profiling identifies predictive biomarkers of response to anti-PD1 therapy in cancer patients.
Tan, Theranostics 2020 - “...receptor signaling pathway; negative regulation of activated T cell proliferation 4 SIX2 Homeobox protein SIX2 Q9NPC8 transcription factor (PC00218) binding (GO:0005488); transcription regulator activity (GO:0140110) 5 EIF4E2 Eukaryotic translation initiation factor 4E type 2 (eIF-4E type 2) O60573 translation initiation factor binding (GO:0005488); transcription regulator activity...”
SIX2_MOUSE / Q62232 Homeobox protein SIX2; Sine oculis homeobox homolog 2 from Mus musculus (Mouse) (see 13 papers)
49% identity, 17% coverage
- function: Transcription factor that plays an important role in the development of several organs, including kidney, skull and stomach. During kidney development, maintains cap mesenchyme multipotent nephron progenitor cells in an undifferentiated state by opposing the inductive signals emanating from the ureteric bud and cooperates with WNT9B to promote renewing progenitor cells proliferation. Acts through its interaction with TCF7L2 and OSR1 in a canonical Wnt signaling independent manner preventing transcription of differentiation genes in cap mesenchyme such as WNT4. Also acts independently of OSR1 to activate expression of many cap mesenchyme genes, including itself, GDNF and OSR1. During craniofacial development plays a role in growth and elongation of the cranial base through regulation of chondrocyte differentiation (PubMed:20515681). During stomach organogenesis, controls pyloric sphincter formation and mucosal growth through regulation of a gene network including NKX2-5, BMPR1B, BMP4, SOX9 and GREM1 (PubMed:19660448). During branchial arch development, acts to mediate HOXA2 control over the insulin-like growth factor pathway (PubMed:18321982). May also be involved in limb tendon and ligament development (PubMed:7720577). Plays a role in cell proliferation and migration (By similarity).
subunit: Interacts with TCF7L2; in a canonical Wnt signaling independent manner; prevents transcription of differentiation genes in cap mesenchyme. Interacts with OSR1; form a strong repressor complex with TCF7L2, TLE2 and TLE3 to prevent the activation of Wnt/beta- catenin target genes in the cap mesenchyme. Interacts with HOXA11, EYA1 and EYA3.
disruption phenotype: Six2 knockout heterozygous mice not exhibit any obvious abnormalities. However, Six2 knockout nullizygous mice die soon after birth.
NP_001038160 homeobox protein SIX2 from Gallus gallus
49% identity, 18% coverage
- Combinatorial activity of Six1-2-4 genes in cephalic neural crest cells controls craniofacial and brain development.
Garcez, Cellular and molecular life sciences : CMLS 2014 - GeneRIF: Combinatorial activity of Six1, Six2, and Six4 genes in cephalic neural crest cells controls craniofacial and brain development.
- Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Abril, BMC genomics 2010 - “...homeobox protein 2 isoform c [Homo sapiens NP_001157150 5,00E-08 90_7545 SIX homeobox 2 [Gallus gallus] NP_001038160 7,00E-36 F6AJIXP02HBGHT SJCHGC06100 protein [Schistosoma japonicum] AAW24487 6,00E-11 90_3395 UBX domain containing 8, isoform CRA_d [Mus musculus] EDL41153 3,00E-14 90_1176 UBX domain-containing protein 4 [Mus musculus] NP_080666 1,00E-06 90_2625 ubx6(yeast)-related...”
NP_001153690 TGIF-like from Nasonia vitripennis
42% identity, 16% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different species were not...”
AT1G75430 BLH11 (BEL1-LIKE HOMEODOMAIN 11); transcription factor from Arabidopsis thaliana
39% identity, 19% coverage
- Conservation and Diversification of Circadian Rhythmicity Between a Model Crassulacean Acid Metabolism Plant Kalanchoë fedtschenkoi and a Model C3 Photosynthesis Plant Arabidopsis thaliana
Moseley, Frontiers in plant science 2018 - “...Transcriptional coactivator/pterin dehydratase 6 Kaladp0039s0495 8 AT1G68550 16 Integrase-type DNA-binding superfamily protein 8 Kaladp0095s0706 8 AT1G75430 16 BEL1-like homeodomain 11 8 Kaladp0037s0533 8 AT5G28300 16 Duplicated homeodomain-like superfamily protein 8 Kaladp1129s0043 8 AT4G17060 20 FRIGIDA interacting protein 2 12 Kaladp0095s0494 8 AT4G32570 20 TIFY domain protein...”
- Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra
Wildhagen, Tree physiology 2018 - “...PROTEIN-LIKE 4 0.86 3.35E50 Potri.007G138800 0.48 1.81E02 AT2G42800 Receptor like protein 29 Potri.008G211800 0.48 1.63E02 AT1G75430 BEL1-LIKE HOMEODOMAIN 11 (BLH11) 0.83 9.01E46 Potri.002G030900 0.60 2.03E03 AT2G36870 Xyloglucan endotransglucosylase/hydrolase 32 Potri.009G006600 0.51 1.08E02 AT1G77920 bZIP family transcription factor 0.85 7.85E50 Potri.002G090700 0.63 9.38E04 AT2G40610 Expansin A8 Potri.013G154700...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...16 ] [ 16 ] [ 14 ] AT5G020309 BLH10 [ 16 ] AT1G19700 BLH11 AT1G75430 Plant KNOX1 proteins have been largely characterized in monocotyledons and dicotyledons as key players in developmental processes where a fine equilibrium between undifferentiated and differentiated cell fate is required [...”
- Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana
Wynn, PloS one 2011 - “...All panels are Col-0 wild type tissue unless otherwise marked. BELL-LIKE HOMEODOMAIN 11 (BLH11) ( AT1G75430) expression was detected weakly in the inflorescence meristem and stage 1 and 2 floral meristems (data not shown). Expression is more strongly detected in sepal primordia during stages 3 and...”
- “...11 (data not shown). 10.1371/journal.pone.0026231.g013 Figure 13 Results of in situ hybridization with BLH11 ( AT1G75430 ) antisense probe. Numbers indicate floral stages. All panels show transverse (cross sectional) tissue orientation. Arrowheads indicate medial domain expression. Arrows indicate valve domain expression. ov - ovule; sp -...”
- Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants
Skinner, BMC plant biology 2009 - “...-2.35 1.07 1.06 (7) At4g36740 ATHB40 homeobox-leucine zipper Class I family -3.80 -1.89 -4.73 (11) At1g75430 --- homeodomain protein -2.02 1.03 1.04 (10) At5g41410 BEL1 homeodomain protein (ovule development) -2.66 -1.12 -1.11 (7) At5g17300 --- myb family -2.01 -1.21 -1.91 (3) At4g37260 MYB73 myb R2R3 family...”
- Transgenic increases in seed oil content are associated with the differential expression of novel Brassica-specific transcripts
Sharma, BMC genomics 2008 - “...acyl-CoA oxidase (At4g16760) and putative 3-ketoacyl-CoA reductase 1 (AY196196). Genes encoding a homeodomain-like transcription factor (At1g75430) and ATP-citrate lyase (At3g06650/DY00115) were also found to be up regulated in DGAT#17 at 22 daa or 26 daa (Figure 4 ). Figure 4 Expression of genes previously correlated with...”
- Genetic subtraction profiling identifies genes essential for Arabidopsis reproduction and reveals interaction between the female gametophyte and the maternal sporophyte
Johnston, Genome biology 2007 - “...Transcriptional Regulation At5g06070 Zinc Finger (C2H2 Type) Family Protein (RBE) 2 0 0 0 0 At1g75430 Homeodomain Protein 1 0 0 0 0 At2g01500 Homeodomain-Leucine Zipper (WOX6, PFA2) 1 0 0 0 1 At2g24840 MADS-Box Protein Type I (AGL61) 2 0 1 1 1 At1g02580 MEDEA...”
Q24248 Homeobox protein araucan from Drosophila melanogaster
NP_524045 araucan, isoform A from Drosophila melanogaster
35% identity, 10% coverage
- Identification of FOXO targets that generate diverse features of the diapause phenotype in the mosquito Culex pipiens
Sim, Proceedings of the National Academy of Sciences of the United States of America 2015 - “...sg 3.1245, 23,739-24,487 Homeobox protein Mitotic checkpoint Q24248 Q1JQB2 sg 3.1, 3,012,366-3,012,647 sg 3.788, 185,527-185,833 Takeout-like protein O76879 sg...”
- Drosophila araucan and caupolican integrate intrinsic and signalling inputs for the acquisition by muscle progenitors of the lateral transverse fate.
Carrasco-Rando, PLoS genetics 2011 - GeneRIF: Data show that genes araucan and caupolican as novel muscle identity genes that confer lateral transverse muscle identity, and the acquisition of this fate requires that Araucan/Caupolican repress other muscle identity genes such as slouch and vestigial.
- Prepatterning the Drosophila notum: the three genes of the iroquois complex play intrinsically distinct roles.
Ikmi, Developmental biology 2008 (PubMed)- GeneRIF: When caupolican and/or mirror expression is reduced, araucan loss of function has an effect on thoracic bristles development. Moreover, the overexpression of araucan is able to rescue caupolican loss of function.
- tailup, a LIM-HD gene, and Iro-C cooperate in Drosophila dorsal mesothorax specification.
de, Development (Cambridge, England) 2007 (PubMed)- GeneRIF: The data support a model in which the EGFR and Dpp signalling pathways, with their respective downstream Iro-C and tup genes, converge and cooperate to commit cells to the notum developmental fate.
- Mutual repression between msh and Iro-C is an essential component of the boundary between body wall and wing in Drosophila.
Villa-Cuesta, Development (Cambridge, England) 2005 (PubMed)- GeneRIF: Mutual repression between msh and Iro-C is an essential component of the boundary between body wall and wing in Drosophila.
XP_641195 homeodomain containing protein from Dictyostelium discoideum AX4
39% identity, 9% coverage
SIX1B_DANRE / Q6NZ04 Homeobox protein six1b; Homeobox protein six1a; Sine oculis homeobox homolog 1a; Sine oculis homeobox homolog 1b from Danio rerio (Zebrafish) (Brachydanio rerio) (see 6 papers)
NP_996978 homeobox protein six1b from Danio rerio
49% identity, 18% coverage
XP_002691065 homeobox protein SIX1 from Bos taurus
44% identity, 21% coverage
NP_001186647 homeobox protein SIX1 from Sus scrofa
49% identity, 18% coverage
SIX1_HUMAN / Q15475 Homeobox protein SIX1; Sine oculis homeobox homolog 1 from Homo sapiens (Human) (see 11 papers)
49% identity, 18% coverage
- function: Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development (By similarity). Plays an important role in the development of several organs, including kidney, muscle and inner ear (By similarity). Depending on context, functions as a transcriptional repressor or activator (By similarity). Lacks an activation domain, and requires interaction with EYA family members for transcription activation (PubMed:15141091). Mediates nuclear translocation of EYA1 and EYA2 (PubMed:19497856). Binds the 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the MYOG promoter and CIDEA enhancer (PubMed:15141091, PubMed:19497856, PubMed:23435380, PubMed:27923061). Regulates the expression of numerous genes, including MYC, CCND1 and EZR (By similarity). Acts as an activator of the IGFBP5 promoter, probably coactivated by EYA2 (By similarity). Repression of precursor cell proliferation in myoblasts is switched to activation through recruitment of EYA3 to the SIX1-DACH1 complex (By similarity). During myogenesis, seems to act together with EYA2 and DACH2 (By similarity). Regulates the expression of CCNA1 (PubMed:15123840). Promotes brown adipocyte differentiation (By similarity).
subunit: Interacts with DACH1 (By similarity). Interacts with EYA1 (By similarity). Interacts with EYA2 (PubMed:19497856, PubMed:23435380). Interacts with CDH1 (PubMed:17130831). Interacts with TBX18 (PubMed:26235987). Interacts with CEBPA (PubMed:27923061). Interacts with CEBPB (PubMed:27923061). Interacts with EBF2 (PubMed:27923061).
SIX1_MOUSE / Q62231 Homeobox protein SIX1; Sine oculis homeobox homolog 1 from Mus musculus (Mouse) (see 11 papers)
NP_033215 homeobox protein SIX1 from Mus musculus
NP_446211 homeobox protein SIX1 from Rattus norvegicus
44% identity, 21% coverage
- function: Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development (PubMed:12215533, PubMed:12668636, PubMed:12834866, PubMed:14628042, PubMed:14695375). Plays an important role in the development of several organs, including kidney, muscle and inner ear (PubMed:12668636, PubMed:12783782, PubMed:12834866, PubMed:14628042, PubMed:14695375). Depending on context, functions as a transcriptional repressor or activator (PubMed:14628042). Lacks an activation domain, and requires interaction with EYA family members for transcription activation (By similarity). Mediates nuclear translocation of EYA1 and EYA2 (By similarity). Binds the 5'-TCA[AG][AG]TTNC-3' motif present in the MEF3 element in the MYOG promoter and CIDEA enhancer (By similarity). Regulates the expression of numerous genes, including MYC, CCNA1, CCND1 and EZR (PubMed:16488997). Acts as an activator of the IGFBP5 promoter, probably coactivated by EYA2 (PubMed:11978764). Repression of precursor cell proliferation in myoblasts is switched to activation through recruitment of EYA3 to the SIX1-DACH1 complex (PubMed:14628042). During myogenesis, seems to act together with EYA2 and DACH2. Regulates the expression of CCNA1 (By similarity). Promotes brown adipocyte differentiation (PubMed:27923061).
subunit: Interacts with DACH1 (PubMed:14628042). Interacts with EYA1 (PubMed:15141091). Interacts with EYA2 (By similarity). Interacts with CDH1 (By similarity). Interacts with TBX18 (By similarity). Interacts with CEBPA (PubMed:27923061). Interacts with CEBPB (PubMed:27923061). Interacts with EBF2 (PubMed:27923061).
disruption phenotype: Perinatal lethality. Mice show failure in renal organogenesis, a severe reduction of most migratory hypaxial muscles including those of the forelimb, diaphragm and tongue, and severe rib- cage deformation. Besides, mice display craniofacial defects, including loss of inner ear structures. Pax2, Six2 and Sall1 expression is markedly reduced in the metanephric mesenchyme at 10.5 dpc during kidney development. Mice lacking both Six1 and Eya1 show defects in kidney development, complete absence of hypaxial muscle, severe reduction in epaxial muscle and a 5-10-fold by volume smaller pituarity than the wild-type gland. - miR-128-3p alleviates airway inflammation in asthma by targeting SIX1 to regulate mitochondrial fission and fusion.
Liu, International immunopharmacology 2024 (PubMed)- GeneRIF: miR-128-3p alleviates airway inflammation in asthma by targeting SIX1 to regulate mitochondrial fission and fusion.
- Detrimental role of SIX1 in hepatic lipogenesis and fibrosis of non-alcoholic fatty liver disease.
Gao, Liver international : official journal of the International Association for the Study of the Liver 2023 (PubMed)- GeneRIF: Detrimental role of SIX1 in hepatic lipogenesis and fibrosis of non-alcoholic fatty liver disease.
- SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state.
Hsu, Cell reports 2022 - GeneRIF: SIX1 reprograms myogenic transcription factors to maintain the rhabdomyosarcoma undifferentiated state.
- Hsa_circ_0017639 regulates cisplatin resistance and tumor growth via acting as a miR-1296-5p molecular sponge and modulating sine oculis homeobox 1 expression in non-small cell lung cancer.
Chang, Bioengineered 2022 - GeneRIF: Hsa_circ_0017639 regulates cisplatin resistance and tumor growth via acting as a miR-1296-5p molecular sponge and modulating sine oculis homeobox 1 expression in non-small cell lung cancer.
- Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis.
Wilson, JCI insight 2022 - GeneRIF: Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis.
- Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4α and SIX1/4.
Camolotto, Gut 2021 - GeneRIF: Reciprocal regulation of pancreatic ductal adenocarcinoma growth and molecular subtype by HNF4alpha and SIX1/4.
- Six1 Promotes Epithelial-Mesenchymal Transition in Bronchial Epithelial Cells via the TGFβ1/Smad Signalling Pathway.
Wang, International archives of allergy and immunology 2021 (PubMed)- GeneRIF: Six1 Promotes Epithelial-Mesenchymal Transition in Bronchial Epithelial Cells via the TGFbeta1/Smad Signalling Pathway.
- Dynamic changes in cis-regulatory occupancy by Six1 and its cooperative interactions with distinct cofactors drive lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.
Li, Nucleic acids research 2020 - GeneRIF: This study provides a mechanistic understanding of how Six1 cooperates with distinct cofactors in feedforward loops to control lineage-specific gene expression programs during progressive differentiation of the auditory sensory epithelium.
- More
- SIX1 induced HULC modulates neuropathic pain and Schwann cell oxidative stress after sciatic nerve injury.
Zhang, Gene 2023 (PubMed)- GeneRIF: SIX1 induced HULC modulates neuropathic pain and Schwann cell oxidative stress after sciatic nerve injury.
- SIX1 attenuates inflammation and rheumatoid arthritis by silencing MyD88-dependent TLR1/2 signaling.
Zhan, International immunopharmacology 2022 (PubMed)- GeneRIF: SIX1 attenuates inflammation and rheumatoid arthritis by silencing MyD88-dependent TLR1/2 signaling.
- Expression of Eya1 and Six1 is decreased in distal airways of rats with experimental pulmonary hypoplasia.
Friedmacher, Journal of pediatric surgery 2014 (PubMed)- GeneRIF: Downregulation of Eya1 and Six1 gene expression in nitrofen-induced PH suggests that decreased Eya1 and Six1 expression during the late pseudoglandular stage may interfere with epithelial branching and distal airway maturation, thus resulting in PH.
NCU05257 homeobox and C2H2 transcription factor from Neurospora crassa OR74A
33% identity, 5% coverage
- Regulatory functions of homeobox domain transcription factors in fungi
Calvo, Applied and environmental microbiology 2024 (secret) - mus-52 disruption and metabolic regulation in Neurospora crassa: Transcriptional responses to extracellular phosphate availability
Martins, PloS one 2018 - “...factor protein (NCU02142) coding gene, which was also down-regulated in the high-Pi condition. Although the NCU05257 gene displayed a fold change value (log2 = 1.47) lower than our expression threshold, it was nevertheless considered in our analysis. Conversely, four genes were up-regulated in low-Pi condition, highlighting...”
- “...2489 and mutant FGSC 9568 strains. Among these, seven genes (NCU00038; NCU001386; NCU02142; NCU02499; NCU03643; NCU05257, and NCU08507) were concomitantly modulated in both phosphate availability conditions, with NCU00038 as the only single DEG up-regulated in both Pi conditions ( Fig 3 ). Most of the TFs...”
- Discovering functions of unannotated genes from a transcriptome survey of wild fungal isolates
Ellison, mBio 2014 - “...this strategy in the context of an unannotated transcription factor, we focused on the gene NCU05257, which encodes a predicted zinc finger and homeobox DNA-binding protein and which fell into an expression cluster containing 58 other genes in our analysis of expression among wild N.crassa strains...”
- “...enriched for genes annotated in amino acid metabolism; see Data SetS1 and TableS2 ), and NCU05257 was previously reported to be a putative target of the N.crassa amino acid biosynthesis regulator CPC1 ( 23 ). To test the regulatory impact of NCU05257 directly, we used transcriptome...”
NP_071873 iroquois-class homeodomain protein IRX-6 isoform 1 from Mus musculus
38% identity, 13% coverage
IRX6_MOUSE / Q9ER75 Iroquois-class homeodomain protein IRX-6; Homeodomain protein IRXB3; Iroquois homeobox protein 6 from Mus musculus (Mouse) (see 2 papers)
38% identity, 13% coverage
- function: Transcription factor (PubMed:23172916). Binds to the iroquois binding site (IBS) motif of target genes to regulate gene expression; functions as a transcriptional activator or repressor (PubMed:23172916). Modulates expression of RCVRN, VSX1, BHLHE22/BHLHB5 and TACR3/Nk3r (PubMed:23172916). Required downstream of retinal bipolar cell specification for the terminal differentiation of type 2, type 3a and possibly type 6 bipolar cells (PubMed:23172916).
NP_001038150 homeobox protein SIX1 from Gallus gallus
49% identity, 18% coverage
NP_001092203 mohawk homeobox a from Danio rerio
38% identity, 17% coverage
Smp_149230 iroquois homeobox family transcription factor from Schistosoma mansoni
41% identity, 9% coverage
NCU00097 BEAK-1 from Neurospora crassa OR74A
35% identity, 21% coverage
- Clustering analysis of large-scale phenotypic data in the model filamentous fungus Neurospora crassa
Carrillo, BMC genomics 2020 - “...genes that are consistently co-regulated across multiple datasets. In Cluster 14, the transcription factors bek-1 (NCU00097) [ 59 ] and bek-2 (NCU07139), the guanosine diphosphatase gda-1 (NCU03713), hypothetical protein NCU06390 and the S/T kinase stk-53 (NCU09064) share the same expression profile during conidial germination and sexual...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...coli CS Orth NCU11289 23565 fail aldo-keto reductase E. coli CS Orth Catalytic Activity/transporter Activity NCU00097 11110 fail BEAK-1 bek-1 Transc Factors NCU02017 11108 fail CBF/NF-Y family transcription factor ada-2 Transc Factors NCU00056 21444 fail condensing enzyme with mitochondrial function cem-1 E. coli CS Orth NCU00467...”
- Functional Profiling of Transcription Factor Genes in Neurospora crassa
Carrillo, G3 (Bethesda, Md.) 2017 - “...different transcription factor families contribute to proper perithecial beak development; the homeodomain mutant bek-1 / NCU00097 ( Krystofova and Borkovich 2006 ), the C6 mutant bek-2 / NCU07139 , the BHLH mutant vsd-3 / NCU08999 and the BZIP mutant ada-1 / NCU00499 completely lacked perithecial beaks,...”
- Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa
Wang, Eukaryotic cell 2014 - “...(48), expression of TFs related to sexual development (NCU00097, NCU04561, NCU09739, NCU07392, and NCU044731) showed 5- to 20-fold changes across all time...”
- Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex
Smith, Eukaryotic cell 2010 - “...TF NCU08807 cre-1 TF/NCU08806 rhp-55 NCU07392 adv-1 TF NCU00097 bek-1TF NCU07705 TF NCU01154 sub-1 TF NCU06534 TF/NCU06536 NCU04731 sah-2 TF NCU07728 sre TF...”
- A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors
Colot, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...(NCU06411), CBF CAAT-binding factor (NCU02017), and homeobox (NCU00097 and NCU03593). Genes showing ascospore lethality are shown in the oval. The numbers...”
NP_523714 vismay, isoform A from Drosophila melanogaster
42% identity, 13% coverage
XP_005538442 similar to BEL1-related homeotic protein from Cyanidioschyzon merolae strain 10D
38% identity, 18% coverage
- A unique life cycle transition in the red seaweed Pyropia yezoensis depends on apospory
Mikami, Communications biology 2019 - “...Arabidopsis thaliana , AtKNAT3 X92392; Chondrus crispus , CcBELL1 XP_005711328; Cyanidioschyzon merolae , CmKNOX (CMR153C) XP_005538442, CmBELL1 (CMH049C) XP_005536034, CmBELL2 (CMR176C) XP_005538457. PopKNOX (esisotig02479) and PouKNOX (esisotig04347) are KNOX homologs of Porphyra purpurea and Porphyra umbilicalis , respectively, which were derived from NoriBLAST ( http://dbdata.rutgers.edu/nori/ )....”
IRX4A_XENLA / Q90XW6 Iroquois-class homeodomain protein irx-4-A; Iroquois homeobox protein 4-A from Xenopus laevis (African clawed frog) (see 3 papers)
37% identity, 12% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Does not appear to play a role in pronephros kidney development.
NP_808263 homeobox protein Mohawk from Mus musculus
38% identity, 17% coverage
- The Transcription Factor Mohawk Facilitates Skeletal Muscle Repair via Modulation of the Inflammatory Environment.
Lynch, International journal of molecular sciences 2024 - GeneRIF: The Transcription Factor Mohawk Facilitates Skeletal Muscle Repair via Modulation of the Inflammatory Environment.
- Involvement of homeobox transcription factor Mohawk in palatogenesis.
Adachi, Congenital anomalies 2022 (PubMed)- GeneRIF: Involvement of homeobox transcription factor Mohawk in palatogenesis.
- Mohawk impedes angiofibrosis by preventing the differentiation of tendon stem/progenitor cells into myofibroblasts.
Mechakra, Scientific reports 2022 - GeneRIF: Mohawk impedes angiofibrosis by preventing the differentiation of tendon stem/progenitor cells into myofibroblasts.
- Mkx-Deficient Mice Exhibit Hedgehog Signaling-Dependent Ectopic Ossification in the Achilles Tendons.
Liu, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2019 - GeneRIF: Mkx-Deficient Mice Exhibit Hedgehog Signaling-Dependent Ectopic Ossification in the Achilles Tendons.
- The transcription factor mohawk homeobox regulates homeostasis of the periodontal ligament.
Koda, Development (Cambridge, England) 2017 - GeneRIF: Mkx prevents periodontal ligament degeneration by regulating osteogenesis.
- Gtf2ird1-Dependent Mohawk Expression Regulates Mechanosensing Properties of the Tendon.
Kayama, Molecular and cellular biology 2016 - GeneRIF: Gtf2ird1 is essential for Mkx transcription, while also linking mechanical forces to Mkx-mediated tendon homeostasis and regeneration.
- Gene targeting of the transcription factor Mohawk in rats causes heterotopic ossification of Achilles tendon via failed tenogenesis.
Suzuki, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: accelerates tendon differentiation and prevents chondrogenic/osteogenic differentiation
- Mohawk promotes the maintenance and regeneration of the outer annulus fibrosus of intervertebral discs.
Nakamichi, Nature communications 2016 - GeneRIF: Data show that homeobox protein Mohawk (Mkx) is mainly expressed in the outer annulus fibrosus (OAF) of humans and mice.
- More
MKX_MOUSE / Q8BIA3 Homeobox protein Mohawk from Mus musculus (Mouse) (see paper)
38% identity, 17% coverage
- function: May act as a morphogenetic regulator of cell adhesion. Participates in the early events that lead to differentiation.
NP_001122206 homeobox protein SIX2b from Danio rerio
44% identity, 21% coverage
IRX4_XENTR / Q688D0 Iroquois-class homeodomain protein irx-4; Iroquois homeobox protein 4 from Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (see paper)
37% identity, 12% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Does not appear to play a role in pronephros kidney development.
NP_001229631 homeobox protein Mohawk from Homo sapiens
38% identity, 17% coverage
- COBL, MKX and MYOC Are Potential Regulators of Brown Adipose Tissue Development Associated with Obesity-Related Metabolic Dysfunction in Children.
Abdul, International journal of molecular sciences 2023 - GeneRIF: COBL, MKX and MYOC Are Potential Regulators of Brown Adipose Tissue Development Associated with Obesity-Related Metabolic Dysfunction in Children.
- Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity.
Lee, Science translational medicine 2020 - GeneRIF: Mohawk is a transcription factor that promotes meniscus cell phenotype and tissue repair and reduces osteoarthritis severity.
- Mohawk promotes the maintenance and regeneration of the outer annulus fibrosus of intervertebral discs.
Nakamichi, Nature communications 2016 - GeneRIF: Data show that homeobox protein Mohawk (Mkx) is mainly expressed in the outer annulus fibrosus (OAF) of humans and mice.
- Transcription factor Mohawk controls tenogenic differentiation of bone marrow mesenchymal stem cells in vitro and in vivo.
Otabe, Journal of orthopaedic research : official publication of the Orthopaedic Research Society 2015 - GeneRIF: Transcription factor Mohawk controls tenogenic differentiation of bone marrow mesenchymal stem cells in vitro and in vivo.
- Mohawk promotes the tenogenesis of mesenchymal stem cells through activation of the TGFβ signaling pathway.
Liu, Stem cells (Dayton, Ohio) 2015 (PubMed)- GeneRIF: these data shed light on previously unrecognized roles of Mkx in tendinopathy, tenogenesis, and tendon repair as well as in regulating the TGFbeta pathway.
- Transcription factor Mohawk and the pathogenesis of human anterior cruciate ligament degradation.
Nakahara, Arthritis and rheumatism 2013 - GeneRIF: Reduced expression of MKX is a feature of degenerated anterior cruciate ligament in osteoarthritis-affected joints.
- Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
Jugessur, PloS one 2010 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- In silico characterization of an Iroquois family-related homeodomain protein.
Weinmann, International journal of molecular medicine 2005 (PubMed)- GeneRIF: In silico characterization of the C10orf48 sequence
FWA_ARATH / Q9FVI6 Homeobox-leucine zipper protein HDG6; HD-ZIP protein HDG6; Homeobox protein FWA; Homeodomain GLABRA 2-like protein 6; Homeodomain transcription factor HDG6; Protein HOMEODOMAIN GLABROUS 6 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G25530, NP_567722 FLOWERING WAGENINGEN from Arabidopsis thaliana
NP_567722 FWA; DNA binding / protein binding / protein homodimerization/ transcription factor from Arabidopsis thaliana
41% identity, 9% coverage
- function: Probable transcription factor involved in the regulation of time of flowering through the photoperiod flowering pathway. May repress FT.
subunit: Interacts with FT. - Targeted DNA demethylation of the Arabidopsis genome using the SunTag-dCpf1-TET1cd system
Zheng, microPublication biology 2023 - “...it away (-). Data shown as mean SD (n = 3 technical replicates). FWA : AT4G25530; CACTA1 : AT2G12210; IPP2 : AT3G02780; TUB2 : AT5G62690. Values shown are means SD from three replicates. Asterisks represent significant differences determined by Students t -test (** P < 0.01)....”
- “...caused by loss of DNA methylation in the promoter of the FLOWERING WAGENINGEN ( FWA, AT4G25530) gene (Johnson et al., 2014), which provides a new genetic source for crop breeding. CRISPR/dCas9-based SunTag-TET1cd system has been recently applied to achieve targeted DNA demethylation and up-regulation of the...”
- Genome editing in plants using the compact editor CasΦ
Li, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...( 34 ) in Col-0 plants versus the fwa-4 epi-mutant plants at the FWA gene (AT4G25530) promoter region. The relative positions of the Cas-2 guide RNAs are illustrated in the schematic below. ( B ) Cas-2 editing efficiencies at the target loci in the FWA promoter...”
- DDT-RELATED PROTEIN4-IMITATION SWITCH alters nucleosome distribution to relieve transcriptional silencing in Arabidopsis
Zhang, The Plant cell 2023 - “...(DDR1), AT1G67780 (DDR3), AT5G08630 (DDW1), AT3G06400 (CHR11), AT5G18620 (CHR17), AT5G64360 (DNAJ1), AT2G01710 (DNAJ2), AT2G17690 (SDC), AT4G25530 (FWA), AT5G49160 (MET1), AT5G14620 (DRM2), and AT1G69770 (CMT3). Supplementary Material koad143_Supplementary_Data Click here for additional data file. Acknowledgments We thank the flow cytometry Core at National Center for Protein Sciences...”
- Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton
Wang, Frontiers in plant science 2022 - “...AtPDF2 (At4g04890), AtANL2 (At4g00730), AtHDG1 (At3g61150), AtHDG2 (At1g05230), AtHDG3 (At2g32370), AtHDG4 (At4g17710), AtHDG5 (At5g46880), AtHDG6 (At4g25530), AtHDG7 (At5g52170), AtHDG8 (At3g03260), AtHDG9 (At5g17320), AtHDG10 (At1g34650), AtHDG11 (At1g73360), AtHDG12 (At1g17920), GhHD1 (Gh_A06G1283), GhHOX1 (AF530913), GhHOX3 (Gh_A12G2462). The MBW Regulatory Complex WD40-repeat proteins provide a scaffold in proteinprotein interactions...”
- Proline Affects Flowering Time in Arabidopsis by Modulating FLC Expression: A Clue of Epigenetic Regulation?
Mattioli, Plants (Basel, Switzerland) 2022 - “...Gene Name Acronym AGI Locus Code Floral Pathway GIGANTEA GI AT1G22770 Photoperiodic FLOWERING WAGENINGEN FWA AT4G25530 Photoperiodic CONSTANS CO AT5G15840 Photoperiodic LUMINIDEPENDENS LD AT4G02560 Autonomous FLOWERING CONTROL LOCUS A FCA AT4G16280 Autonomous FLOWERING LOCUS KH DOMAIN FLK AT3G04610 Autonomous FLOWERING LOCUS D FLD AT3G10390 Autonomous Unknown...”
- Coexpression of MEIOTIC-TOPOISOMERASE VIB-dCas9 with guide RNAs specific to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis
Yelina, G3 (Bethesda, Md.) 2022 - “...6(pre-tRNA-gRNA) construct to express previously reported gRNAs targeting 6 Arabidopsis genes (At1g69320, At1g26600, At2g27250, At3g27920, At4g25530, and At5g35620) outside 3a to use as a negative control ( Pyott et al. 2016 ; Hahn et al. 2017 ; Yamaguchi et al. 2017 ; Gallego-Bartolom et al. 2018...”
- DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
He, Nature communications 2022 - “...and down-regulated genes in mddcc . e Snapshots of expression and DNA methylation levels over AT4G25530 ( FWA ) in the indicated mutants. f Representative images of pavement cell morphology of cotyledons from 11-day-old WT, ddcc , met1-9 , and mddcc seedlings. Cell outlines were visualized...”
- Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs
Fei, Nucleic acids research 2021 - “...corresponds to TRV:FWAtr) ( 33 ). FWA-B is a 544-nt fragment of the FWA promoter (At4g25530), which contains two tandem repeats. A shorter version of FWA-B, referred to as FWA-Bs that harbours a single short and long repeat (239 nt) was PCR amplified and subsequently ligated...”
- “...as Bs (TRV-FWA-Bs). ( C ) Schematic diagram of the tandem repeats in FWA promoter (At4g25530) and the repeat-derived sequences used for VIGS. The short (38 nt) and long (198 nt) repeats are indicated as purple and pink arrows, respectively. A 239 nt fragment of the...”
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- The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1
Pan, BMC plant biology 2015 - “...ATML1 (NP_193906), ANL2 (NP_567183), HDG1 (NP_191674), HDG2 (NP_172015), HDG3 (NP_180796), HDG4 (NP_193506), HDG5 (NP_199499), HDG6 (NP_567722), HDG7 (NP_200030), HDG8 (NP_186976), HDG9 (NP_197234), HDG10 (NP_174724), HDG11 (NP_177479) and HDG12 (NP_564041) in Arabidopsis ; ZmOCL1 (CAG38614), ZmOCL2 (CAB96422), ZmOCL3 (CAB96423), and ZmOCL4 (CAB96424) for maize; GaHOX1 (ABY41242), GaHOX2...”
- Role of Homeodomain leucine zipper (HD-Zip) IV transcription factors in plant development and plant protection from deleterious environmental factors
Chew, International journal of molecular sciences 2013 - “...filament, stomatal guard cells of the carpel Not determined [ 24 ] Arabidopsis thaliana FWA/HDG6 NP_567722 Endosperm Endosperm development [ 30 ] Arabidopsis thaliana HDG7 NP_200030 Base of leaf primordia, apical region of the heart-stage embryo, lateral root primordia and tips, seedlings Not determined [ 24...”
- START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Schrick, Genome biology 2004 - “...START 709 230-464 4 - NP_193906 At4g21750 ATML1 HD ZLZ START 762 254-482 4 - NP_567722 At4g25530 FWA HD ZLZ START 686 207-435 4 - NP_197234 At5g17320 - HD ZLZ START 718 235-462 5 - NP_199499 At5g46880 - HD ZLZ START 820 315-549 5 - NP_200030...”
Q9I9C5 Iroquois homologue-1 from Gallus gallus
36% identity, 15% coverage
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710 P51974 n/a Q9PUK5/A0JMA6 n/a Bmp4 P21275 P12644 Q06826 Q90752 P30885/Q90YD6 n/a Cited1 P97769 Q99966 Q4V8P1 n/a n/a...”
SO_DROME / Q27350 Protein sine oculis from Drosophila melanogaster (Fruit fly) (see 2 papers)
NP_476733 sine oculis from Drosophila melanogaster
47% identity, 12% coverage
- function: Required for visual system development. May transcriptionally regulate genes necessary for optic lobe invagination and Bolwig's nerve formation.
disruption phenotype: Flies specifically display visual defects. These range from reduced ocelli and ommatidia number in weak loss-of-function phenotypes to complete absence of compound eyes and bolwig's organ in more severe lethal phenotypes. - Antagonistic regulation of the second mitotic wave by Eyes absent-Sine oculis and Combgap coordinates proliferation and specification in the Drosophila retina.
Davis, Development (Cambridge, England) 2017 - GeneRIF: Uncover a novel role for Eya and So in promoting cell cycle exit in the retinal second mitotic wave (SMW), a synchronized, terminal cell division that occurs several hours after passage of the furrow. We show that Combgap (Cg), a zinc-finger transcription factor, antagonizes Eya-So function in the SMW.
- Conditional knockout of retinal determination genes in differentiating cells in Drosophila.
Jin, The FEBS journal 2016 - GeneRIF: By removing gene function in differentiating cells, the study shows that so is dispensable for larval photoreceptor differentiation, but is required for differentiation during pupal development.
- Onset of atonal expression in Drosophila retinal progenitors involves redundant and synergistic contributions of Ey/Pax6 and So binding sites within two distant enhancers.
Zhou, Developmental biology 2014 - GeneRIF: atonal expression in Drosophila retinal progenitors involves redundant and synergistic contributions of Ey/Pax6 and So binding sites within two distant enhancers
- Regulation of Drosophila eye development by the transcription factor Sine oculis.
Jusiak, PloS one 2014 - GeneRIF: mapping of So-enriched regions throughout the genome in third instar larval eye discs; study found 7,566 So-enriched regions, which map to approximately 5,952 genes, including previously characterized So targets in the eye
- Dual transcriptional activities of SIX proteins define their roles in normal and ectopic eye development.
Anderson, Development (Cambridge, England) 2012 - GeneRIF: Data suggest that during early phases of eye development, So and Optix function, in part, to repress the transcription of non-retinal selector genes, thereby allowing induction of the retina to proceed.
- Segregation of eye and antenna fates maintained by mutual antagonism in Drosophila.
Wang, Development (Cambridge, England) 2012 (PubMed)- GeneRIF: Loss of So in the eye disc caused ectopic antenna development in the eye.
- Sine oculis, a member of the SIX family of transcription factors, directs eye formation.
Weasner, Developmental biology 2007 - GeneRIF: expression of so on its own is sufficient to induce eye development within non-retinal tissues
- Identification of transcriptional targets of the dual-function transcription factor/phosphatase eyes absent.
Jemc, Developmental biology 2007 - GeneRIF: EYA and SO may influence cell proliferation through transcriptional regulation of stg.
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- XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, BMC genomics 2005 - “...138 46 10061 1 YES Q27324 Derailed protein 1.20E-45 23 400 47 14903 1 YES Q27350 Sine oculis protein 3.90E-87 1 20 Sequences without significant homology 48 O77459 transcription factor Ken 60 NP_651346 CG11849-PA 49 AAF46666 CG10527-PA 61 Q23997 Chitinase-like protein DS47 precursor 50 NP_728586 CG9134-PA...”
XP_004238268 BEL1-like homeodomain protein 11 from Solanum lycopersicum
36% identity, 14% coverage
NP_725182 achintya, isoform A from Drosophila melanogaster
42% identity, 13% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...similarity with TGIF of Aedes aegypti (XP_001653660), Culex quinquefasciatus (XP_001849992), Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively....”
- Drosophila TGIF is essential for developmentally regulated transcription in spermatogenesis.
Ayyar, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: results show that TGIF is expressed in the early stages of spermatogenesis consistent with a conserved role in the activation of the spermatogenesis transcription programme
- Requirement for two nearly identical TGIF-related homeobox genes in Drosophila spermatogenesis.
Wang, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: Results suggest that vismay and achintya help to specify the spermatogenesis program by recruiting or stabilizing Always early and Cookie monster to specific target genes that need to be transcriptionally regulated during testes development.
6fqpA / Q15583 Crystal structure of tale homeobox domain transcription factor tgif1 with its consensus DNA (see paper)
37% identity, 80% coverage
NP_001093693 homeobox protein SIX1 from Xenopus tropicalis
49% identity, 18% coverage
ATH1_ARATH / P48731 Homeobox protein ATH1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_195024 homeobox protein ATH1 from Arabidopsis thaliana
AT4G32980 ATH1 (ARABIDOPSIS THALIANA HOMEOBOX GENE 1); DNA binding / sequence-specific DNA binding / transcription factor from Arabidopsis thaliana
36% identity, 15% coverage
- function: Transcription factor which may be involved in the signal transduction pathway downstream of the COP1 gene. Controls floral competency as a specific activator of FLC expression. Is responsive of the nuclear import of SHOOT MERISTEMLESS (STM).
subunit: May form heterodimeric complex with the TALE/KNOX protein STM - Arabidopsis thaliana rosette habit is controlled by combined light and energy signaling converging on transcriptional control of the TALE homeobox gene ATH1.
Shokrian, The New phytologist 2023 (PubMed)- GeneRIF: Arabidopsis thaliana rosette habit is controlled by combined light and energy signaling converging on transcriptional control of the TALE homeobox gene ATH1.
- ATH1 and KNAT2 proteins act together in regulation of plant inflorescence architecture.
Li, Journal of experimental botany 2012 - GeneRIF: The data indicate that the ATH1-KNAT2 complex acts redundantly with KNAT6, both of which are negatively regulated by BP during pedicel development.
- BLADE-ON-PETIOLE1 and 2 regulate Arabidopsis inflorescence architecture in conjunction with homeobox genes KNAT6 and ATH1.
Khan, Plant signaling & behavior 2012 - GeneRIF: BOP1/2 gain-of-function in stems promotes expression of the boundary gene KNOTTED1-LIKE FROM ARABIDOPSIS THALIANA6 (KNAT6) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1).
- Shoot apical meristem function in Arabidopsis requires the combined activities of three BEL1-like homeodomain proteins.
Rutjens, The Plant journal : for cell and molecular biology 2009 (PubMed)- GeneRIF: combined lesions in ATH1, PNY and PNF result in a full phenocopy of shoot apical meristem loss-of-function mutants.
- ARABIDOPSIS THALIANA HOMEOBOX GENE1 establishes the basal boundaries of shoot organs and controls stem growth.
Gómez-Mena, The Plant cell 2008 - GeneRIF: Data show that ATH1 modulates growth at the interface between the stem, meristem, and organ primordia and contributes to the compressed vegetative habit of Arabidopsis thaliana.
- The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC.
Proveniers, The Plant journal : for cell and molecular biology 2007 (PubMed)- GeneRIF: ATH1 controls floral competency as a specific activator of FLOWERING LOCUS C (FLC) expression.
- The SAS chromatin-remodeling complex mediates inflorescence-specific chromatin accessibility for transcription factor binding
Guo, Nucleic acids research 2025 (no snippet) - Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate
Avidan, Plant physiology 2024 - “...and functional terms are of significance to the work described in this paper: ATH1 Gramene: AT4G32980 ATH1 Araport: AT4G32980 RPS6 Gramene: AT4G31700 RPS6 Araport: AT4G31700 clf Gramene: AT2G23380 clf Araport: AT2G23380 AtTPS1 Gramene: AT1G78580 AtTPS1 Araport: AT1G78580 MAF5 Gramene: AT5G65080 MAF5 Araport: AT5G65080 bZIP25 Gramene: AT3G54620...”
- Altered interactions between cis-regulatory elements partially resolve BLADE-ON-PETIOLE genetic redundancy in Capsella rubella
Tran, The Plant cell 2024 - “...and functional terms are of significance to the work described in this paper: ATH1 Gramene: AT4G32980 ATH1 Araport: AT4G32980 SPL9 Gramene: At2g42200 SPL9 Araport: At2g42200 BOP1 Gramene: AT3G57130 BOP1 Araport: AT3G57130 BOP2 Gramene: At2g41370 BOP2 Araport: At2g41370 FIL Gramene: AT2G45190 FIL Araport: AT2G45190 AP2 Gramene: AT4G36920...”
- Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis
Han, Frontiers in plant science 2023 - “...2W cytoplasmic and nuclear-localized NPR1 like protein Chahtane etal., 2018 SNP77376 QQI LN10 ATH1 ( AT4G32980 ) chr4:15914670..15918153 SNP157833 SNP157883 QQI QQI LDV increased levels of ATH1 severely delay flowering Li etal., 2012 0W CPL3 ( AT4G01060 ) chr4:460395..461246 SNP125917 QTN 2W Myb-related protein similar to...”
- “...thaliana ( Han etal., 2008 ). At the same time, the known gene ATH1 ( AT4G32980 , around SNP157833), which is related to LDV and 0W ( Table1 ; Figure3A ; Supplementary Figure1D ), is necessary for controlling the morphology of Arabidopsis flower stalk. In addition,...”
- Unique and overlapping functions for the transcriptional regulators KANADI1 and ULTRAPETALA1 in Arabidopsis gynoecium and stamen gene regulation
Hagelthorn, Plant direct 2023 - “...COL2 1.36 0.00005 GATA AT5G56860 GNC/GATA21 1.19 0.0007 GRF AT3G13960 GRF5 .93 0.00005 Homeodomain TALE AT4G32980 ATH1 .80 0.00005 WOX AT2G33880 WOX9/HB3 .61 0.0005 MADS AT1G77080 AGL27 1.42 0.00005 MYB AT1G01060 LHY .65 0.00005 WRKY AT3G56400 WRKY70 1.33 0.00005 Zn finger C2H2 AT5G59820 ZAT2 1.19 0.0001...”
- “...MYB108 2.62 0.00005 ULT1 and KAN1 induced AP2/ERF ERF AT5G61600 ERF104 1.12 0.0006 Homeodomain TALE AT4G32980 ATH1 .61 0.00085 LBD AT1G65620 AS2 1.15 0.00055 MYB AT5G62320 MYB99 1.06 0.00055 AT5G02840 LCL1/RVE4 .60 0.00015 WRKY AT3G56400 WRKY70 .86 0.00005 ULT1 and KAN1 repressed G2like AT5G16560 KAN1 1.93...”
- RNAseq-Based Working Model for Transcriptional Regulation of Crosstalk between Simultaneous Abiotic UV-B and Biotic Stresses in Plants
Zhou, Genes 2023 - “...2.07 AT5G53500 WD40-2 response to light stimulus, but cytoplasmatic protein Figure S3B 2.11 0.59 1.58 AT4G32980 ATH1 homeobox gene 1, involved in photomorphogenesis 2.62 0.50 2.10 AT1G14440 HB31 Homeobox protein, long-day photoperiodism Figure S4B 2.51 0.23 4.05 AT4G17460 HAT1 class II Homeodomain-ZIP protein, negative regulator Figure...”
- Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed
Prapas, Evolutionary applications 2022 - “...QTL2 AT3G01090 SNF1 KINASE HOMOLOG 10 QTL2 AT4G15880 EARLY IN SHORT DAYS 4 (ESD4) QTL2 AT4G32980 HOMEOBOX GENE 1, ATH1 QTL2 AT5G65050 MADS AFFECTING FLOWERING 2 (MAF2) QTL12 AT1G65480 FLOWERING LOCUS T (FT) QTL6 AT1G12910 LIGHTREGULATED WD 1 (LWD1) QTL6 AT1G26830 CULLIN 3A QTL6 AT2G27550 ATC,...”
- Transcript Profiling Analysis and ncRNAs' Identification of Male-Sterile Systems of Brassica campestris Reveal New Insights Into the Mechanism Underlying Anther and Pollen Development
Zhou, Frontiers in plant science 2022 - “...regulate stomatal differentiation Bra026499 0.661 1.526 Up AT5G23400 - Signal transduction Bra011403 2.550 5.431 Up AT4G32980 Arabidopsis thaliana homeobox 1 ( ATH1 ) Regulation of gibberellin biosynthetic genes The expression of genes was presented as fragments per kilobase of exon model per million mapped fragments. B...”
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SIX1_XENLA / Q9I8H0 Homeobox protein six1; Sine oculis homeobox homolog 1 from Xenopus laevis (African clawed frog) (see paper)
NP_001082027 homeobox protein six1 from Xenopus laevis
49% identity, 18% coverage
- function: Transcription factor that is involved in the regulation of cell proliferation, apoptosis and embryonic development. Depending on context, functions as a transcriptional repressor or activator. Required for the normal formation of pre-placodal ectoderm.
- Six1 and Irx1 have reciprocal interactions during cranial placode and otic vesicle formation.
Sullivan, Developmental biology 2019 - GeneRIF: Homeobox protein SIX1 (Six1) is required for continued Irx1 (Xiro1) expression.
- Pa2G4 is a novel Six1 co-factor that is required for neural crest and otic development.
Neilson, Developmental biology 2017 - GeneRIF: these findings establish an interaction between Pa2G4 and Six1, and demonstrate that it has an important role in the development of tissues affected in Branchiootorenal Spectrum disorder.
- Six1 and Eya1 both promote and arrest neuronal differentiation by activating multiple Notch pathway genes.
Riddiford, Developmental biology 2017 (PubMed)- GeneRIF: Six1 and Eya1 can both promote and arrest neuronal differentiation by activating the Notch pathway genes.
- Microarray identification of novel genes downstream of Six1, a critical factor in cranial placode, somite, and kidney development.
Yan, Developmental dynamics : an official publication of the American Association of Anatomists 2015 - GeneRIF: Microarray identification of novel genes downstream of Six1, a critical factor in cranial placode, somite, and kidney development.
- Six1 is a key regulator of the developmental and evolutionary architecture of sensory neurons in craniates.
Yajima, BMC biology 2014 - GeneRIF: The results indicated the critical role of Six1 in transition of Rohon-Beard cells to dorsal root ganglia (DRG) neurons during Xenopus development and establishment of exclusive DRG system of mice.
- Eya1 and Six1 promote neurogenesis in the cranial placodes in a SoxB1-dependent fashion.
Schlosser, Developmental biology 2008 - GeneRIF: Eya1 and Six1 are required for both the regulation of placodal neuronal progenitor proliferation, through their effects on SoxB1 expression, and subsequent neuronal differentiation.
4egcA / P0AEX9,Q15475 Crystal structure of mbp-fused human six1 bound to human eya2 eya domain (see paper)
47% identity, 10% coverage
- Ligand: alpha-d-glucopyranose (4egcA)
KNAT5_ARATH / P48002 Homeobox protein knotted-1-like 5; Homeodomain-containing protein 1; Protein KNAT5 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT4G32040 KNAT5 (KNOTTED1-LIKE HOMEOBOX GENE 5); transcription activator/ transcription factor from Arabidopsis thaliana
38% identity, 15% coverage
- subunit: May form heterodimeric complex with the TALE/BELL protein BEL1, BLH1 and BLH2. Interacts with OFP1, OFP2, OFP3 and OFP4.
- Protocol for screening and expression studies of T-DNA and tagging-based insertional knox mutants in Arabidopsis thaliana
Sunaryo, 3 Biotech 2021 - “...SALK_110899 Locus AT1G70510 AT1G70510 AT5G25220 AT5G25220 AT4G32040 AT4G32040 AT1G23380 AT1G23380 AT1G62990 AT1G62990 T-DNA b. Expression analysis using qRT-PCR...”
- “...- AT1G70510 - AT1G70510 - AT5G25220 - AT5G25220 - AT4G32040 - AT4G32040 - AT1G23380 - AT1G23380 - AT1G62990 - AT1G62990 - AT1G70510 - AT1G70510 Oligo name...”
- In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families
Bueno, Genes 2021 - “...AtKNAT3 AT5G25220 Mature organs [ 111 ] AtKNAT4 AT5G11060 Mature organs [ 111 ] AtKNAT5 AT4G32040 Mature organs [ 111 ] AtKNAT7 AT1G62990 Mature organs [ 111 ] Picea abies PaKN5 MK580154 n/a [ 115 ] Pinus pinaster PpKN5 MK580155 Shoot apex and primordia of young...”
- Functional divergence and adaptive selection of KNOX gene family in plants
Meng, Open life sciences 2020 - “...in the same subfamily may play similar roles in the same organization. AT5G11060, AT5G25220, and AT4G32040 are from the class II subfamily. Their overall transcription was richer than that of the class I subfamily. The expression level was higher in senescing leaves. AT4G32040 was highly expressed...”
- “...AT1G70510 310 4.9 35,638 II AT5G25220 431 5.86 47,599.8 II AT5G11060 393 5.87 44,385 II AT4G32040 383 6.03 43,283.6 I AT1G23380 329 4.92 37,189.9 I AT1G62360 382 6.19 42,753.1 II AT1G62990 291 6.1 32,908.1 I Glyma14g10430 385 6.39 44,100 I Glyma0041s00360 387 6.43 44,458.4 I Glyma04g05210...”
- Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica
Jia, Frontiers in plant science 2020 - “...AT1G23380 chr1:8,297,241..8,297,241 990 329 KNAT3 AT5G25220 chr5:8,735,944..8,735,944 1,296 431 KNAT4 AT5G11060 chr5:3,509,833..3,509,833 1,182 393 KNAT5 AT4G32040 chr4:15,493,989..15,493,989 1,152 383 KNAT7 AT1G62990 chr1:23,337,167..23,337,167 876 291 KNOX01 MD02G1012900 Chr03:821,764..821,764 1,083 360 KNOX02 MD04G1069700 Chr04:9,546,107..9,546,107 765 254 KNOX03 MD04G1215500 Chr04:29,846,452..29,846,452 993 330 KNOX04 MD05G1352500 Chr05:46,891,824..46,891,824 1,161 386 KNOX05 MD06G1071100...”
- Integration of QTL Mapping and Gene Fishing Techniques to Dissect the Multi-Main Stem Trait in Rapeseed (Brassica napus L.)
Zhao, Frontiers in plant science 2019 - “...AT3G08770 ERD10 BnaA03g51000D AT3G57230 AGL16 BnaA03g58880D AT4G29040 RPT2A BnaA03g38750D AT2G14900 RDK1 BnaA03g51450D AT4G31400 CTF7 BnaA03g51900D AT4G32040 KNAT5 BnaA03g52120D AT4G32551 LUC BnaA03g52290D AT4G32980 ATH1 BnaA03g52520D AT4G33430 BAK1 BnaA03g50910D AT4G34160 CYCD3 BnaA03g53400D AT4G35550 WOX13 BnaA03g53680D AT4G37180 UIF1 BnaA03g49660D AT4G29740 CKX4 cqMMS.A3-2 BnaA03g50360D AT4G30610 BRS1 BnaA03g54090D AT4G37540 LBD39 BnaA03g54110D...”
- Arabidopsis SKP1-like protein13 (ASK13) positively regulates seed germination and seedling growth under abiotic stress
Rao, Journal of experimental botany 2018 - “...stress 9 At3g09350 Hsp70-binding protein1 Abiotic stress 10 At2g45660 Agamous-like 20 Germination, flower development 11 At4g32040 Knotted1-like homeobox gene 5 Root development 12 At3g48330 Protein isoaspartyl methyl transferase 1 Seed vigor and stress 13 At2g47180 Galactinol synthase 1 Abiotic stress 14 At2g47210 Myb-like transcription factor family...”
- Screening of Candidate Leaf Morphology Genes by Integration of QTL Mapping and RNA Sequencing Technologies in Oilseed Rape (Brassica napus L.)
Jian, PloS one 2017 - “...(GRF8) BnaCnng20070D 2.83 1.68 0.00 AT5G11060 KNOTTED1-like homeobox gene 4 (KNAT4) BnaA01g04870D 4.26 4.09 1.92 AT4G32040 KNOTTED1-like homeobox gene 5 (KNAT5) Screening for candidate genes that control leaf morphology by the integration of QTL mapping and RNA sequencing In total, 1,205 genes were identified in QTL...”
- “...which is homologous to AT5G11060 ( KNAT4 ), and BnaA01g04870D , which is homologous to AT4G32040 ( KNAT5 ), are KNOTTED1 -like homeobox genes with important roles in promoting leaf complexity [ 39 ]. KNOX1 genes are expressed in the SAM and maintain indeterminacy of leaf...”
- An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses
Zhan, Nature communications 2015 - “...RNA-seq analysis. For RTPCR analysis, we selected At4g16143 , At5g09330 , At2g42010 , At3g53340 , At4g32040 and At4g35800 . At4g16143 encodes importin alpha isoform 2. At5g09330 encodes NAC domain-containing protein 82. At4g42010 encodes phospholipase D beta 1. At3g53340 encodes nuclear factor Y, subunit B10. At4g32040 encodes...”
- “...The RTPCR assays found that transcripts of At4g16143 , At5g09330 , At2g42010 , At3g53340 , At4g32040 and At4g35800 contain an intron in rbm25-1 and rbm25-2 with or without ABA treatment ( Fig. 5c,e ; Supplementary Fig. 3 ). Thus, the RTPCR results confirmed the RNA-seq data...”
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- The plant MBF1 protein family: a bridge between stress and transcription
Jaimes-Miranda, Journal of experimental botany 2020 - “...et al. (2014) ; Trigg et al. (2017) Arabidopsis thaliana I AT3G58680 (TAIR) MBF1b Yes P48002 (Homeobox), Q39057 (Zn-finger), Q3EAI1-2 (bHLH), Q84TK1 (bHLH), Q8L8A5 (SSXT non-TF), Q9FF62 (Zn-finger), Q9M274 (NAC), Q9SRV2-2 (non-TF) Kim et al. (2007) ; IntAct a : Orchard et al. (2014) ; Trigg...”
- A novel cell-to-cell trafficking assay indicates that the KNOX homeodomain is necessary and sufficient for intercellular protein and mRNA trafficking
Kim, Genes & development 2005 - “...KNAT2 (P46640), KNAT3 (P48000), KNAT4 (P48001), KNAT5 (P48002), KNAT6 (NP_850951), KNAT7 (NP_564805). (B). Trichome rescue assays were performed using HD...”
BLH6_ARATH / O65685 BEL1-like homeodomain protein 6; BEL1-like protein 6 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G34610 BLH6 (BELL1-LIKE HOMEODOMAIN 6); DNA binding / transcription factor from Arabidopsis thaliana
NP_195187 BEL1-like homeodomain 6 from Arabidopsis thaliana
39% identity, 11% coverage
- subunit: May form heterodimeric complexes with TALE/KNOX proteins (By similarity). Interacts with OFP2, OFP4, and OFP5.
- Exploring the diversity of galls on Artemisia indica induced by Rhopalomyia species through morphological and transcriptome analyses
Takeda, Plant direct 2024 - “...Gibberellin homeostasis Dong et al., 2022 Jumonji (JmjC) domaincontaining protein AT1G11950 BEL1like homeodomain protein 6;BLH6 AT4G34610 Secondary cell wall development Liu et al., 2014 bHLH62 AT3G07340 Auxin response factor 4;ARF4 AT5G60450 ABAINDUCIBLE bHLHTYPE;AIB; JAM1 AT2G46510 JA signaling Nakata et al., 2013 PERIANTHIA;PAN AT1G68640 Floral organ number...”
- Global gene regulatory network underlying miR165a in Arabidopsis shoot apical meristem
Sinha, Scientific reports 2023 - “...cytokinin 1.03 AT2G21050 Like AUXIN RESISTANT 2 (LAX2) Auxin influx carrier 1.03 1.06 1.03 -1.83 AT4G34610 BEL1-like homeodomain 6 (BLH6) Negative regulator of xylem vessel cells 1.09 1.01 2.2 AT3G25717 ROTUNDIFOLIA like 16 (RTFL16) 1.09 3.34 3.4 AT3G50870 MONOPOLE (MNP) Regulates shoot apical meristem and flower...”
- Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development
Laubscher, Scientific reports 2018 - “...14 hpt 7 hpt 14 hpt Transcription factors AT1G75410 BEL1-LIKE HOMEODOMAIN 3 (BLH3) 3.4 4.4 AT4G34610 BEL1-LIKE HOMEODOMAIN 6 (BLH6) 18.5 12.9 361.7 AT1G19700 BEL1-LIKE HOMEODOMAIN 10 (BEL10) 3.5 5.7 AT1G66810 CCCH ZINC FINGER 14 (C3H14) 5.2 7.5 34.0 AT1G62990 KNOTTED-LIKE HOMEOBOX OF ARABIDOPSIS THALIANA 7...”
- Reconstitution of a secondary cell wall in a secondary cell wall-deficient Arabidopsis mutant
Sakamoto, Plant & cell physiology 2015 - “...Not restored At1g62990 KNAT7, IXR11 Not restored At1g66810 AtC3H14 Not restored At2g44745 WRKY12 Not restored At4g34610 BLH6 Not restored At1g74660 MIF1 Not restored At1g62360 WAM1 Not restored At1g80730 ZFP1 Not restored We then tested the transcriptional activation ability of SND2 by fusing the gene to the...”
- Identification of novel transcription factors regulating secondary cell wall formation in Arabidopsis
Cassan-Wang, Frontiers in plant science 2013 - “...candidates regulating the biosynthesis of lignin and/or the whole SCW biosynthetic program: BLH6 (Bel-like HomeoBox6; AT4G34610), HB5 (AT5G65310), HB15 (AT1G52150), MYB-like TF (AT3G11280), MYB52 (AT1G17950), and Zinc finger TF (AT3G46620). Results A post-genomic approach to identify novel regulatory genes involved in SCW formation In order to...”
- “...2.2 1.2 0.6 3.0 Low_ns 0 AT5G02030 homeodomain TF (BELLRINGER) 1.4 1.6 0.2 High_p 0 AT4G34610 homeodomain TF (BLH6) 2.0 0.7 0.7 1.4 Low_p 2 AT1G70510 homeodomain TF (KNAT2) 1.4 2.1 0.1 Medium_s 0 AT1G62990 homeodomain TF (KNAT7) 7.9 2.8 2.4 2.6 High_s 0 AT1G62360 homeodomain...”
- TALE and Shape: How to Make a Leaf Different
Di, Plants (Basel, Switzerland) 2013 - “...[ 16 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] AT4G34610 BLH7 [ 16 , 19 ] [ 16 ] [ 16 ] [ 16 ] [ 16 ] AT2G16400 BLH8 /PNF [ 18 ] [ 16 , 18 ] [...”
- Expression of ROS-responsive genes and transcription factors after metabolic formation of H(2)O(2) in chloroplasts
Balazadeh, Frontiers in plant science 2012 - “...HB 1.66 0.24 At4g00150 GRAS 0.57 0.58 At4g32980 HB 0.66 0.12 At4g08250 GRAS 2.11 2.28 At4g34610 HB 0.27 0.20 At4g17230 GRAS 4.77 2.92 At4g35550 HB 0.22 0.40 At4g36710 GRAS 0.22 0.75 At4g37650 GRAS 0.29 0.47 At4g36870 HB 0.11 0.05 At5g17490 GRAS 0.26 1.26 At4g37790 HB 1.19...”
- A role for OVATE FAMILY PROTEIN1 (OFP1) and OFP4 in a BLH6-KNAT7 multi-protein complex regulating secondary cell wall formation in Arabidopsis thaliana.
Liu, Plant signaling & behavior 2015 - GeneRIF: This study shows that OFP1 and OFP4 enhance the repression activity of BLH6, supporting a role for these OFPs as components of a putative multi-protein transcription regulatory complex containing BLH6 and KNAT7.
- BEL1-LIKE HOMEODOMAIN6 and KNOTTED ARABIDOPSIS THALIANA7 interact and regulate secondary cell wall formation via repression of REVOLUTA.
Liu, The Plant cell 2014 - GeneRIF: BLH6 and KNAT7 bind to the REV promoter and repress REV expression.
XP_002425861 Homeobox protein TGIF2LX, putative from Pediculus humanus corporis
40% identity, 17% coverage
- BmTGIF, a Bombyx mori homolog of Drosophila DmTGIF, regulates progression of spermatogenesis
Zhang, PloS one 2012 - “...Anopheles gambiae (XP_308755), D. melanogaster (NP_725182), Tribolium castaneum (NP_001153689), Apis mellifera (XP_001122713), Pediculus humanus corporis (XP_002425861), Nasonia vitripennis (NP_001153690), Daphnia pulex (EFX88970), Xenopus laevis (NP_001087637), Danio rerio (NP_955861), Homo sapiens (NP_068581) and Mus musculus (NP_775572), respectively. Although the sequence identities of the TGIF proteins from different...”
IRX5_XENLA / Q90XW5 Iroquois-class homeodomain protein irx-5; Iroquois homeobox protein 5 from Xenopus laevis (African clawed frog) (see 6 papers)
42% identity, 12% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Does not appear to play a role in pronephros kidney development. Involved in craniofacial and gonadal development. Modulates the migration of progenitor cell populations in branchial arches and gonads by repressing CXCL12.
XP_005711328 hypothetical protein from Chondrus crispus
35% identity, 13% coverage
- A unique life cycle transition in the red seaweed Pyropia yezoensis depends on apospory
Mikami, Communications biology 2019 - “...PpBELL2 XP_001777380, PpBELL3 XM_001769443, PpBELL4 XP_001762111; Arabidopsis thaliana , AtKNAT3 X92392; Chondrus crispus , CcBELL1 XP_005711328; Cyanidioschyzon merolae , CmKNOX (CMR153C) XP_005538442, CmBELL1 (CMH049C) XP_005536034, CmBELL2 (CMR176C) XP_005538457. PopKNOX (esisotig02479) and PouKNOX (esisotig04347) are KNOX homologs of Porphyra purpurea and Porphyra umbilicalis , respectively, which were...”
IRX5_MOUSE / Q9JKQ4 Iroquois-class homeodomain protein IRX-5; Homeodomain protein IRXB2; Iroquois homeobox protein 5 from Mus musculus (Mouse) (see 4 papers)
NP_061296 iroquois-class homeodomain protein IRX-5 from Mus musculus
40% identity, 12% coverage
- function: Establishes the cardiac repolarization gradient by its repressive actions on the KCND2 potassium-channel gene. Required for retinal cone bipolar cell differentiation. May regulate contrast adaptation in the retina and control specific aspects of visual function in circuits of the mammalian retina. Involved in craniofacial and gonadal development (By similarity). Modulates the migration of progenitor cell populations in branchial arches and gonads by repressing CXCL12.
disruption phenotype: Disruption causes increased KCND2 potassium- channel expression in endocardial myocardium leading to abolition of the cardiac repolarization gradient, a selective increase of the major cardiac repolarization current, I(to,f), and increased susceptibility to arrhythmias. - IRX5 suppresses osteogenic differentiation of hBMSCs by inhibiting protein synthesis.
Jiang, Journal of cellular physiology 2024 (PubMed)- GeneRIF: IRX5 suppresses osteogenic differentiation of hBMSCs by inhibiting protein synthesis.
- IRX5 promotes DNA damage repair and activation of hair follicle stem cells.
Chen, Stem cell reports 2023 - GeneRIF: IRX5 promotes DNA damage repair and activation of hair follicle stem cells.
- Irx5 and transient outward K+ currents contribute to transmural contractile heterogeneities in the mouse ventricle.
Kim, American journal of physiology. Heart and circulatory physiology 2022 (PubMed)- GeneRIF: Irx5 and transient outward K(+) currents contribute to transmural contractile heterogeneities in the mouse ventricle.
- Deficiency of Irx5 protects mice from obesity and associated metabolic abnormalities.
Son, International journal of obesity (2005) 2022 (PubMed)- GeneRIF: Deficiency of Irx5 protects mice from obesity and associated metabolic abnormalities.
- Irx3 and Irx5 in Ins2-Cre+ cells regulate hypothalamic postnatal neurogenesis and leptin response.
Son, Nature metabolism 2021 (PubMed)- GeneRIF: Irx3 and Irx5 in Ins2-Cre(+) cells regulate hypothalamic postnatal neurogenesis and leptin response.
- Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira, Science (New York, N.Y.) 2021 - GeneRIF: Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
- Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads.
Koth, Development (Cambridge, England) 2020 - GeneRIF: Canonical Wnt/beta-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads.
- IRX3 and IRX5 collaborate during ovary development and follicle formation to establish responsive granulosa cells in the adult mouse†.
Fu, Biology of reproduction 2020 - GeneRIF: IRX3 and IRX5 collaborate during ovary development and follicle formation to establish responsive granulosa cells in the adult mousedagger.
- More
NP_991261 iroquois-class homeodomain protein IRX-4a from Danio rerio
38% identity, 13% coverage
FGSG_09043 hypothetical protein from Fusarium graminearum PH-1
36% identity, 11% coverage
- Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
Lawler, BMC systems biology 2013 - “...FG6 FGSG_02814 HLH 4 FG1, FG2.11, FG6, FG6 FGSG_05567 HLH 4 FG1, FG2.11, FG6, FG6 FGSG_09043 Homeobox/zf-C2H2 1 FG2.11 FGSG_06359 HSF_DNA-bind 1 FG6 FGSG_13911 Myb_DNA-binding 1 FG2.01 FGSG_01298 zf-C2H2 1 FG6 FGSG_01341 zf-C2H2 2 FG1, FG2.10 FGSG_01350 zf-C2H2 2 FG1, FG2.10 FGSG_02743 zf-C2H2 2 FG1, FG2.10...”
XP_006255259 iroquois-class homeodomain protein IRX-5 isoform X1 from Rattus norvegicus
40% identity, 14% coverage
NP_620410 homeobox protein TGIF2LX from Homo sapiens
37% identity, 24% coverage
- Regulation of long non-coding RNAs XIST and ROR induced by homeodomain protein TGIF2LX in colorectal cancer.
Tabarestani, Journal of cancer research and therapeutics 2022 (PubMed)- GeneRIF: Regulation of long non-coding RNAs XIST and ROR induced by homeodomain protein TGIF2LX in colorectal cancer.
- In vivo identification of novel TGIF2LX target genes in colorectal adenocarcinoma using the cDNA-AFLP method.
Mobini, Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology 2018 (PubMed)- GeneRIF: To the best of our knowledge, this is the first report that proposes Nir1, Nir2, and Fhit genes might be regulated by homeodomain protein TGIF2LX in colorectal adenocarcinoma cells.
- Association of TGIFLX/Y mRNA expression with prostate cancer.
Ousati, Medical oncology (Northwood, London, England) 2009 (PubMed)- GeneRIF: most prostate tumors (73.5%) express at least one of these genes (TGIFLX and TGIFLY), although different patterns of mRNA expression were observed. These results suggest an association of TGIFLX/Y expression with the progression of prostate cancer.
- Association of TGIFLX/Y mRNA expression with azoospermia in infertile men.
Aarabi, Molecular reproduction and development 2008 (PubMed)- GeneRIF: Association of TGIFLX/Y mRNA expression with azoospermia in infertile men.(
IRX5_HUMAN / P78411 Iroquois-class homeodomain protein IRX-5; Homeodomain protein IRX-2A; Homeodomain protein IRXB2; Iroquois homeobox protein 5 from Homo sapiens (Human) (see paper)
NP_005844 iroquois-class homeodomain protein IRX-5 isoform 1 from Homo sapiens
40% identity, 12% coverage
- function: Establishes the cardiac repolarization gradient by its repressive actions on the KCND2 potassium-channel gene. Required for retinal cone bipolar cell differentiation. May regulate contrast adaptation in the retina and control specific aspects of visual function in circuits of the mammalian retina (By similarity). Could be involved in the regulation of both the cell cycle and apoptosis in prostate cancer cells. Involved in craniofacial and gonadal development. Modulates the migration of progenitor cell populations in branchial arches and gonads by repressing CXCL12.
- IRX5 suppresses osteogenic differentiation of hBMSCs by inhibiting protein synthesis.
Jiang, Journal of cellular physiology 2024 (PubMed)- GeneRIF: IRX5 suppresses osteogenic differentiation of hBMSCs by inhibiting protein synthesis.
- The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
Nagel, International journal of molecular sciences 2022 - GeneRIF: The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
- Human model of IRX5 mutations reveals key role for this transcription factor in ventricular conduction.
Al, Cardiovascular research 2021 (PubMed)- GeneRIF: Human model of IRX5 mutations reveals key role for this transcription factor in ventricular conduction.
- A duplication on chromosome 16q12 affecting the IRXB gene cluster is associated with autosomal dominant cone dystrophy with early tritanopic color vision defect.
Kohl, Human molecular genetics 2021 - GeneRIF: A duplication on chromosome 16q12 affecting the IRXB gene cluster is associated with autosomal dominant cone dystrophy with early tritanopic color vision defect.
- Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira, Science (New York, N.Y.) 2021 - GeneRIF: Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
- Iroquois Homeobox 5 Negatively Regulated by miRNA-147 Promotes the Proliferation, Metastasis, and Invasion by Oral Squamous Cell Carcinoma.
Zhu, Journal of biomedical nanotechnology 2021 (PubMed)- GeneRIF: Iroquois Homeobox 5 Negatively Regulated by miRNA-147 Promotes the Proliferation, Metastasis, and Invasion by Oral Squamous Cell Carcinoma.
- Transcription factorIRX5 promotes hepatocellular carcinoma proliferation and inhibits apoptosis by regulating the p53 signalling pathway.
Zhu, Cell biochemistry and function 2020 - GeneRIF: Transcription factorIRX5 promotes hepatocellular carcinoma proliferation and inhibits apoptosis by regulating the p53 signalling pathway.
- IRX5 prompts genomic instability in colorectal cancer cells.
Sun, Journal of cellular biochemistry 2020 (PubMed)- GeneRIF: IRX5 prompts genomic instability in colorectal cancer cells.
- More
IRX2_MOUSE / P81066 Iroquois-class homeodomain protein IRX-2; Homeodomain protein IRXA2; Iroquois homeobox protein 2; Iroquois-class homeobox protein Irx6 from Mus musculus (Mouse) (see 4 papers)
NP_034704 iroquois-class homeodomain protein IRX-2 from Mus musculus
40% identity, 12% coverage
IRX3_MOUSE / P81067 Iroquois-class homeodomain protein IRX-3; Homeodomain protein IRXB1; Iroquois homeobox protein 3 from Mus musculus (Mouse) (see 8 papers)
NP_032419 iroquois-class homeodomain protein IRX-3 isoform 2 from Mus musculus
33% identity, 13% coverage
- function: Transcription factor involved in SHH-dependent neural patterning (PubMed:10830170, PubMed:15201216). Together with NKX2-2 and NKX6-1 acts to restrict the generation of motor neurons to the appropriate region of the neural tube (PubMed:10830170, PubMed:15201216). Belongs to the class I proteins of neuronal progenitor factors, which are repressed by SHH signals (PubMed:10830170, PubMed:15201216). Involved in the transcriptional repression of MNX1 in non-motor neuron cells (PubMed:15201216). Acts as a regulator of energy metabolism (PubMed:24646999).
disruption phenotype: Mice are viable and fertile but display a significant reduction of body weight, primarily through the loss of fat mass and increase in basal metabolic rate with browning of white adipose tissue. - IRX3 promotes adipose tissue browning and inhibits fibrosis in obesity-resistant mice.
Yan, The international journal of biochemistry & cell biology 2024 (PubMed)- GeneRIF: IRX3 promotes adipose tissue browning and inhibits fibrosis in obesity-resistant mice.
- Irx3 promotes gap junction communication between uterine stromal cells to regulate vascularization during embryo implantation†.
Brown, Biology of reproduction 2022 - GeneRIF: Irx3 promotes gap junction communication between uterine stromal cells to regulate vascularization during embryo implantationdagger.
- Irx3 and Irx5 in Ins2-Cre+ cells regulate hypothalamic postnatal neurogenesis and leptin response.
Son, Nature metabolism 2021 (PubMed)- GeneRIF: Irx3 and Irx5 in Ins2-Cre(+) cells regulate hypothalamic postnatal neurogenesis and leptin response.
- Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira, Science (New York, N.Y.) 2021 - GeneRIF: Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
- Macrophage IRX3 promotes diet-induced obesity and metabolic inflammation.
Yao, Nature immunology 2021 (PubMed)- GeneRIF: Macrophage IRX3 promotes diet-induced obesity and metabolic inflammation.
- The homeobox factor Irx3 maintains adipogenic identity.
Bjune, Metabolism: clinical and experimental 2020 (PubMed)- GeneRIF: Irx3 is required for preadipocyte identity and differentiation capacity.
- Canonical Wnt/β-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads.
Koth, Development (Cambridge, England) 2020 - GeneRIF: Canonical Wnt/beta-catenin activity and differential epigenetic marks direct sexually dimorphic regulation of Irx3 and Irx5 in developing mouse gonads.
- IRX3 and IRX5 collaborate during ovary development and follicle formation to establish responsive granulosa cells in the adult mouse†.
Fu, Biology of reproduction 2020 - GeneRIF: IRX3 and IRX5 collaborate during ovary development and follicle formation to establish responsive granulosa cells in the adult mousedagger.
- More
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...Ptn P63089 P21246 P63090 P32760 P48532/A4IH83 n/a Ccnd1 P25322 P24385 P39948 P55169 P50755/Q6GLD3 n/a Irx3 P81067 P78415 n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710...”
IRX2_XENLA / Q6DCQ1 Iroquois-class homeodomain protein irx-2; Irx2-A; Iroquois homeobox protein 2; Xiro2 from Xenopus laevis (African clawed frog) (see 6 papers)
40% identity, 13% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Acts early in neural plate development to induce expression of some but not all proneural genes, and specify a neural precursor state. Also up- regulates repressors that prevent neuronal differentiation. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Probably dispensable for pronephric kidney development.
Q9BZI1 Iroquois-class homeodomain protein IRX-2 from Homo sapiens
XP_011512281 iroquois-class homeodomain protein IRX-2 isoform X1 from Homo sapiens
40% identity, 12% coverage
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...P25322 P24385 P39948 P55169 P50755/Q6GLD3 n/a Irx3 P81067 P78415 n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710 P51974 n/a Q9PUK5/A0JMA6 n/a Bmp4 P21275 P12644 Q06826...”
- Iroquois Homeobox Protein 2 Identified as a Potential Biomarker for Parkinson's Disease.
Sim, International journal of molecular sciences 2020 - GeneRIF: Iroquois Homeobox Protein 2 Identified as a Potential Biomarker for Parkinson's Disease.
- IRX2-mediated upregulation of MMP-9 and VEGF in a PI3K/AKT-dependent manner.
Liu, Molecular medicine reports 2015 (PubMed)- GeneRIF: IRX2 modulates the expression levels of MMP2 and VEGF in an AKTdependent manner.
- Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells.
Werner, BMC cancer 2015 - GeneRIF: IRX2 transcription factor might represent a novel metastasis associated protein that acts as a negative regulator of cellular motility and as a repressor of chemokine expression and loss of IRX2 expression could therefore contribute to early hematogenous dissemination of breast cancer by sustaining chemokine secretion and enabling mobilization of tumor cells.
- Knockdown of IRX2 inhibits osteosarcoma cell proliferation and invasion by the AKT/MMP9 signaling pathway.
Liu, Molecular medicine reports 2014 (PubMed)- GeneRIF: The mechanism by which IRX2 promoted cell proliferation and invasion by activating AKT and MMP9 was detected.
- Gene expression profiles predictive of outcome and age in infant acute lymphoblastic leukemia: a Children's Oncology Group study.
Kang, Blood 2012 - GeneRIF: Results revealed 3 genes highly predictive of event-free survival (EFS), beyond age and MLL status: FLT3, IRX2, and TACC2.
- A genome-wide scan maps a novel high myopia locus to 5p15.
Lam, Investigative ophthalmology & visual science 2008 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Frequent amplifications and abundant expression of TRIO, NKD2, and IRX2 in soft tissue sarcomas.
Adamowicz, Genes, chromosomes & cancer 2006 (PubMed)- GeneRIF: IRX2 represents a candidate target of 5p amplifications in soft tissue sarcomas and might play a crucial role during the progression of this disease.
IRX2_XENTR / Q66IK1 Iroquois-class homeodomain protein irx-2; Iroquois homeobox protein 2 from Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (see paper)
40% identity, 12% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Acts early in neural plate development to induce expression of some but not all proneural genes, and specify a neural precursor state. Also up- regulates repressors that prevent neuronal differentiation. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Probably dispensable for pronephric kidney development.
Q9PU52 Iroquois homologue 2 from Gallus gallus
XP_015137852 iroquois-class homeodomain protein IRX-2 isoform X1 from Gallus gallus
40% identity, 12% coverage
AT2G16400 BLH7 (bell1-like homeodomain 7); DNA binding / transcription factor from Arabidopsis thaliana
37% identity, 12% coverage
FOXG_07428 hypothetical protein from Fusarium oxysporum f. sp. lycopersici 4287
43% identity, 6% coverage
CUP9 putative uncharacterized protein CUP9 from Candida albicans (see paper)
XP_721352 Cup9p from Candida albicans SC5314
38% identity, 21% coverage
- CharProtDB CGD description: Protein of unknown function, upregulated in clinical isolates from HIV+ patients with oral candidiasis; transcription reduced upon yeast-hyphal switch; ketoconazole-induced; Plc1p-regulated; shows colony morphology-related Ssn6p regulation
- Identification of Candida albicans regulatory genes governing mucosal infection.
Meir, Cellular microbiology 2018 (PubMed)- GeneRIF: Candida albicans transcription regulator CUP9 is a key determinant of mucosal colonisation. Deletion of cup9 resulted in the formation of more foci of colonisation and heightened persistence in infected tongues. Furthermore, the cup9 mutant produced longer and denser filaments in the oral mucosa without eliciting an enhanced local immune response.
NP_957351 iroquois-class homeodomain protein IRX-2a from Danio rerio
40% identity, 13% coverage
KNAT4_ARATH / P48001 Homeobox protein knotted-1-like 4; Protein KNAT4 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT5G11060 KNAT4 (KNOTTED1-LIKE HOMEOBOX GENE 4); transcription activator/ transcription factor from Arabidopsis thaliana
38% identity, 14% coverage
- subunit: May form heterodimeric complex with the TALE/BELL proteins (By similarity). Interacts with OFP1, OFP2, OFP4 and OFP12 (PubMed:15781858). Interacts with KNATM-B (PubMed:18398054).
- A novel cell-to-cell trafficking assay indicates that the KNOX homeodomain is necessary and sufficient for intercellular protein and mRNA trafficking
Kim, Genes & development 2005 - “...KNAT1 (AAM03027), KNAT2 (P46640), KNAT3 (P48000), KNAT4 (P48001), KNAT5 (P48002), KNAT6 (NP_850951), KNAT7 (NP_564805). (B). Trichome rescue assays were...”
- A comprehensive analysis of transcriptomic data for comparison of plants with different photosynthetic pathways in response to drought stress
Karami, PloS one 2023 - “...PIF5 , PIL6 bHLH At3g62420 ATBZIP53 bZIP At5g08790 anac081 , ATAF2 NAC At5g09330 anac082 NAC At5g11060 KNAT4 Homeobox At5g16540 ZFN3 C2H2 At5g39660 CDF2 C2C2-Dof At5g41030 - TCP At5g47220 ATERF-2 , ATERF2 , ERF2 AP2-EREBP At4g24020 NLP7 NLP At4g32010 HSI2-L1 , HSL1 , VAL2 ABI3VP1 At4g36870 BLH2...”
- “...CDF2 C2C2-Dof At4g36920 AP2 , FL1 , FLO2 AP2-EREBP At5g09330 anac082 NAC At5g16470 - C2H2 At5g11060 KNAT4 Homeobox Through analyzing down-regulated meta-DEGs, we identified 79 and 42 miRNAs belonging to 39 and 28 miRNA families that target 65 and 37 down-regulated genes involved in various biological...”
- Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis
Xu, Biomolecules 2021 - “...PMT6/PLT6 (AT4G36670) Lipid MIOX2 (AT2G19800), ITPK3 (AT4G08170), SFH14 (AT5G56160) Light BG1 (AT5G12050), ERD7 (AT2G17840), KNAT4 (AT5G11060), DFL2 (AT4G03400), PKS1 (AT2G02950), PKS2 (AT1G14280), BRN2 (AT1G03457), TEM1 (AT1G25560), BBX30 (AT4G15248) CO 2 /HCO 3 /pH sensing CA3 (AT1G23730), SLAH3 (AT5G24030) Cell cycle CDKG1 (AT5G63370) Secondary metabolism AtGES (AT1G61120),...”
- “...(ERF), AT2G38470 (WRKY), AT2G46400 (WRKY), AT4G23810 (WRKY), AT5G03150 (C2H2), AT5G67450 (C2H2), AT2G40140 (C3H), AT5G53210 (bHLH), AT5G11060 (TALE), AT1G46480 (WOX), AT3G10590 (MYB-related), AT5G66350 (SRS), AT2G17040 (NAC), AT3G21150 (C2C2 $ ), AT4G14465 (AT-hook $ ) AT1G22810 (ERF), AT1G43160 (ERF), AT1G72360 (ERF), AT4G06746 (ERF), AT4G32800 (ERF), AT5G25810 (ERF), AT5G53290...”
- In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families
Bueno, Genes 2021 - “...114 ] ii. Class II Arabidopsis thaliana AtKNAT3 AT5G25220 Mature organs [ 111 ] AtKNAT4 AT5G11060 Mature organs [ 111 ] AtKNAT5 AT4G32040 Mature organs [ 111 ] AtKNAT7 AT1G62990 Mature organs [ 111 ] Picea abies PaKN5 MK580154 n/a [ 115 ] Pinus pinaster PpKN5...”
- Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson
Li, Plant biotechnology journal 2021 - “...Transcription factor KANADI 3 SV: Premature stop codon, with 3n+1 indel in CDS BrKNAT4 BraA03g00439P AT5G11060 Homeobox protein knotted1like 4 SV: Premature stop codon BrREV BraA10g01717P AT5G60690 Homeoboxleucine zipper REVOLUTA SV: Premature stop codon BrYABBY1 BraA03g02273P AT2G45190 Axial regulator YABBY 1 SV: Premature stop codon John...”
- Functional divergence and adaptive selection of KNOX gene family in plants
Meng, Open life sciences 2020 - “...suggested that members in the same subfamily may play similar roles in the same organization. AT5G11060, AT5G25220, and AT4G32040 are from the class II subfamily. Their overall transcription was richer than that of the class I subfamily. The expression level was higher in senescing leaves. AT4G32040...”
- “...AT4G08150 398 6.02 45,835.5 I AT1G70510 310 4.9 35,638 II AT5G25220 431 5.86 47,599.8 II AT5G11060 393 5.87 44,385 II AT4G32040 383 6.03 43,283.6 I AT1G23380 329 4.92 37,189.9 I AT1G62360 382 6.19 42,753.1 II AT1G62990 291 6.1 32,908.1 I Glyma14g10430 385 6.39 44,100 I Glyma0041s00360...”
- Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica
Jia, Frontiers in plant science 2020 - “...AT1G70510 chr1:26,576,486..26,576,486 933 310 KNAT6 AT1G23380 chr1:8,297,241..8,297,241 990 329 KNAT3 AT5G25220 chr5:8,735,944..8,735,944 1,296 431 KNAT4 AT5G11060 chr5:3,509,833..3,509,833 1,182 393 KNAT5 AT4G32040 chr4:15,493,989..15,493,989 1,152 383 KNAT7 AT1G62990 chr1:23,337,167..23,337,167 876 291 KNOX01 MD02G1012900 Chr03:821,764..821,764 1,083 360 KNOX02 MD04G1069700 Chr04:9,546,107..9,546,107 765 254 KNOX03 MD04G1215500 Chr04:29,846,452..29,846,452 993 330 KNOX04 MD05G1352500...”
- Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID
Mair, eLife 2019 - “...AT5G08130 BIM1 bHLH transcription factor N Y AT1G75080 BZR1 Transcription factor N, C Y Y AT5G11060 KNAT4 Homeobox transcription factor N, C Y AT2G41900 OXS2, TCF7 Zinc finger transcription factor (N), C Y AT1G79000 HAC1, PCAT2 Transcriptional co-activator (histone acetyltransferase) N, C Y AT4G04920 MED16, SFR6...”
- Cytokinin-overinduced transcription factors and thalianol cluster genes in CARBOXYL-TERMINAL DOMAIN PHOSPHATASE-LIKE 4-silenced Arabidopsis roots during de novo shoot organogenesis
Fukudome, Plant signaling & behavior 2018 - “...43 AT3G60390 HAT3 I homeobox-leucine zipper protein 3 AT5G11060 KNAT4 II homeobox protein knotted-1-like 4 AT1G80590 WRKY66 I WRKY DNA-binding protein 66...”
- More
XP_017456222 homeobox protein Mohawk from Rattus norvegicus
38% identity, 17% coverage
NP_077311 iroquois-class homeodomain protein IRX-6 from Homo sapiens
38% identity, 13% coverage
IRX5A_DANRE / Q1LXU5 Iroquois homeobox protein 5a from Danio rerio (Zebrafish) (Brachydanio rerio) (see 4 papers)
40% identity, 13% coverage
- function: Transcription factor (PubMed:26555055). Binds to consensus iroquois binding site (IBS) motifs 5'-ACANNTGT-3' or 5'-ACANNNTGT-3' in regulatory elements of target genes (PubMed:26555055). Required, together with irx7, for hyoid joint formation; they act cell autonomously to repress expression of cartilage matrix genes, such as collagen col2a1a, within immature chondrocytes of the joint interzone (PubMed:26555055). May compete with or modify Sox9a activity, thereby reducing Sox9a-mediated activation of col2a1a (PubMed:26555055). Probably acts in the developing hyoid joint downstream of Bmp signaling (PubMed:26555055). In concert with irx6a, plays a role in visual performance (PubMed:33891002).
IRX5_XENTR / Q4LDQ3 Iroquois-class homeodomain protein irx-5; Iroquois homeobox protein 5 from Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (see paper)
40% identity, 12% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Patterns the neuroectoderm in both the anterior/posterior and dorsal/ventral axes. Does not appear to play a role in pronephros kidney development. Involved in craniofacial and gonadal development (By similarity). Modulates the migration of progenitor cell populations in branchial arches and gonads by repressing CXCL12.
P78414 Iroquois-class homeodomain protein IRX-1 from Homo sapiens
38% identity, 12% coverage
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...P81067 P78415 n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710 P51974 n/a Q9PUK5/A0JMA6 n/a Bmp4 P21275 P12644 Q06826 Q90752 P30885/Q90YD6 n/a Cited1 P97769 Q99966 Q4V8P1...”
IRX1_MOUSE / P81068 Iroquois-class homeodomain protein IRX-1; Homeodomain protein IRXA1; Iroquois homeobox protein 1 from Mus musculus (Mouse) (see 4 papers)
NP_034703 iroquois-class homeodomain protein IRX-1 from Mus musculus
38% identity, 12% coverage
NP_001307054 iroquois-class homeodomain protein IRX-3a from Danio rerio
33% identity, 15% coverage
VDAG_04891 uncharacterized protein from Verticillium dahliae VdLs.17
40% identity, 6% coverage
- Transcription factors containing both C2H2 and homeobox domains play different roles in Verticillium dahliae
Tang, mSphere 2024 - “...-homeobox transcription f actors in the genome of VdLs.17 are VDAG_00465, VDAG_02532, VDAG_02889, VDAG_04660, VDAG_04837, VDAG_04891, and VDAG_07897, named VdChtf1 to VdChtf7, respectively (Fig. S1A and B). To further investigate their functions, we knocked them out using Agrobacterium-mediated genetic transformation ( 23 ) and confirmed the...”
CPAR2_301340 uncharacterized protein from Candida parapsilosis
32% identity, 23% coverage
- Alternative sulphur metabolism in the fungal pathogen Candida parapsilosis
Lombardi, Nature communications 2024 - “...to copper, as previously observed in C. albicans 37 (Fig. 1B ). Disrupting CUP9 ( CPAR2_301340 ), MAC1 ( CPAR2_301500 ) and PBS2 ( CPAR2_806750 ) increases sensitivity to cadmium 41 (Fig. 1B ). Disrupting the phosphatidylinositol (PI) 3-kinase VPS34 ( CPAR2_206880 ) also induced hypersensitivity...”
NP_649256 Six4, isoform A from Drosophila melanogaster
53% identity, 9% coverage
F4JWP8 Homeobox protein knotted-1-like 3 from Arabidopsis thaliana
38% identity, 13% coverage
- Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves
Resjö, International journal of molecular sciences 2019 - “...protein NA 0.53 PGSC0003DMP400014290 AMP dependent CoA ligase NA 0.53 PGSC0003DMP400009317 Superoxide dismutase NA 0.53 F4JWP8 Homeobox protein knotted-1-like 3 NA 0.53 Q9LXG7 Aldose 1-epimerase family protein NA 0.52 PGSC0003DMP400006170 60S ribosomal protein L7A NA 0.51 Q43286 Histone H2A NA 0.50 PGSC0003DMP400042811 60S ribosomal protein L18...”
NP_571429 SIX homeobox 7 from Danio rerio
37% identity, 23% coverage
O04136 Homeobox protein knotted-1-like 3 from Malus domestica
38% identity, 13% coverage
- Genomic approach to study floral development genes in Rosa sp.
Dubois, PloS one 2011 - “...1,24 0,24 BQ104603 0,00 1,65 2,31 1,19 1,00 EC588955 0,00 1,61 0,19 1,01 0,67 BQ106662 (O04136) Homeobox protein knotted-1-like 3 (KNAP3)) 1,58 1,09 1,02 0,17 CF349422 (Q9SWH0) Plasma membrane proton ATPase 1,53 1,54 1,03 0,13 BQ106489 0,00 1,52 0,98 2,22 EC586088 (Q41695) Pectinacetylesterase precursor 1,48 1,58...”
- Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison.
Pilati, BMC genomics 2007 - “...3 (Fragment) 3,12E-114 1617931_at TC40185 8 Q9M276 Homeobox-leucine zipper protein ATHB-12 4,41E-34 1615625_at TC39581 8 O04136 Homeobox protein knotted-1 like 3 (KNAP3) 6,59E-86 1613036_at TC39310 4 Q56R05 Putative pollen specific LIM domain-containing protein 2,68E-90 1606561_at TC41613 7 O81384 Putative basic helix-loop-helix DNA binding protein TCP2 1,25E-20...”
SS1G_03098 hypothetical protein from Sclerotinia sclerotiorum 1980 UF-70
38% identity, 4% coverage
- Changes in the Sclerotinia sclerotiorum transcriptome during infection of Brassica napus
Seifbarghi, BMC genomics 2017 - “...- SS1G_06124 mads-box mef2 type transcription factor (SRF type) - - - - - 3.5 SS1G_03098 homeobox transcription factor - - - - - 2.2 SS1G_03835 homeobox C2H2 transcription factor - - - - - 3.1 SS1G_06987 yippee zinc-binding protein - - - - - 2.4...”
- A cupin domain-containing protein with a quercetinase activity (VdQase) regulates Verticillium dahliae's pathogenicity and contributes to counteracting host defenses
El, Frontiers in plant science 2015 - “...FG09047.1 unnamed protein product hypothetical protein FG09043.1 conserved hypothetical protein conserved hypothetical protein hypothetical protein SS1G_03098 homeobox C2H2 transcription factor, putative homeobox and C2H2 transcription factor hypothetical protein CHGG_04773 hypothetical protein SNOG_06363 hypothetical protein BC1G_06341 homeobox C2H2 transcription factor, putative Pc06g01320, similar to copper homeostasis Pc22g06630,...”
- “...FG09047.1 hypothetical protein SNOG_10151 hypothetical protein CHGG_04773 hypothetical protein MGG_01730 hypothetical protein BC1G_06341 hypothetical protein SS1G_03098 Gibberella zeae PH-1 Gibberella zeae PH-1 Gibberella zeae PH-1 Neurospora crassa OR74A Pyrenophora tritici-repentis Pt-1C-BFP Gibberella zeae PH-1 Phaeosphaeria nodorum SN15 Chaetomium globosum CBS 148.51 Magnaporthe grisea 70-15 Botryotinia fuckeliana...”
A0A0B7A551 Uncharacterized protein (Fragment) from Arion vulgaris
33% identity, 15% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...PREDICTED: mucin-5AC Pax Aplysia_californica Mollusca_Gastropoda A0A0B6YZY1 Uncharacterized protein (Fragment) GN = ORF42948 Pax2/5/8?(f) Arion_vulgaris Mollusca_Gastropoda A0A0B7A551 Uncharacterized protein (Fragment) GN = ORF96941 Pax3/7(f) Arion_vulgaris Mollusca_Gastropoda A0A0B7A6X2 Uncharacterized protein (Fragment) GN = ORF96938 Pax3/7(f) Arion_vulgaris Mollusca_Gastropoda A0A0B7A6Y7 Uncharacterized protein (Fragment) GN = ORF96935 Pax3/7(f) Arion_vulgaris Mollusca_Gastropoda A0A0B6Y326...”
NP_571956 iroquois homeobox 7 from Danio rerio
35% identity, 20% coverage
KNOS3_ORYSJ / Q94LW3 Homeobox protein knotted-1-like 3; Homeobox protein HOS66 from Oryza sativa subsp. japonica (Rice) (see 2 papers)
36% identity, 18% coverage
six1-2 / CAD89530.1 six1-2 protein from Dugesia japonica (see paper)
37% identity, 14% coverage
KNAT3_ARATH / P48000 Homeobox protein knotted-1-like 3; Protein KNAT3 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_197904 homeobox protein knotted-1-like 3 from Arabidopsis thaliana
AT5G25220, NP_197904 KNAT3 (KNOTTED1-LIKE HOMEOBOX GENE 3); transcription activator/ transcription factor from Arabidopsis thaliana
38% identity, 13% coverage
- subunit: May form heterodimeric complex with the TALE/BELL proteins (By similarity). Interacts with OFP1, OFP2, OFP4, OFP12 and OFP14 (PubMed:15781858). Interacts with KNATM-B (PubMed:18398054).
- A novel cell-to-cell trafficking assay indicates that the KNOX homeodomain is necessary and sufficient for intercellular protein and mRNA trafficking
Kim, Genes & development 2005 - “...STM (Q38874), KNAT1 (AAM03027), KNAT2 (P46640), KNAT3 (P48000), KNAT4 (P48001), KNAT5 (P48002), KNAT6 (NP_850951), KNAT7 (NP_564805). (B). Trichome rescue...”
- The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis.
Zhang, Journal of experimental botany 2022 (PubMed)- GeneRIF: The Class II KNOX family members KNAT3 and KNAT7 redundantly participate in Arabidopsis seed coat mucilage biosynthesis.
- The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence deposition of secondary cell walls that provide mechanical support to Arabidopsis stems.
Wang, The Plant journal : for cell and molecular biology 2020 (PubMed)- GeneRIF: The Class II KNOX genes KNAT3 and KNAT7 work cooperatively to influence deposition of secondary cell walls that provide mechanical support to Arabidopsis stems.
- The class II KNOX transcription factors KNAT3 and KNAT7 synergistically regulate monolignol biosynthesis in Arabidopsis.
Qin, Journal of experimental botany 2020 (PubMed)- GeneRIF: The class II KNOX transcription factors KNAT3 and KNAT7 synergistically regulate monolignol biosynthesis in Arabidopsis.
- BLH1 and KNAT3 modulate ABA responses during germination and early seedling development in Arabidopsis.
Kim, The Plant journal : for cell and molecular biology 2013 (PubMed)- GeneRIF: BLH1 and KNAT3 together modulate seed germination and early seedling development by directly regulating ABI3 expression.
- Halophyte-based crop managements induce biochemical, metabolomic and proteomic changes in tomato plants under saline conditions
Barba-Espín, Physiologia plantarum 2025 - “...Arabidopsis homolog (s) Upregulated by T H Solyc07g007120.3.1 Class II knottedlike homeodomain protein 100.00 1.20E03 AT5G25220 Solyc03g118640.3.1 Ketosebisphosphate aldolase classII family protein 7.11 7.18E03 AT1G18270 Solyc01g111700.2.1 26S proteasome nonATPase regulatory subunit 3 6.63 6.69E03 AT1G20200 AT1G75990 Solyc09g083120.3.1 Acylaminoacidreleasing enzyme 6.24 6.96E03 AT4G14570 Solyc11g065600.2.1 Xyloglucan endotransglucosylasehydrolase 4...”
- LcMPK3 and LcMPK6 positively regulate fruitlet abscission in litchi
Wang, Molecular horticulture 2024 - “...homolog protein 2S AT3G45640 LITCHI013207 NAC domain-containing protein 72 AT4G27410 LITCHI016932 Homeobox protein knotted-1-like 3 AT5G25220 LITCHI027845 DNL-type zinc finger protein AT3G54826 LITCHI029103 ethylene response factor AT4G17500 LITCHI027285 Probable aquaporin PIP2-5 AT3G54820 LITCHI018676 Aquaporin TIP1-1 AT2G36830 LITCHI021068 Expansin-B3 AT4G28250 LITCHI001804 Glucan endo-1,3-beta-glucosidase 7 AT4G34480 LITCHI013896 Glucan...”
- The pan-genome and local adaptation of Arabidopsis thaliana
Kang, Nature communications 2023 - “...of different ecotypes across diverse habitats. As an example of SV-overlap influencing adaptation, KNAT3 ( AT5G25220 ) is a class II knotted1-like gene that uses BLH1 to directly regulates ABI3 expression to modulate seed germination and early seedling development. The knat3 mutants are less sensitive to...”
- Protocol for screening and expression studies of T-DNA and tagging-based insertional knox mutants in Arabidopsis thaliana
Sunaryo, 3 Biotech 2021 - “...SALK_110899 SALK_110899 Locus AT1G70510 AT1G70510 AT5G25220 AT5G25220 AT4G32040 AT4G32040 AT1G23380 AT1G23380 AT1G62990 AT1G62990 T-DNA b. Expression...”
- “...- AT4G08150 - AT4G08150 - AT1G70510 - AT1G70510 - AT5G25220 - AT5G25220 - AT4G32040 - AT4G32040 - AT1G23380 - AT1G23380 - AT1G62990 - AT1G62990 - AT1G70510 -...”
- In Vitro Plant Regeneration in Conifers: The Role of WOX and KNOX Gene Families
Bueno, Genes 2021 - “...[ 114 ] PtKN4 AY680387/AY680398 n/a [ 114 ] ii. Class II Arabidopsis thaliana AtKNAT3 AT5G25220 Mature organs [ 111 ] AtKNAT4 AT5G11060 Mature organs [ 111 ] AtKNAT5 AT4G32040 Mature organs [ 111 ] AtKNAT7 AT1G62990 Mature organs [ 111 ] Picea abies PaKN5 MK580154...”
- Functional divergence and adaptive selection of KNOX gene family in plants
Meng, Open life sciences 2020 - “...that members in the same subfamily may play similar roles in the same organization. AT5G11060, AT5G25220, and AT4G32040 are from the class II subfamily. Their overall transcription was richer than that of the class I subfamily. The expression level was higher in senescing leaves. AT4G32040 was...”
- “...pI a Mw (Da) I AT4G08150 398 6.02 45,835.5 I AT1G70510 310 4.9 35,638 II AT5G25220 431 5.86 47,599.8 II AT5G11060 393 5.87 44,385 II AT4G32040 383 6.03 43,283.6 I AT1G23380 329 4.92 37,189.9 I AT1G62360 382 6.19 42,753.1 II AT1G62990 291 6.1 32,908.1 I Glyma14g10430...”
- Genome-Wide Identification of the MdKNOX Gene Family and Characterization of Its Transcriptional Regulation in Malus domestica
Jia, Frontiers in plant science 2020 - “...AT4G08150 chr4:5,147,699..5,147,699 1,197 398 KNAT2 AT1G70510 chr1:26,576,486..26,576,486 933 310 KNAT6 AT1G23380 chr1:8,297,241..8,297,241 990 329 KNAT3 AT5G25220 chr5:8,735,944..8,735,944 1,296 431 KNAT4 AT5G11060 chr5:3,509,833..3,509,833 1,182 393 KNAT5 AT4G32040 chr4:15,493,989..15,493,989 1,152 383 KNAT7 AT1G62990 chr1:23,337,167..23,337,167 876 291 KNOX01 MD02G1012900 Chr03:821,764..821,764 1,083 360 KNOX02 MD04G1069700 Chr04:9,546,107..9,546,107 765 254 KNOX03 MD04G1215500...”
- Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions
Albihlal, Journal of experimental botany 2018 - “...AT1G29640 AT3G15770 AT3G15770 AT5G22940 F8H AT1G32640 MYC2 AT3G15790 MBD11 AT5G24530 DMR6 AT1G32920 AT1G32920 AT3G16240 DELTA-TIP AT5G25220 KNAT3 AT1G72450 JAZ6 AT3G22380 TIC AT5G47220 ERF2 AT1G77280 AT1G77280 AT3G24518 AT3G24518 AT5G47225 AT5G47225 AT1G78070 AT1G78070 AT3G24520 HSFC1 AT5G48250 BBX8 AT1G80440 AT1G80440 AT3G49790 AT3G49790 AT5G49520 WRKY48 AT2G14210 AGL44 AT3G50750 BEH1 AT5G53400...”
- More
R7TKD0 Transcription factor Pax3/7 (Fragment) from Capitella teleta
39% identity, 26% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...Pax2(f) Helobdella_robusta Annelida_Clitellata R7VKC0 Uncharacterized protein Pax1/9(f) Capitella_teleta Annelida_Polychaeta R7T7W6 Uncharacterized protein Pax2/5/8(f) Capitella_teleta Annelida_Polychaeta R7TKD0 Uncharacterized protein Pax3/7(f) Capitella_teleta Annelida_Polychaeta R7TWR1 Uncharacterized protein Pax(f) Capitella_teleta Annelida_Polychaeta R7UF83 Uncharacterized protein PoxN Capitella_teleta Annelida_Polychaeta K1QWY6 Paired box protein Pax-6 eyg Crassostrea_gigas Mollusca_Bivalvia K1QYI7 Paired box protein Pax-2-A...”
NP_998265 iroquois-class homeodomain protein IRX-3b from Danio rerio
38% identity, 16% coverage
NP_631960 homeobox protein TGIF2LY from Homo sapiens
Q8IUE0 Homeobox protein TGIF2LY from Homo sapiens
32% identity, 34% coverage
- Association of TGIFLX/Y mRNA expression with prostate cancer.
Ousati, Medical oncology (Northwood, London, England) 2009 (PubMed)- GeneRIF: most prostate tumors (73.5%) express at least one of these genes (TGIFLX and TGIFLY), although different patterns of mRNA expression were observed. These results suggest an association of TGIFLX/Y expression with the progression of prostate cancer.
- Association of TGIFLX/Y mRNA expression with azoospermia in infertile men.
Aarabi, Molecular reproduction and development 2008 (PubMed)- GeneRIF: Association of TGIFLX/Y mRNA expression with azoospermia in infertile men.(
- Geometric deep learning of protein-DNA binding specificity
Mitra, Nature methods 2024 - “...subsequently, improve DeepPBS prediction). We demonstrated this process for the human TGIF2LY protein (UniProt ID Q8IUE0 , unstructured region trimmed; Supplementary Section 8 ) in Fig. 3e . In round 1, we applied RFNA to this protein sequence alongside the IG DNA sequence for the HD...”
- “..., 7OH9 and 1APL . UniProt accession codes for protein sequences discussed (folded with RFNA): Q8IUE0 , Q6H878 , O43680 and Q4H376 . Accession codes for discussed experimental specificity data from JASPAR2022 and HOCOMOCOv11: MA1897.1 , MA1568.1 , MA1031.1 , MA1572.1 , MA0112.2 , MA0112.3 ,...”
GRMZM2G159431 homeobox protein HD1 from Zea mays
36% identity, 18% coverage
- Dissection of the genetic architecture of peduncle vascular bundle-related traits in maize by a genome-wide association study
Sun, Plant biotechnology journal 2022 - “...involved in lignin polymerization and synthesis (Endo etal ., 2019 ). The Arabidopsis homolog of GRMZM2G159431 was identified as KNAT7 , which has recently been implicated in the direct regulation of xylan biosynthesis genes affecting the SCW and seed coat mucilage of Arabidopsis (He etal .,...”
- “...etal ., 2011 ; Xiao etal ., 2016 ; Tables S6S9 ). The homolog of GRMZM2G159431 (in qPVB1 ) is KNAT7 , whose function has already been mentioned in candidate gene analysis section. Of the 36 QTL detected in more than one study, 13 ( qPVB6...”
- Functional divergence and adaptive selection of KNOX gene family in plants
Meng, Open life sciences 2020 - “...GRMZM2G055243 316 5.69 34,522.6 II GRMZM2G370332 310 5.84 33,791.9 II GRMZM2G433591 363 9.78 39,958.3 II GRMZM2G159431 310 5.73 34,336.7 I Pp1s235_27V6 508 5.55 57,539.1 I Pp1s33_357V6 445 5.44 50,715.3 II Pp1s154_83V6 636 5.59 72,405.5 II Pp1s77_59V6 518 5.24 58,858.8 ORF = open reading frame; aa =...”
P78415 Iroquois-class homeodomain protein IRX-3 from Homo sapiens
NP_077312 iroquois-class homeodomain protein IRX-3 from Homo sapiens
36% identity, 12% coverage
- Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.
Harmon, eLife 2017 - “...from which the sequence was drawn EDEDSEKEEEEEDKEMEELQEEKECEKPQGDEEEEEEEEE 0.80 0.60 0.93 P37275 DEEGNAYGSEREEEDEEEDEEDGKRELELEEEELGGEEED 0.70 0.55 0.88 P78415 REKDREKYSQREQERDRQQNDQNRPSEKGEKEEKSKAKEE 0.65 0.00 0.93 Q9H0G5 DRVVVTDDSDERRLKGAEDKSEEGEDNRSSESEEESEGEE 0.60 0.30 0.88 Q9BQG0 EAYRLSLEADRAKREAHEREMAEQFRLEQIRKEQEEEREA 0.55 0.10 0.88 Q9UNN5 RRQRRWEDIFNQHEEELRQVDKDKEDESSDNDEVFHSIQA 0.50 0.15 0.73 Q7Z2Y5 NNRKGRGGNRGREFRGEENGIDCNQVDKPSDRGKRARGRG 0.45 0.15 0.76 Q5T6F2 QKQKLRLLSSVKPKTGEKSRDDALEAIKGNLDGFSRDAKM 0.40 0.10 0.75 Q9UMZ2...”
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...P63089 P21246 P63090 P32760 P48532/A4IH83 n/a Ccnd1 P25322 P24385 P39948 P55169 P50755/Q6GLD3 n/a Irx3 P81067 P78415 n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710 P51974...”
- The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
Nagel, International journal of molecular sciences 2022 - GeneRIF: The Hematopoietic TALE-Code Shows Normal Activity of IRX1 in Myeloid Progenitors and Reveals Ectopic Expression of IRX3 and IRX5 in Acute Myeloid Leukemia.
- IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism.
Ma, Frontiers in endocrinology 2022 - GeneRIF: IRX3 plays an important role in the pathogenesis of metabolic-associated fatty liver disease by regulating hepatic lipid metabolism.
- Clinical utility of irx3 in keratoconus.
Markoulli, Clinical & experimental optometry 2021 (PubMed)- GeneRIF: Clinical utility of irx3 in keratoconus.
- IRX3 Overexpression Enhances Ucp1 Expression In Vivo.
Zhang, Frontiers in endocrinology 2021 - GeneRIF: IRX3 Overexpression Enhances Ucp1 Expression In Vivo.
- Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
Sobreira, Science (New York, N.Y.) 2021 - GeneRIF: Extensive pleiotropism and allelic heterogeneity mediate metabolic effects of IRX3 and IRX5.
- The homeobox factor Irx3 maintains adipogenic identity.
Bjune, Metabolism: clinical and experimental 2020 (PubMed)- GeneRIF: Irx3 is required for preadipocyte identity and differentiation capacity.
- Hypothalamic IRX3: A New Player in the Development of Obesity.
de, Trends in endocrinology and metabolism: TEM 2020 (PubMed)- GeneRIF: Hypothalamic IRX3: A New Player in the Development of Obesity.
- Associations of nicotidamide-N-methyltransferase, FTO, and IRX3 genetic variants with body mass index and resting energy expenditure in Mexican subjects.
Bañales-Luna, Scientific reports 2020 - GeneRIF: Associations of nicotidamide-N-methyltransferase, FTO, and IRX3 genetic variants with body mass index and resting energy expenditure in Mexican subjects.
- More
NP_001073284 mix-type homeobox gene 2 from Danio rerio
39% identity, 21% coverage
NP_001084204 iroquois-class homeodomain protein irx-3 from Xenopus laevis
33% identity, 15% coverage
V4AMZ8 Uncharacterized protein (Fragment) from Lottia gigantea
36% identity, 24% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...eyg Lottia_gigantea Mollusca_Gastropoda V4A9T6 Uncharacterized protein Pax1/9 Lottia_gigantea Mollusca_Gastropoda V3ZI38 Uncharacterized protein Pax2/5/8(f) Lottia_gigantea Mollusca_Gastropoda V4AMZ8 Uncharacterized protein Pax3/7(f) Lottia_gigantea Mollusca_Gastropoda V3ZQV3 Uncharacterized protein Pax6(f) Lottia_gigantea Mollusca_Gastropoda Contig4275(24639772470937) LgGsHFWreduced.5213 Pax Lottia_gigantea Mollusca_Gastropoda V4B0D1 Uncharacterized protein Pax(f) Lottia_gigantea Mollusca_Gastropoda V3ZWA2 Uncharacterized protein PoxN(f) Lottia_gigantea Mollusca_Gastropoda Q25411 Pax6-like...”
IRX3_XENLA / O42261 Iroquois-class homeodomain protein irx-3; Iroquois homeobox protein 3; Xiro3 from Xenopus laevis (African clawed frog) (see 6 papers)
33% identity, 15% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Both up- regulates and down-regulates gene expression during neural development. Acts early in neural plate development to induce proneural gene expression and specify a neural precursor state. Also up-regulates repressors that prevent neuronal differentiation. Required during at least two stages of pronephros kidney development; during neurula stages, maintains transcription of key renal genes to define the size and identity of the pronephric anlage, probably in part through regulation of bmp-signaling. Subsequently required for proper formation of the intermediate tubule segment of the pronephros.
CLUG_02322 Homeobox KN domain family protein from Clavispora lusitaniae
39% identity, 28% coverage
NP_001081933 SIX homeobox 6 L homeolog from Xenopus laevis
38% identity, 23% coverage
XP_068068923 homeobox protein SIX6a isoform X1 from Danio rerio
38% identity, 19% coverage
Q9SYT6 Homeobox protein liguleless 3 from Zea mays
42% identity, 17% coverage
XP_005685997 homeobox protein SIX6 isoform X1 from Capra hircus
38% identity, 22% coverage
SIX6_CHICK / O93307 Homeobox protein SIX6; Optic homeobox 2; Sine oculis homeobox homolog 6; Six9 protein from Gallus gallus (Chicken) (see 2 papers)
38% identity, 22% coverage
- function: May be involved in eye development.
NP_571635 mix-type homeobox gene 1 from Danio rerio
38% identity, 21% coverage
XP_038529716 homeobox protein SIX6 from Canis lupus familiaris
38% identity, 22% coverage
SIX6_MOUSE / Q9QZ28 Homeobox protein SIX6; Optic homeobox 2; Sine oculis homeobox homolog 6; Six9 protein from Mus musculus (Mouse) (see 3 papers)
NP_035514 homeobox protein SIX6 from Mus musculus
38% identity, 22% coverage
- function: May be involved in eye development.
subunit: Interacts with TLE4 and TLE5. - The Homeodomain Transcription Factors Vax1 and Six6 Are Required for SCN Development and Function.
Pandolfi, Molecular neurobiology 2020 - GeneRIF: The Homeodomain Transcription Factors Vax1 and Six6 Are Required for SCN Development and Function.
- Six2 regulates Pax9 expression, palatogenesis and craniofacial bone formation.
Sweat, Developmental biology 2020 - GeneRIF: Six2 regulates Pax9 expression, palatogenesis and craniofacial bone formation.
- Deletion of the Homeodomain Protein Six6 From GnRH Neurons Decreases GnRH Gene Expression, Resulting in Infertility.
Pandolfi, Endocrinology 2019 - GeneRIF: Six6 plays distinct roles in maintaining fertility in the GnRH neuron vs in the migratory environment of the GnRH neuron by maintaining expression of GnRH and survival of GnRH neurons, respectively.
- Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation.
Diacou, Cell reports 2018 - GeneRIF: Six3 and Six6 together directly or indirectly suppress Wnt/beta-catenin signaling but promote retinogenic factors for the maintenance of multipotent neuroretinal progenitors.
- Homeodomain Proteins SIX3 and SIX6 Regulate Gonadotrope-specific Genes During Pituitary Development.
Xie, Molecular endocrinology (Baltimore, Md.) 2015 - GeneRIF: SIX3 and SIX6 play distinct but compensatory roles in regulating transcription of gonadotrope-specific genes as gonadotrope cells differentiate.
- Aberrant development of the suprachiasmatic nucleus and circadian rhythms in mice lacking the homeodomain protein Six6.
Clark, Journal of biological rhythms 2013 - GeneRIF: Six6-null mice display abnormal patterns of circadian behavior.
- Direct transcriptional regulation of Six6 is controlled by SoxB1 binding to a remote forebrain enhancer.
Lee, Developmental biology 2012 - GeneRIF: SoxB1 transcription factors are direct activators of Six6 expression in the ventral forebrain
- Hypothalamic dysregulation and infertility in mice lacking the homeodomain protein Six6.
Larder, The Journal of neuroscience : the official journal of the Society for Neuroscience 2011 - GeneRIF: Six6 plays an important role in the regulation of GnRH expression and hypothalamic control of fertility.
- More
XP_017172856 homeobox protein SIX3 isoform X1 from Mus musculus
38% identity, 16% coverage
- The homeodomain transcription factor Six3 regulates hypothalamic Pomc expression and its absence from POMC neurons induces hyperphagia and mild obesity in male mice.
Yu, Molecular metabolism 2024 - GeneRIF: The homeodomain transcription factor Six3 regulates hypothalamic Pomc expression and its absence from POMC neurons induces hyperphagia and mild obesity in male mice.
- Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation.
Shrestha, Stem cells (Dayton, Ohio) 2023 - GeneRIF: Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation.
- Deletion of the homeodomain gene Six3 from kisspeptin neurons causes subfertility in female mice.
Lavalle, Molecular and cellular endocrinology 2022 - GeneRIF: Deletion of the homeodomain gene Six3 from kisspeptin neurons causes subfertility in female mice.
- Homeobox Gene Six3 is Required for the Differentiation of D2-Type Medium Spiny Neurons.
Song, Neuroscience bulletin 2021 - GeneRIF: Homeobox Gene Six3 is Required for the Differentiation of D2-Type Medium Spiny Neurons.
- The transcription factors SIX3 and VAX1 are required for suprachiasmatic nucleus circadian output and fertility in female mice.
Hoffmann, Journal of neuroscience research 2021 - GeneRIF: The transcription factors SIX3 and VAX1 are required for suprachiasmatic nucleus circadian output and fertility in female mice.
- Haploinsufficiency of Homeodomain Proteins Six3, Vax1, and Otx2 Causes Subfertility in Mice via Distinct Mechanisms.
Hoffmann, Neuroendocrinology 2019 - GeneRIF: Heterozygous deletion of Otx2, Vax1, or Six3 is sufficient to produce subfertility. Review shows that that all 3 have reduced numbers of GnRH neurons and are subfertile. However, there is specificity to the subfertility by sex and by mechanisms of action.
- Haploinsufficiency of SIX3 Abolishes Male Reproductive Behavior Through Disrupted Olfactory Development, and Impairs Female Fertility Through Disrupted GnRH Neuron Migration.
Pandolfi, Molecular neurobiology 2018 - GeneRIF: Six3 is haploinsufficient for main olfactory epithelium development, GnRH neuron migration, and fertility.
- SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression.
Xu, Development (Cambridge, England) 2018 - GeneRIF: SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression
- More
SIX6_HUMAN / O95475 Homeobox protein SIX6; Homeodomain protein OPTX2; Optic homeobox 2; Sine oculis homeobox homolog 6 from Homo sapiens (Human) (see paper)
NP_031400 homeobox protein SIX6 from Homo sapiens
38% identity, 22% coverage
- function: May be involved in eye development
subunit: Interacts with TLE4 and TLE5. - Association of SIX1-SIX6 polymorphisms with peripapillary retinal nerve fibre layer thickness in children.
Lu, The British journal of ophthalmology 2023 (PubMed)- GeneRIF: Association of SIX1-SIX6 polymorphisms with peripapillary retinal nerve fibre layer thickness in children.
- Association of Polymorphisms at the SIX1/SIX6 Locus With Normal Tension Glaucoma in a Korean Population.
Shin, Journal of glaucoma 2022 (PubMed)- GeneRIF: Association of Polymorphisms at the SIX1/SIX6 Locus With Normal Tension Glaucoma in a Korean Population.
- Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.
Panagiotou, Molecular vision 2022 - GeneRIF: Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.
- Mutually exclusive epigenetic modification on SIX6 with hypermethylation for precancerous stage and metastasis emergence tracing.
Dong, Signal transduction and targeted therapy 2022 - GeneRIF: Mutually exclusive epigenetic modification on SIX6 with hypermethylation for precancerous stage and metastasis emergence tracing.
- Lack of association between SIX1/SIX6 locus polymorphisms and pseudoexfoliation syndrome in a population from the Republic of Korea.
Lee, Medicine 2022 - GeneRIF: Lack of association between SIX1/SIX6 locus polymorphisms and pseudoexfoliation syndrome in a population from the Republic of Korea.
- SIX6-related anophthalmia/microphthalmia: second report on a deletion in a consanguineous family.
Deepthi, Ophthalmic genetics 2021 (PubMed)- GeneRIF: SIX6-related anophthalmia/microphthalmia: second report on a deletion in a consanguineous family.
- Age-dependent regional retinal nerve fibre changes in SIX1/SIX6 polymorphism.
Charng, Scientific reports 2020 - GeneRIF: Age-dependent regional retinal nerve fibre changes in SIX1/SIX6 polymorphism.
- SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome.
Laukkanen, Leukemia & lymphoma 2020 (PubMed)- GeneRIF: SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome.
- More
- Novel SIX6 mutations cause recessively inherited congenital cataract, microcornea, and corneal opacification with or without coloboma and microphthalmia.
Panagiotou, Molecular vision 2022 - “...using CLUSTALW . Molecular modeling The structural model of human SIX6 protein (Uniprot accession number O95475 ) was derived by homology modeling using M4T [ 13 , 14 ]. The crystal structure of the human SIX1-EYA2 protein complex [ 15 ] and the crystal structure of...”
XP_063118601 homeobox protein SIX3 isoform X1 from Rattus norvegicus
38% identity, 15% coverage
BC1G_06341 Bchox2 from Botrytis cinerea B05.10
36% identity, 4% coverage
- A cupin domain-containing protein with a quercetinase activity (VdQase) regulates Verticillium dahliae's pathogenicity and contributes to counteracting host defenses
El, Frontiers in plant science 2015 - “...factor, putative homeobox and C2H2 transcription factor hypothetical protein CHGG_04773 hypothetical protein SNOG_06363 hypothetical protein BC1G_06341 homeobox C2H2 transcription factor, putative Pc06g01320, similar to copper homeostasis Pc22g06630, DNA binding domain hypothetical protein AN9328.2 hypothetical protein FG07909.1 homeobox C2H2 transcription factor, putative AhpA, protection against organic peroxides...”
- “...protein hypothetical protein FG09047.1 hypothetical protein SNOG_10151 hypothetical protein CHGG_04773 hypothetical protein MGG_01730 hypothetical protein BC1G_06341 hypothetical protein SS1G_03098 Gibberella zeae PH-1 Gibberella zeae PH-1 Gibberella zeae PH-1 Neurospora crassa OR74A Pyrenophora tritici-repentis Pt-1C-BFP Gibberella zeae PH-1 Phaeosphaeria nodorum SN15 Chaetomium globosum CBS 148.51 Magnaporthe grisea...”
NP_001018421 homeobox protein SIX6b from Danio rerio
38% identity, 22% coverage
Q9PUR3 Iroquois-related homeobox transcription factor IRX3 (Fragment) from Gallus gallus
38% identity, 56% coverage
- Representing kidney development using the gene ontology.
Alam-Faruque, PloS one 2014 - “...P63090 P32760 P48532/A4IH83 n/a Ccnd1 P25322 P24385 P39948 P55169 P50755/Q6GLD3 n/a Irx3 P81067 P78415 n/a Q9PUR3 O42261/Q6NVN3 n/a Irx2 P81066 Q9BZI1 n/a Q9PU52 Q6DCQ1/Q66IK1 n/a Irx1 P81068 P78414 n/a Q9I9C5 Q9YGK8/Q6F2E3 n/a Pax2 P32114 Q02962 D4ACZ2 Q9PTX1 O57685 O57682/Q28IR6 n/a Pax8 Q00288 Q06710 P51974 n/a Q9PUK5/A0JMA6...”
NP_997067 iroquois-class homeodomain protein IRX-1a isoform 1 from Danio rerio
36% identity, 14% coverage
- A cascade of irx1a and irx2a controls shh expression during retinogenesis.
Choy, Developmental dynamics : an official publication of the American Association of Anatomists 2010 (PubMed)- GeneRIF: Observations suggest that Irx2 functions downstream of irx1a to control shh expression in the retina. Study proposed a novel transcriptional cascade of ath5-irx1a-irx2a in the regulation of hedgehog waves during vertebrate retinal development.
- Expression of ventral diencephalon-enriched genes in zebrafish.
Li, Developmental dynamics : an official publication of the American Association of Anatomists 2010 (PubMed)- GeneRIF: Data revealed that expression of DNA binding inhibitor 3, early B cell factor 2, Ebf3, Iroquois related homeobox 1, Kruppel-like factor 7 , mab-21-like 1 , fatty acid binding protein 7 and stathmin-like 4,were enriched in the diencephalon of zebrafish.
- Zebrafish homologue irx1a is required for the differentiation of serotonergic neurons.
Cheng, Developmental dynamics : an official publication of the American Association of Anatomists 2007 (PubMed)- GeneRIF: irx1a is not required for the initial specification but it is required for the complete differentiation of 5HT neurons
- The homeobox gene irx1a is required for the propagation of the neurogenic waves in the zebrafish retina.
Cheng, Mechanisms of development 2006 (PubMed)- GeneRIF: Our results reveal a role for Iroquois genes in controlling hedgehog expression during vertebrate retinogenesis.
KNOSD_ORYSJ / Q0J6N4 Homeobox protein knotted-1-like 13; Homeobox protein OSH45 from Oryza sativa subsp. japonica (Rice) (see paper)
38% identity, 15% coverage
- function: Isoform 3 acts as a transcription activator, but isoforms 1 and 2 do not.
XP_015147858 LOW QUALITY PROTEIN: iroquois-class homeodomain protein IRX-3 from Gallus gallus
36% identity, 12% coverage
IRX3_XENTR / Q6NVN3 Iroquois-class homeodomain protein irx-3; Iroquois homeobox protein 3 from Xenopus tropicalis (Western clawed frog) (Silurana tropicalis) (see paper)
33% identity, 15% coverage
- function: Acts partially redundantly with other irx members in neural patterning. Required for formation of the posterior forebrain, midbrain, hindbrain, and to a lesser extent, spinal cord. Both up- regulates and down-regulates gene expression during neural development. Acts early in neural plate development to induce proneural gene expression and specify a neural precursor state. Also up-regulates repressors that prevent neuronal differentiation. Required during at least two stages of pronephros kidney development; during neurula stages, maintains transcription of key renal genes to define the size and identity of the pronephric anlage, probably in part through regulation of bmp-signaling. Subsequently required for proper formation of the intermediate tubule segment of the pronephros.
KNOS8_ORYSJ / Q10ED2 Homeobox protein knotted-1-like 8; Homeobox protein OSH43 from Oryza sativa subsp. japonica (Rice) (see paper)
38% identity, 18% coverage
LOC107436457 homeobox protein SIX6-like from Parasteatoda tepidariorum
38% identity, 15% coverage
so / CAB89515.1 homeodomain transcription factor from Girardia tigrina (see paper)
37% identity, 14% coverage
SIX3_MOUSE / Q62233 Homeobox protein SIX3; Sine oculis homeobox homolog 3 from Mus musculus (Mouse) (see 18 papers)
38% identity, 17% coverage
- function: Transcriptional regulator which can act as both a transcriptional repressor and activator by binding a ATTA homeodomain core recognition sequence on these target genes. During forebrain development represses WNT1 expression allowing zona limitans intrathalamica formation and thereby ensuring proper anterio-posterior patterning of the diencephalon and formation of the rostral diencephalon (PubMed:18094027). Acts as a direct upstream activator of SHH expression in the rostral diencephalon ventral midline and that in turn SHH maintains its expression (PubMed:18775421). In addition, Six3 activity is required for the formation of the telencephalon. During postnatal stages of brain development is necessary for ependymal cell maturation by promoting the maturation of radial glia into ependymal cells through regulation of neuroblast proliferation and migration (PubMed:22071110). Acts on the proliferation and differentiation of neural progenitor cells through activating transcription of CCND1 AND CCND2 (PubMed:17576749). During early lens formation plays a role in lens induction and specification by activating directly PAX6 in the presumptive lens ectoderm (PubMed:17066077). In turn PAX6 activates SIX3 resulting in activation of PDGFRA and CCND1 promoting cell proliferation (PubMed:12072567). Also is required for the neuroretina development by directly suppressing WNT8B expression in the anterior neural plate territory (PubMed:20890044). Its action during retina development and lens morphogenesis is TLE5 and TLE4-dependent manner. Furthermore, during eye development regulates several genes expression. Before and during early lens development represses the CRYGF promoter by binding a SIX repressor element (PubMed:11139622). Directly activates RHO transcription, or cooperates with CRX or NRL (PubMed:17666527). Six3 also functions in the formation of the proximodistal axis of the optic cup (PubMed:12163408), and promotes the formation of optic vesicles-like structures (PubMed:11458394). During pituitary development, acts in parallel or alternatively with HESX1 to control cell proliferation through Wnt/beta-catenin pathway (PubMed:18694563). Plays a role in eye development by suppressing WNT1 expression and in dorsal-ventral patterning by repressing BMP signaling pathway (By similarity).
subunit: Interacts with EYA4; translocates EYA4 from the cytoplasm to the nucleus and promotes activation of their target genes. Interacts with MTA1 and HDAC2; represses its own transcription. Interacts with MTA1; facilitates the binding of SIX3 to the core DNA motif of SIX3 promoter. Interacts with EYA1; promotes EYA1 translocation to the nucleus. Interacts with TLE1 and TLE5 (via Q domain); can act in combination with either TLE1 and/or TLE5 leading to transcriptional repression or activation, respectively (By similarity). Interacts (via homeobox) with NR4A3; differentially regulates the transcriptional activities NR4A3 (By similarity). Interacts with GMNN (By similarity). Interacts with TLE4.
disruption phenotype: Embryos die at birth and lack most head structures anterior to the midbrain, including the eyes and nose (PubMed:12569128). Embryonic SHH and SIX3 double heterozygous mice exhibit a semilobar holoprosencephaly-like phenotype and a dorsoventral patterning defects in telencephalon (PubMed:18694563). Embryonic WNT1 and SIX3 double homozygous mice lack cerebellum and colliculus and have a severely reduced midbrain (PubMed:18094027). Conditional knockout in eye exhibit drastically reduced lens size, cataracts, or absence of the lens (PubMed:17066077). Embryo of SIX3 and HESX1 heterozygous mice exhibit severe growth retardation after weaning, with additional gonadal and thyroid gland defects, resulting in a lethal phenotype (PubMed:18775421). - Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...pigments such as melanins defects in Tyr results in various forms of albinism 1 isoform Q62233 Six3 homeobox protein SIX3 87 transcriptional regulator -- 2 isoforms O54751 Crx cone-rod homeobox protein 87 transcription factor that transactivates a sequence upstream of several photoreceptor-specific genes -- 1 isoform...”
PAX7_HUMAN / P23759 Paired box protein Pax-7; HuP1 from Homo sapiens (Human) (see 3 papers)
NP_001128726 paired box protein Pax-7 isoform 3 from Homo sapiens
33% identity, 14% coverage
- function: Transcription factor that is involved in the regulation of muscle stem cells proliferation, playing a role in myogenesis and muscle regeneration.
subunit: Can bind to DNA as a heterodimer with PAX3. Interacts with PAXBP1; the interaction links PAX7 to a WDR5-containing histone methyltransferase complex (By similarity). Interacts with DAXX (PubMed:10393185). - In vitro-generated human muscle reserve cells are heterogeneous for Pax7 with distinct molecular states and metabolic profiles.
Bouche, Stem cell research & therapy 2023 - GeneRIF: In vitro-generated human muscle reserve cells are heterogeneous for Pax7 with distinct molecular states and metabolic profiles.
- PAX7, a Key for Myogenesis Modulation in Muscular Dystrophies through Multiple Signaling Pathways: A Systematic Review.
Rahman, International journal of molecular sciences 2023 - GeneRIF: PAX7, a Key for Myogenesis Modulation in Muscular Dystrophies through Multiple Signaling Pathways: A Systematic Review.
- Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors.
Mavrommatis, eLife 2023 - GeneRIF: Human skeletal muscle organoids model fetal myogenesis and sustain uncommitted PAX7 myogenic progenitors.
- Defining and identifying satellite cell-opathies within muscular dystrophies and myopathies.
Ganassi, Experimental cell research 2022 - GeneRIF: Defining and identifying satellite cell-opathies within muscular dystrophies and myopathies.
- Does PAX7 and NKX2.2 immunoreactivity in Ewing sarcoma have prognostic significance?
Machado, Virchows Archiv : an international journal of pathology 2022 (PubMed)- GeneRIF: Does PAX7 and NKX2.2 immunoreactivity in Ewing sarcoma have prognostic significance?
- Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers.
van, Scientific reports 2022 - GeneRIF: Facioscapulohumeral dystrophy transcriptome signatures correlate with different stages of disease and are marked by different MRI biomarkers.
- Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
Manceau, PLoS genetics 2022 - GeneRIF: Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
- Genomic Safe Harbor Expression of PAX7 for the Generation of Engraftable Myogenic Progenitors.
Kim, Stem cell reports 2021 - GeneRIF: Genomic Safe Harbor Expression of PAX7 for the Generation of Engraftable Myogenic Progenitors.
- More
- Characterising the efficacy and bioavailability of bioactive peptides identified for attenuating muscle atrophy within a Vicia faba-derived functional ingredient.
Corrochano, Current research in food science 2021 - “...Myogenic factor 5 Human P15173 MYOG Myogenin Human P23760 PAX3 Paired box protein Pax-3 Human P23759 PAX7 Paired box protein Pax-7 Human Q06413 MEF2C Myocyte-specific enhancer factor 2C Human The two approaches were finally combined to carry out the final prediction and identify the most efficacious...”
KNOS1_ORYSJ / Q9FP29 Homeobox protein knotted-1-like 1; Homeobox protein HOS16; Homeobox protein OSH6 from Oryza sativa subsp. japonica (Rice) (see paper)
42% identity, 17% coverage
- function: Probable transcription factor that may be involved in shoot formation during early embryogenesis.
NP_989600 paired box protein Pax-3 isoform a from Gallus gallus
33% identity, 14% coverage
- Pax3 overexpression induces cell aggregation and perturbs commissural axon projection during embryonic spinal cord development.
Lin, The Journal of comparative neurology 2017 (PubMed)- GeneRIF: Pax3 regulates neural circuit formation during embryonic development
- Pax3 and Pax7 interact reciprocally and regulate the expression of cadherin-7 through inducing neuron differentiation in the developing chicken spinal cord.
Lin, The Journal of comparative neurology 2016 (PubMed)- GeneRIF: Pax3 has an important role in regulating morphogenesis and cell differentiation in the developing spinal cord.
- Pax3 isoforms in sensory neurogenesis: expression and function in the ophthalmic trigeminal placode.
Adams, Developmental dynamics : an official publication of the American Association of Anatomists 2014 - GeneRIF: PAx3 full length and Pax3V1 isoforms inhibit neuronal differentiation; Pax3V2 isoform is permissive for neuronal differentiation and is expressed in trigeminal placode.
- Housing system influences abundance of Pax3 and Pax7 in postnatal chicken skeletal muscles.
Yin, Poultry science 2014 (PubMed)- GeneRIF: PAX3 and PAX7 mRNA abundance increases with age were less pronounced in caged system chickens than in pen and free-range chickens from day 56 to 84; free-range chickens showed more pronounced increase in gene expression with age than did pen chickens.
- Genetic and physical interaction of Meis2, Pax3 and Pax7 during dorsal midbrain development.
Agoston, BMC developmental biology 2012 - GeneRIF: The results described here suggest a model in which interdependent regulatory loops involving Pax3 and Pax7 in the dorsal mesencephalic vesicle modulate Meis2 expression.
- Interplay of Nkx3.2, Sox9 and Pax3 regulates chondrogenic differentiation of muscle progenitor cells.
Cairns, PloS one 2012 - GeneRIF: the balance of Pax3, Nkx3.2 and Sox9 may act as a molecular switch during the chondrogenic differentiation of muscle progenitor cells, which may be important for fracture healing.
- Mutual repression between Pax3 and Pax6 is involved in the positioning of ophthalmic trigeminal placode in avian embryo.
Wakamatsu, Development, growth & differentiation 2011 (PubMed)- GeneRIF: the mutual repression between Pax3and Pax6 has important roles in the specification and the positioning of the ophthalmic trigeminal placode.
- Retention of Pax3 expression in satellite cells of muscle spindles.
Kirkpatrick, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 2010 - GeneRIF: Pax3-positive SCs are involved in fiber maintenance.
- More
Smp_147790 putative homothorax homeobox protein from Schistosoma mansoni
58% identity, 3% coverage
- A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture
Attenborough, eLife 2024 - “...(Smp_247590), tiptop (Smp_180690), hes-related (Smp_024860), p53-1 (Smp_139530), Zfp-1 (Smp_145470), and a putative homothorax homeobox protein/six-31 (Smp_147790). The simultaneous co-expression of multiple transcription factors indicates a multipotent progenitor stage ( Kumar et al., 2017 ). Enriched in, or specific to, Kappa cells were genes involved in glycolysis...”
- “...( Figure 6figure supplement 2 ). A putative orthologue of a planaria transcription factor six-3-1 (Smp_147790), a marker for early epidermal progenitors ( Cheng et al., 2018 ) was expressed in the Delta/Phi stem cells and miracidia tegument ( Figure 6figure supplement 2 ). All of...”
- A single-cell atlas of the miracidium larva of the human blood flukeSchistosoma mansoni: cell types, developmental pathways and tissue architecture
Attenborough, 2023
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory