PaperBLAST
PaperBLAST Hits for 86 a.a. (AGSDSEEGLL...)
Show query sequence
>86 a.a. (AGSDSEEGLL...)
AGSDSEEGLLKRKQRRYRTTFTSYQLEELERAFQKTHYRDVFTREELAMRLDLTEARVQV
WFQNRRAKWRKREKAGAQTHPPGLPF
Running BLASTp...
Found 250 similar proteins in the literature:
ARX_MOUSE / O35085 Homeobox protein ARX; Aristaless-related homeobox from Mus musculus (Mouse) (see 3 papers)
NP_031518 homeobox protein ARX from Mus musculus
99% identity, 15% coverage
- function: Transcription factor (By similarity). Binds to specific sequence motif 5'-TAATTA-3' in regulatory elements of target genes, such as histone demethylase KDM5C (By similarity). Positively modulates transcription of KDM5C (PubMed:31691806). Activates expression of KDM5C synergistically with histone lysine demethylase PHF8 and perhaps in competition with transcription regulator ZNF711; synergy may be related to enrichment of histone H3K4me3 in regulatory elements (By similarity). Required for normal brain development (PubMed:12379852). Plays a role in neuronal proliferation, interneuronal migration and differentiation in the embryonic forebrain (PubMed:12379852, PubMed:31691806). May also be involved in axonal guidance in the floor plate (PubMed:9256348).
disruption phenotype: Hemizygous knockout males were born at 19.5 dpc and died within a half day (PubMed:12379852). Neonatal males have small brains, small olfactory bulbs, small testes, hypoplasia of the seminal vesicle and abnormally enlarged seminiferous tubules (PubMed:12379852). Abnormal morphology in each of the developing brain regions in which ARX is normally expressed (PubMed:12379852). Suppressed proliferation and nearly normal migration of neuroepithelial cells in the neocortex (PubMed:12379852). Aberrant formation of many nerve fiber tracts at 19.5 dpc (PubMed:12379852). Abnormal primary migration of GABAergic interneurons from the ganglionic eminence (PubMed:12379852). Abolished expression of wingless-related WNT8B and LIM homeobox protein LHX9 in the thalamic eminence at 12.5 dpc, and decreased expression of DLX1 in the ventral thalamus at 12.5 dpc (PubMed:12379852). Testes have a dysplastic interstitium, probably owing to a considerable decrease in cells containing an abundant cytoplasm as the interstitium is occupied predominantly by fibroblast-like cells (PubMed:12379852). Expression of Leydig cell marker HSD3B1 is severely diminished in the interstitial region of testes, suggesting that Leydig cell differentiation is blocked (PubMed:12379852). Expression of KDM5C is reduced at both mRNA and protein levels (PubMed:31691806). Increased expression of SYN1, SCN2A and some isoforms of BDNF (PubMed:31691806). - Arx expansion mutation perturbs cortical development by augmenting apoptosis without activating innate immunity in a mouse model of X-linked infantile spasms syndrome.
Siehr, Disease models & mechanisms 2020 - GeneRIF: Arx expansion mutation perturbs cortical development by augmenting apoptosis without activating innate immunity in a mouse model of X-linked infantile spasms syndrome.
- Identification and validation of the phosphorylation sites on Aristaless-related homeobox protein.
Shi, Bioscience reports 2020 - GeneRIF: Identification and validation of the phosphorylation sites on Aristaless-related homeobox protein.
- Arx Expression Suppresses Ventralization of the Developing Dorsal Forebrain.
Lim, Scientific reports 2019 - GeneRIF: Here the authors show that ARX participates in establishing dorsoventral identity in the mouse forebrain.
- The maternal immune activation model uncovers a role for the Arx gene in GABAergic dysfunction in schizophrenia.
Nakamura, Brain, behavior, and immunity 2019 (PubMed)- GeneRIF: The maternal immune activation model uncovers a role for the Arx gene in GABAergic dysfunction in schizophrenia.
- Present status and expectation of aristaless-related homeobox (ARX) in endocrine pancreas.
Xu, The International journal of developmental biology 2019 (PubMed)- GeneRIF: isruption and mutation of aristaless-related homeobox (ARX) are found to lead to the deletion and reduction of alpha-cells both in mice models and in humans [Review].
- A new mouse model of ARX dup24 recapitulates the patients' behavioral and fine motor alterations.
Dubos, Human molecular genetics 2018 - GeneRIF: To understand the functional consequences of this mutation, we generated a partially humanized mouse model carrying the c.428_451dup24 duplication (Arxdup24/0) that we characterized at the behavior, neurological and molecular level. Arxdup24/0 males presented with hyperactivity, enhanced stereotypies and altered contextual fear memory
- Aristaless Related Homeobox (ARX) Interacts with β-Catenin, BCL9, and P300 to Regulate Canonical Wnt Signaling.
Cho, PloS one 2017 - GeneRIF: ARX positively regulates Wnt/ beta-catenin signaling and the C-terminal domain of ARX interacts with the armadillo repeats in beta-catenin to promote Wnt/beta-catenin signaling. In addition, we found BCL9 and P300 also interact with ARX to modulate Wnt/beta-catenin signaling.
- Converting Adult Pancreatic Islet α Cells into β Cells by Targeting Both Dnmt1 and Arx.
Chakravarthy, Cell metabolism 2017 - GeneRIF: Arx and Dnmt1 that are sufficient for achieving targeted generation of beta cells from adult pancreatic alpha cells.
- More
NP_001093644 homeobox protein ARX from Rattus norvegicus
99% identity, 15% coverage
ARX_HUMAN / Q96QS3 Homeobox protein ARX; Aristaless-related homeobox from Homo sapiens (Human) (see 9 papers)
NP_620689 homeobox protein ARX from Homo sapiens
99% identity, 15% coverage
- function: Transcription factor (PubMed:22194193, PubMed:31691806). Binds to specific sequence motif 5'-TAATTA-3' in regulatory elements of target genes, such as histone demethylase KDM5C (PubMed:22194193, PubMed:31691806). Positively modulates transcription of KDM5C (PubMed:31691806). Activates expression of KDM5C synergistically with histone lysine demethylase PHF8 and perhaps in competition with transcription regulator ZNF711; synergy may be related to enrichment of histone H3K4me3 in regulatory elements (PubMed:31691806). Required for normal brain development (PubMed:11889467, PubMed:12379852, PubMed:14722918). Plays a role in neuronal proliferation, interneuronal migration and differentiation in the embryonic forebrain (By similarity). May also be involved in axonal guidance in the floor plate (By similarity).
- Structure analysis of the proteins associated with polyA repeat expansion disorders.
Hernandez, Journal of biomolecular structure & dynamics 2022 - “...). PolyA proteins UniProt ID WTTL 1 MPTL 2 Associated Diseases 3 ARX (Tract 1) Q96QS3 16 17 NS-XLID; PRT MR/RTS/dys; ISSX/WS; IEDE; OS; (OMIM #308350; #300419; #309510) ARX (Tract 2) Q96QS3 12 20 ARX (Tract 3) Q96QS3 7 23 ARX (Tract 4) Q96QS3 9 21...”
- Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions
Darling, Molecules (Basel, Switzerland) 2017 - “...placing this transcription factors into the oncogene category. Homeobox protein ARX (Aristaless-related homeobox, UniProt ID: Q96QS3) is predicted by MobiDB consensus to have 59.07% disordered residues. It is not surprising since ARX has two long Ala-rich regions (residues 100155 and 425544), as well as a long...”
- “...) Transcription factor SOX3 (UniProt ID: P41225); ( G ) Homeobox protein ARX (UniProt ID: Q96QS3); ( H ) Human FOXL2 (UniProt ID: P58012); ( I ) PABP2/PABPN1 (UniProt ID: Q86U42); ( J ) Small conductance calcium-activated potassium channel protein 3 (SK3, UniProt ID: Q9UGI6); (...”
- Trinucleotide repeats: a structural perspective.
Almeida, Frontiers in neurology 2013 - “...Residues 322328 (2l7z) Infantile spasm syndrome (ARX) GCG Protein coding region (polyA) ARX Aristaless-related homeobox (Q96QS3, 562 residues) Differentiation, neurogenesis, transcription, transcription regulation 1016 1723 No structural information Myotonic dystrophy type 1 (DM1) CTG 3UTR DMPK Myotonic dystrophy protein kinase (DMPK) (Q09013, 639 residues) No associated...”
- Further characterisation of ARX-related disorders in females due to inherited or de novo variants.
Gras, Journal of medical genetics 2024 (PubMed)- GeneRIF: Further characterisation of ARX-related disorders in females due to inherited or de novo variants.
- Predicting recurrence in pancreatic neuroendocrine tumours: role of ARX and alternative lengthening of telomeres (ALT).
Neyaz, Histopathology 2023 (PubMed)- GeneRIF: Predicting recurrence in pancreatic neuroendocrine tumours: role of ARX and alternative lengthening of telomeres (ALT).
- Further Delineation of Duplications of ARX Locus Detected in Male Patients with Varying Degrees of Intellectual Disability.
Poeta, International journal of molecular sciences 2022 - GeneRIF: Further Delineation of Duplications of ARX Locus Detected in Male Patients with Varying Degrees of Intellectual Disability.
- Screening of the duplication 24 pb of ARX gene in Moroccan patients with X-linked Intellectual Disability.
Benmakhlouf, BMC research notes 2021 - GeneRIF: Screening of the duplication 24 pb of ARX gene in Moroccan patients with X-linked Intellectual Disability.
- Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures.
Poeta, Genes 2021 - GeneRIF: Analysis of a Set of KDM5C Regulatory Genes Mutated in Neurodevelopmental Disorders Identifies Temporal Coexpression Brain Signatures.
- Increased NKX6.1 expression and decreased ARX expression in alpha cells accompany reduced beta-cell volume in human subjects.
Fujita, Scientific reports 2021 - GeneRIF: Increased NKX6.1 expression and decreased ARX expression in alpha cells accompany reduced beta-cell volume in human subjects.
- Assessment of ARX expression, a novel biomarker for metastatic risk in pancreatic neuroendocrine tumors, in endoscopic ultrasound fine-needle aspiration.
Hackeng, Diagnostic cytopathology 2020 - GeneRIF: Assessment of ARX expression, a novel biomarker for metastatic risk in pancreatic neuroendocrine tumors, in endoscopic ultrasound fine-needle aspiration.
- Alternative Lengthening of Telomeres and Differential Expression of Endocrine Transcription Factors Distinguish Metastatic and Non-metastatic Insulinomas.
Hackeng, Endocrine pathology 2020 - GeneRIF: Alternative Lengthening of Telomeres and Differential Expression of Endocrine Transcription Factors Distinguish Metastatic and Non-metastatic Insulinomas.
- More
NP_001086450 aristaless related homeobox L homeolog from Xenopus laevis
97% identity, 16% coverage
NP_001079329 aristaless related homeobox S homeolog from Xenopus laevis
95% identity, 16% coverage
NP_571459 aristaless-related homeobox protein from Danio rerio
94% identity, 19% coverage
AL_DROME / Q06453 Homeobox protein aristaless from Drosophila melanogaster (Fruit fly) (see paper)
NP_722629 aristaless from Drosophila melanogaster
74% identity, 20% coverage
- function: Involved in the morphogenesis of proximal and distal pattern elements in a subset of appendages. Also has a role in early imaginal disk development.
disruption phenotype: Flies display a reduction in size of the arista and scutellum, a reduction or complete absence of the tarsal claws, irregularities of the sternopleural bristles and of the wing vein, and a bending of the wing blade. - Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.
Miyazono, The EMBO journal 2010 - GeneRIF: In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions.
- A concerted action of a paired-type homeobox gene, aristaless, and a homolog of Hox11/tlx homeobox gene, clawless, is essential for the distal tip development of the Drosophila leg.
Kojima, Developmental biology 2005 (PubMed)- GeneRIF: Data show that Aristaless and Clawless proteins form a complex capable of binding to specific DNA targets, which cannot be well recognized solely by Aristaless or Clawless.
- Chip-mediated partnerships of the homeodomain proteins Bar and Aristaless with the LIM-HOM proteins Apterous and Lim1 regulate distal leg development.
Pueyo, Development (Cambridge, England) 2004 (PubMed)- GeneRIF: homeodomain proteins Bar and Aristaless and the LIM-HOM proteins Apterous and Lim1 regulate distal leg development
- Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network
Xu, Journal of structural and functional genomics 2014 - “...a structure comprising residues 87 to 144 of the aristaless homeodomain protein [ 52 ] (Q06453), Al(87144), from Drosophila melanogaster bound to DNA (PDB ID: 3LNQ: RMSD of 1.9 for the C atoms of 58 structurally aligned residues). The corresponding structure based sequence alignment reveals a...”
LOC552251 homeobox protein aristaless from Apis mellifera
82% identity, 18% coverage
- Transcriptomic Analysis of Genes Associated with Stinger Development at Different Life Stages of Apis mellifera
Zhou, International journal of molecular sciences 2024 - “...pupae (D_TAS_P_1 d), respectively. To verify the reliability of the transcriptome data, ten genes, including LOC552251 , Dll , lac2 , TH , Y-y , DDC , LOC552685 , CPR22 , tra2 , and Dsx , were randomly selected and validated with samples of W_S_P_1 d,...”
- “...Dll, LOC726710 ), LIM/homeobox protein Awh ( LOC725532 and LOC725574 ), homeobox protein aristaless ( LOC552251 ), homeobox protein MSX-2 ( LOC724148 ), and transcription factor AP - 2 - epsilon ( LOC410893 ) ( Figure 5 A and Table S9 ). In order to investigate...”
NP_477330 PvuII-PstI homology 13 from Drosophila melanogaster
78% identity, 20% coverage
LOC102223853 dorsal root ganglia homeobox protein-like from Xiphophorus maculatus
69% identity, 25% coverage
NP_001025475 homeobox protein aristaless-like 4 from Bos taurus
77% identity, 19% coverage
ALX4_MOUSE / O35137 Homeobox protein aristaless-like 4; ALX-4 from Mus musculus (Mouse) (see paper)
NP_031468 homeobox protein aristaless-like 4 from Mus musculus
77% identity, 19% coverage
- function: Transcription factor involved in skull and limb development
subunit: Binds DNA - Alx4 relays sequential FGF signaling to induce lacrimal gland morphogenesis.
Garg, PLoS genetics 2017 - GeneRIF: Inactivation of ALX4/Alx4 causes lacrimal gland aplasia in both human and mouse. These results reveal a key role of Alx4 in mediating FGF-Shp2-FGF signaling in the neural crest for lacrimal gland development.
- A novel allele of Alx4 results in reduced Fgf10 expression and failure of eyelid fusion in mice.
Curtain, Mammalian genome : official journal of the International Mammalian Genome Society 2015 - GeneRIF: novel allele of Alx4 results in reduced Fgf10 expression and failure of eyelid fusion in mice
- Genetic analysis of the role of Alx4 in the coordination of lower body and external genitalia formation.
Matsumaru, European journal of human genetics : EJHG 2014 - GeneRIF: Alx4 genetically interacts with and Shh and Gli3 during genital tubercle formation.
- Multiple abnormalities due to a nonsense mutation in the Alx4 gene.
Chen, Genetics and molecular research : GMR 2013 (PubMed)- GeneRIF: A mutagenesis study characterizes a polydactylous phenotype that is caused by a nonsense mutation in the Alx4 gene.
- Loss of Alx4, a stromally-restricted homeodomain protein, impairs mammary epithelial morphogenesis.
Joshi, Developmental biology 2006 (PubMed)- GeneRIF: Alx4, is required for normal branching morphogenesis of the ductal epithelia during pubescent mammary gland development.
- Genetic interaction of Gli3 and Alx4 during limb development.
Panman, The International journal of developmental biology 2005 (PubMed)- GeneRIF: the loss of the severe preaxial polydactyly characteristic of Gli3-/- limbs in double mutant embryos establishes that this type of polydactyly requires Alx4 function.
- Function and regulation of Alx4 in limb development: complex genetic interactions with Gli3 and Shh.
Kuijper, Developmental biology 2005 (PubMed)- GeneRIF: Function and regulation of Alx4 in limb development entail complex genetic interactions with Gli3 and Shh.
- Progression of calvarial bone development requires Foxc1 regulation of Msx2 and Alx4.
Rice, Developmental biology 2003 (PubMed)- GeneRIF: Progression of calvarial bone development requires Foxc1 regulation of Msx2 and Alx4.
ALX4_HUMAN / Q9H161 Homeobox protein aristaless-like 4 from Homo sapiens (Human) (see 4 papers)
NP_068745 homeobox protein aristaless-like 4 from Homo sapiens
77% identity, 18% coverage
- function: Transcription factor involved in skull and limb development. Plays an essential role in craniofacial development, skin and hair follicle development.
subunit: Binds DNA. - Characterization of the Secretome, Transcriptome, and Proteome of Human β Cell Line EndoC-βH1.
Ryaboshapkina, Molecular & cellular proteomics : MCP 2022 - “...UniProt Symbol Rank UniProt Symbol 1 Q5TEC6 H3-2 51 P62851 RPS25 101 P07237 P4HB 2 Q9H161 ALX4 52 P13533 MYH6 102 O43405 COCH 3 Q6ZNA1 ZNF836 53 Q6ZVC0 NYAP1 103 P62249 RPS16 4 Q96JB3 HIC2 54 P30049 ATP5F1D 104 P11142 HSPA8 5 P25398 RPS12 55 P60660...”
- Solution NMR structures of homeodomains from human proteins ALX4, ZHX1, and CASP8AP2 contribute to the structural coverage of the Human Cancer Protein Interaction Network
Xu, Journal of structural and functional genomics 2014 - “...human homeodomains comprising (i) residues 209280 of homeobox protein aristaless-like 4 (ALX4) (UniProtKB accession number: Q9H161), (ii) residues 462532 (homeodomain 2) of the zinc fingers and homeoboxes protein 1 (ZHX1) (Q9UKY1), and (iii) the C-terminal domain comprising residues 19161982 of caspase 8-associated protein 2 (CASP8AP2) (Q9UKL3)...”
- Dominant frontonasal dysplasia with ectodermal defects results from increased activity of ALX4.
Peled, American journal of medical genetics. Part A 2023 (PubMed)- GeneRIF: Dominant frontonasal dysplasia with ectodermal defects results from increased activity of ALX4.
- Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1.
Walters, American journal of medical genetics. Part A 2021 (PubMed)- GeneRIF: Vertical transmission of a large calvarial ossification defect due to heterozygous variants of ALX4 and TWIST1.
- De novo ALX4 variant detected in child with non-syndromic craniosynostosis.
Fonteles, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas 2021 (PubMed)- GeneRIF: De novo ALX4 variant detected in child with non-syndromic craniosynostosis.
- miR-1470 regulates cell proliferation and apoptosis by targeting ALX4 in hepatocellular carcinoma.
Lu, Biochemical and biophysical research communications 2020 (PubMed)- GeneRIF: miR-1470 regulates cell proliferation and apoptosis by targeting ALX4 in hepatocellular carcinoma.
- Variants in ALX4 and their association with genitourinary defects.
Chen, Andrology 2020 - GeneRIF: Variants in ALX4 and their association with genitourinary defects.
- Overexpression of circ_0001445 decelerates hepatocellular carcinoma progression by regulating miR-942-5p/ALX4 axis.
Xu, Biotechnology letters 2020 (PubMed)- GeneRIF: Overexpression of circ_0001445 decelerates hepatocellular carcinoma progression by regulating miR-942-5p/ALX4 axis.
- Overexpression of Aristaless-Like Homeobox-4 Inhibits Proliferation, Invasion, and EMT in Hepatocellular Carcinoma Cells.
Shi, Oncology research 2017 - GeneRIF: overexpression of ALX4 inhibited the proliferation, invasion, and epithelial-mesenchymal transition (EMT) in HCC cells. ALX4 had an inhibitory effect on the sonic hedgehog (Shh) signaling pathway.
- ALX4, an epigenetically down regulated tumor suppressor, inhibits breast cancer progression by interfering Wnt/β-catenin pathway.
Yang, Journal of experimental & clinical cancer research : CR 2017 - GeneRIF: We reveal for the first time that ALX4 acts as a novel functional tumor suppressor inactivated by DNA methylation and is an independent prognostic factor in breast cancer
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XP_023014225 paired mesoderm homeobox protein 2A-like from Leptinotarsa decemlineata
76% identity, 19% coverage
A6NNA5 Dorsal root ganglia homeobox protein from Homo sapiens
67% identity, 32% coverage
XP_063131133 dorsal root ganglia homeobox protein isoform X1 from Rattus norvegicus
70% identity, 30% coverage
DRGX_MOUSE / Q8BYH0 Dorsal root ganglia homeobox protein; Dorsal root ganglion 11; Homeobox protein DRG11; Paired-related homeobox protein-like 1 from Mus musculus (Mouse) (see 3 papers)
XP_006518475 dorsal root ganglia homeobox protein isoform X2 from Mus musculus
70% identity, 30% coverage
- function: Transcription factor required for the formation of correct projections from nociceptive sensory neurons to the dorsal horn of the spinal cord and normal perception of pain.
subunit: Interacts with RGMB.
disruption phenotype: Defects in the projection pattern of nociceptive sensory neurons to the dorsal horn of the developing spinal cord leading to reduced sensitivity to painful stimuli. They die within 3 weeks of birth. Mice lacking Drgx exhibit reduced expression of Rgmb in dorsal root ganglion sensory neurons. - A role for prolyl isomerase PIN1 in the phosphorylation-dependent modulation of PRRXL1 function.
Soares-Dos-Reis, The Biochemical journal 2017 (PubMed)- GeneRIF: The findings provide evidence for a putative novel role of PIN1 in the development of the nociceptive system and indicate phosphorylation-mediated conformational changes as a mechanism for regulating the PRRXL1 role in the process.
- Zinc finger transcription factor Casz1 expression is regulated by homeodomain transcription factor Prrxl1 in embryonic spinal dorsal horn late-born excitatory interneurons.
Monteiro, The European journal of neuroscience 2016 (PubMed)- GeneRIF: Study shows that Casz1 lies downstream of Prrxl1 in the differentiation pathway of a large subset of dorsal late-born excitatory neurons and provides a framework for further studies of Casz1 in assembly of the dorsal root ganglion-spinal circuit.
- Increased fronto-hippocampal connectivity in the Prrxl1 knockout mouse model of congenital hypoalgesia.
Monteiro, Pain 2016 (PubMed)- GeneRIF: The results of this study suggest that Prrxl1 knockout mouse model of congenital hypoalgesia may have an effect on brain plasticity that is the inverse of what is usually observed in animal models of chronic pain.
- Abolition of lemniscal barrellette patterning in Prrxl1 knockout mice: Effects upon ingestive behavior.
Bakalar, Somatosensory & motor research 2015 (PubMed)- GeneRIF: The results of this study showed that Prrxl1(-/-) animal is a valuable model system for examining the genetic assembly and functional role of trigeminal lemniscal circuits in the normal control of eating in mammals.
- Ser¹¹⁹ phosphorylation modulates the activity and conformation of PRRXL1, a homeodomain transcription factor.
Soares-dos-Reis, The Biochemical journal 2014 (PubMed)- GeneRIF: Data suggest phosphorylation at serine-119 is a determinant of Prrxl1 conformation/transcriptional activity in embryonic dorsal root ganglia and dorsal spinal cord nociceptive neurons and may regulate Prrxl1 during nociceptive system development.
- Paired related homeobox protein-like 1 (Prrxl1) controls its own expression by a transcriptional autorepression mechanism.
Monteiro, FEBS letters 2014 (PubMed)- GeneRIF: Prrxl1 uses distinct regulatory regions to repress its own expression in dorsal root ganglia and dorsal spinal cord.
- Dual role of Tlx3 as modulator of Prrxl1 transcription and phosphorylation.
Regadas, Biochimica et biophysica acta 2014 (PubMed)- GeneRIF: Tlx3 uses distinct mechanisms to tightly modulate Prrxl1 activity, either by controlling its transcriptional levels or by increasing Prrxl1 phosphorylation state.
- Several cis-regulatory elements control mRNA stability, translation efficiency, and expression pattern of Prrxl1 (paired related homeobox protein-like 1).
Regadas, The Journal of biological chemistry 2013 - GeneRIF: Prrxl1 transcription is regulated by three alternative promoters, which control the expression of three distinct Prrxl1 5'-UTR variants.
- More
XP_001340966 homeobox protein aristaless-like 4 from Danio rerio
80% identity, 18% coverage
- Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene
McGonnell, Evolution & development 2011 - “...phylogenetic analysis, were: chicken Alx1 (XP_425445.2) and Alx4 (NP_989493.1); zebrafish Alx1 (NP_001038539.1), Alx3 (XP_695330.1), Alx4a (XP_001340966.1), and Alx4b (NP_001082826.1). For lizard ( Anolis carolinensis ) and frog ( X. tropicalis ) sequences, tblastn searches using human Alx proteins against whole genome sequence in GenBank (lizard) or...”
- “...zgc: 162606 (GenBank: NP_001082826) is most closely related to the protein named zebrafish Alx4 (GenBank: XP_001340966). The implication is that zebrafish has two Alx4 genes, which we name Alx4a (GenBank: XM_001340930) and Alx4b (GenBank: NM_001089357). The duplication of Alx4 genes is also observed in the genomes...”
NP_726006 retinal homeobox from Drosophila melanogaster
65% identity, 8% coverage
ARXH_CAEEL / Q21836 Homeobox ARX homolog alr-1; Aristaless-related homeobox alr-1 from Caenorhabditis elegans (see 4 papers)
NP_509860 Homeobox ARX homolog alr-1 from Caenorhabditis elegans
66% identity, 22% coverage
- function: Transcription factor (By similarity). Involved in activating or repressing transcription of genes in neurons (PubMed:15790968, PubMed:21368126). Regulates expression of nuclear hormone receptor odr- 7 and LIM homeodomain protein lin-11 in AWA and ASG chemosensory neurons (PubMed:15790968, PubMed:21368126). In concert with lin-11 and forkhead domain protein unc-130 plays a role in specifying AWA and ASG cell fates (PubMed:15790968). Plays a role in modulating dendritic morphology and functions of AWA neurons (PubMed:15790968). Involved in regulating GABAergic motor neuron development, acting in parallel with nuclear hormone receptor unc-55 (PubMed:15790968, PubMed:31691806). Required to maintain the functional and structural integrity of the amphid organs during larval development (PubMed:16055504). Plays a role in anterior hypodermal morphogenesis (PubMed:16055504). Required for touch sensation (PubMed:21368126, PubMed:31691806). May act as a transcriptional activator in touch receptor neurons (TRNs), forming a positive feedback loop with transcription factor mec-3, thereby restricting the variability of expression of target genes such as mec-3 (PubMed:21368126). Positively modulates expression of H3K4 demethylase rbr-2 in early embryogenesis and during larval development (PubMed:31691806).
- Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression.
Topalidou, Proceedings of the National Academy of Sciences of the United States of America 2011 - GeneRIF: Because ALR-1 and similar proteins (Drosophila Aristaless and human ARX) are needed for the expression of other transcription factors, we propose that proteins in this family may act to ensure differentiation more generally
- Shared gene expression in distinct neurons expressing common selector genes.
Topalidou, Proceedings of the National Academy of Sciences of the United States of America 2011 - GeneRIF: FLP neurons ectopically express the auxiliary transcription factor ALR-1 which ensures, but does not direct, differentiation to touch receptor neurons.
- The Caenorhabditis elegans aristaless orthologue, alr-1, is required for maintaining the functional and structural integrity of the amphid sensory organs.
Tucker, Molecular biology of the cell 2005 - GeneRIF: role in the proper morphogenesis of the anterior hypodermis; may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs
XP_005156907 dorsal root ganglia homeobox protein isoform X1 from Danio rerio
71% identity, 26% coverage
NP_788420 homeobrain from Drosophila melanogaster
74% identity, 18% coverage
Q62798 Dorsal root ganglia homeobox protein from Rattus norvegicus
69% identity, 30% coverage
- Acetaminophen Induced Hepatotoxicity in Wistar Rats--A Proteomic Approach.
Ilavenil, Molecules (Basel, Switzerland) 2016 - “...inhibitor precursor (TFPI) 29 72 7.6 Q02445 4 2204 Homeobox protein DRG11 21 28.6 5.9 Q62798 5 608 SEC14-like protein 3 39 6 3 Low-density lipoprotein receptor-related protein 4 precursor 42 45.1 4.8 Q9Z1J8 7 2308 Splice isoform 1; Variant Displayed 27 31.6 6.1 Q8VHQ7-00-00-00 8...”
- “...CYP2D3 25 22 57 6.7 P12938 2 8305 Homeobox protein DRG11 24 19 29 9.5 Q62798 3 3705 4-Aminobutyrate aminotransferase 35 35 56 6.4 P50554 4 3312 Serine/threonine protein phosphatase 32 34 31.5 6.7 P13353 5 6101 Acyl CoA 41 39 18.38 7.8 Q64559 6 5504...”
ALX3_HUMAN / O95076 Homeobox protein aristaless-like 3; Proline-rich transcription factor ALX3 from Homo sapiens (Human) (see paper)
NP_006483 homeobox protein aristaless-like 3 from Homo sapiens
76% identity, 19% coverage
- function: Transcriptional regulator with a possible role in patterning of mesoderm during development.
- Oncogenic role of ALX3 in cervical cancer cells through KDM2B-mediated histone demethylation of CDC25A.
Qi, BMC cancer 2021 - GeneRIF: Oncogenic role of ALX3 in cervical cancer cells through KDM2B-mediated histone demethylation of CDC25A.
- Exome sequencing revealed a novel nonsense variant in ALX3 gene underlying frontorhiny.
Ullah, Journal of human genetics 2018 (PubMed)- GeneRIF: Genome scan using 250k Nsp1 array followed by exome and Sanger sequence analysis revealed a novel homozygous nonsense variant (c.604C>T, p.Gln202*) in the ALX3 gene resulting in frontorhiny in the family. This is the first mutation in the ALX3 gene, underlying frontorhiny, in Pakistani population.
- Exclusion of mutations in TGIF, ALX3, and ALX4 genes in patients with the syndrome of frontonasal dysgenesis, callosal agenesis, basal encephalocele, and eye anomalies.
Ribeiro-Bicudo, American journal of medical genetics. Part A 2012 (PubMed)- GeneRIF: Exclusion of mutations in ALX3 gene in patients with the syndrome of frontonasal dysgenesis, callosal agenesis, basal encephalocele, and eye anomalies
- 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)
- Frontorhiny, a distinctive presentation of frontonasal dysplasia caused by recessive mutations in the ALX3 homeobox gene.
Twigg, American journal of human genetics 2009 - GeneRIF: ALX3 is essential for normal facial development in humans and that deficiency causes a clinically recognizable phenotype, which we term frontorhiny.
- The homeoprotein Alx3 expressed in pancreatic beta-cells regulates insulin gene transcription by interacting with the basic helix-loop-helix protein E47.
Mirasierra, Molecular endocrinology (Baltimore, Md.) 2006 (PubMed)- GeneRIF: Chromatin immunoprecipitation assays indicated that Alx3 in mouse pancreatic islets occupies the promoter of the mouse insulin genes.
- GeneRIF: Alx3 participates in the regulation of insulin gene expression in pancreatic beta-cells.
- The homeoprotein Alx3 contains discrete functional domains and exhibits cell-specific and selective monomeric binding and transactivation.
Pérez-Villamil, The Journal of biological chemistry 2004 (PubMed)- GeneRIF: Rat Alx3 undergoes restrictive or permissive interactions with nuclear proteins that determine its binding to and transactivation from TAAT target sites selected in a cell-specific manner.
- Combined restriction landmark genomic scanning and virtual genome scans identify a novel human homeobox gene, ALX3, that is hypermethylated in neuroblastoma.
Wimmer, Genes, chromosomes & cancer 2002 (PubMed)- GeneRIF: The lack of a chromosome 1-derived fragment of ALX3 in restriction landmark genomic scanning and virtual genome scans of neuroblastomas is attributable to hypermethylation.
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- Systematic identification of conditionally folded intrinsically disordered regions by AlphaFold2.
Alderson, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...94 ). ALX3 encodes for a transcription factor named homeobox protein aristaless-like 3 (ALX3, UniProt: O95076) that plays a key role in development ( 95 ). The L168V mutation maps to a DNA-binding homeodomain of ALX3 (residues 153 to 212), for which there is no experimental...”
NP_001007013 homeobox protein aristaless-like 3 from Rattus norvegicus
76% identity, 19% coverage
NP_031467 homeobox protein aristaless-like 3 from Mus musculus
76% identity, 19% coverage
- Alx3 deficiency disrupts energy homeostasis, alters body composition, and impairs hypothalamic regulation of food intake.
Mirasierra, Cellular and molecular life sciences : CMLS 2024 - GeneRIF: Alx3 deficiency disrupts energy homeostasis, alters body composition, and impairs hypothalamic regulation of food intake.
- Parenchymal and stromal tissue regeneration of tooth organ by pivotal signals reinstated in decellularized matrix.
He, Nature materials 2019 - GeneRIF: Alx3, a transcription factor of the homeobox gene family, was pivotal for prenatal tooth development but subsided in the adult.Alx3 promoted stroma regeneration via VEGF signaling.
- Embryonic defence mechanisms against glucose-dependent oxidative stress require enhanced expression of Alx3 to prevent malformations during diabetic pregnancy.
García-Sanz, Scientific reports 2017 - GeneRIF: Study shows that ALX3 deficiency provides a novel molecular mechanism for developmental defects arising from maternal hyperglycaemia.
- Glucose-dependent downregulation of glucagon gene expression mediated by selective interactions between ALX3 and PAX6 in mouse alpha cells.
Mirasierra, Diabetologia 2016 (PubMed)- GeneRIF: Glucose-stimulated expression of ALX3 in alpha cells provides a regulatory mechanism for the downregulation of glucagon gene expression by interfering with PAX6-mediated transactivation on the glucagon G1 promoter element.
- Pdx1 and USF transcription factors co-ordinately regulate Alx3 gene expression in pancreatic β-cells.
Fernández-Pérez, The Biochemical journal 2014 (PubMed)- GeneRIF: Pdx1, USF1 and USF2 co-ordinately regulate Alx3 gene expression in pancreatic beta-cells.
- Differential configurations involving binding of USF transcription factors and Twist1 regulate Alx3 promoter activity in mesenchymal and pancreatic cells.
García-Sanz, The Biochemical journal 2013 (PubMed)- GeneRIF: Alx3 promoter activity in mesenchymal and pancreatic cells is regulatd by USF transcription factors and Twist1
- BMP-2 Induced Expression of Alx3 That Is a Positive Regulator of Osteoblast Differentiation.
Matsumoto, PloS one 2013 - GeneRIF: results indicate that Alx3 expression is enhanced by BMP-2 via the BMP receptors mediated-Smad signaling and that Alx3 is a positive regulator of osteoblast differentiation induced by BMP-2
- Alx3-deficient mice exhibit decreased insulin in beta cells, altered glucose homeostasis and increased apoptosis in pancreatic islets.
Mirasierra, Diabetologia 2011 (PubMed)- GeneRIF: ALX3 participates in the regulation of the expression of essential genes for the function of pancreatic islets, and its deficiency alters the regulation of glucose homeostasis in vivo.
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XP_017213137 paired box protein Pax-3a isoform X1 from Danio rerio
75% identity, 15% coverage
- A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish.
Miyadai, Development (Cambridge, England) 2023 - GeneRIF: A gene regulatory network combining Pax3/7, Sox10 and Mitf generates diverse pigment cell types in medaka and zebrafish.
- BMP, Wnt and FGF signals are integrated through evolutionarily conserved enhancers to achieve robust expression of Pax3 and Zic genes at the zebrafish neural plate border.
Garnett, Development (Cambridge, England) 2012 - GeneRIF: BMP, Wnt and FGF signaling are needed for expression of the neural plate border specifiers pax3a and zic3 in zebrafish
- Yes-associated protein 65 (YAP) expands neural progenitors and regulates Pax3 expression in the neural plate border zone.
Gee, PloS one 2011 - GeneRIF: evidence of YAP's role in regulating pax3 neural crest expression
- Sequential actions of Pax3 and Pax7 drive xanthophore development in zebrafish neural crest.
Minchin, Developmental biology 2008 - GeneRIF: Pax3 in zebrafish is required for specification of two specific lineages of neural crest, xanthophores and enteric neurons.
Q91574 ALX homeobox protein 1 from Xenopus laevis
68% identity, 22% coverage
ALX1_GEOFO / P0DMV5 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Geospiza fortis (Medium ground-finch) (see paper)
68% identity, 23% coverage
- function: Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes. Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures (By similarity). May therefore play a role in beak development and regulate beak shape (PubMed:25686609).
subunit: Binds DNA as a homodimer; required for transcriptional activation.
ALX1_MOUSE / Q8C8B0 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Mus musculus (Mouse) (see 2 papers)
NP_766141 ALX homeobox protein 1 isoform 1 from Mus musculus
68% identity, 23% coverage
- function: Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes (PubMed:12929931). Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures. Early on in development, it plays a role in forebrain mesenchyme survival (PubMed:8673125). May also induce epithelial to mesenchymal transition (EMT) through the expression of SNAI1 (By similarity).
subunit: Binds DNA as a homodimer; required for transcriptional activation (By similarity). Interacts (via homeobox domain) with EP300; acetylates ALX1 and stimulates its transcriptional activity (PubMed:12929931).
disruption phenotype: Mice lacking Alx1 die within 24 hours of birth. The overt phenotype is acrania and degeneration of unprotected brain tissues. This is most probably the cause of the death since no other abnormality in limbs and visceral tissues is observed. The defect in cranial bone formation may be a consequence of extensive loss of forebrain head mesenchyme due to cell death and neural tube closure defects earlier during development. The penetrance of the acrania/meroanencephaly phenotype is variable between mice strains. Heterozygous mice appear normal and fertile. - ALX1-transcribed LncRNA AC132217.4 promotes osteogenesis and bone healing via IGF-AKT signaling in mesenchymal stem cells.
Zhang, Cellular and molecular life sciences : CMLS 2022 - GeneRIF: ALX1-transcribed LncRNA AC132217.4 promotes osteogenesis and bone healing via IGF-AKT signaling in mesenchymal stem cells.
- Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1.
Capellini, Development (Cambridge, England) 2010 - GeneRIF: Scapula development is governed by genetic interactions of Pbx1 with its family members and with Emx2 via their cooperative control of Alx1
- The OAR/aristaless domain of the homeodomain protein Cart1 has an attenuating role in vivo.
Brouwer, Mechanisms of development 2003 (PubMed)- GeneRIF: We now demonstrate the function of the aristaless domain in vivo by ectopically expressing normal and mutated forms of Cart1 and Alx3
- P300/CBP acts as a coactivator to cartilage homeoprotein-1 (Cart1), paired-like homeoprotein, through acetylation of the conserved lysine residue adjacent to the homeodomain.
Iioka, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2003 (PubMed)- GeneRIF: p300/CBP stimulate Cart1-dependent transcription activity, and this transactivation is inhibited by E1A and Tax, oncoproteins that suppress the activity of p300/CBP
ALX1_HUMAN / Q15699 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Homo sapiens (Human) (see 4 papers)
NP_008913 ALX homeobox protein 1 from Homo sapiens
68% identity, 23% coverage
- function: Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes (PubMed:8756334, PubMed:9753625). Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures. Early on in development, it plays a role in forebrain mesenchyme survival (PubMed:20451171). May also induce epithelial to mesenchymal transition (EMT) through the expression of SNAI1 (PubMed:23288509).
subunit: Binds DNA as a homodimer; required for transcriptional activation (PubMed:9753625). Interacts (via homeobox domain) with EP300; acetylates ALX1 and stimulates its transcriptional activity. - Disruption of ALX1 causes extreme microphthalmia and severe facial clefting: expanding the spectrum of autosomal-recessive ALX-related frontonasal dysplasia.
Uz, American journal of human genetics 2010 - Promoter Methylation-mediated Silencing of the MiR-192-5p Promotes Endometrial Cancer Progression by Targeting ALX1.
Ni, International journal of medical sciences 2021 - GeneRIF: Promoter Methylation-mediated Silencing of the MiR-192-5p Promotes Endometrial Cancer Progression by Targeting ALX1.
- Knockdown of aristaless-like homeobox1 inhibits epithelial-mesenchymal transition through Wnt/β-catenin signaling pathway in melanoma cells.
Jiao, Biochemical and biophysical research communications 2019 (PubMed)- GeneRIF: ALX1 is highly expressed in human melanoma tissues and cell lines. Knockdown of ALX1 suppressed the proliferation and invasion of melanoma cells.
- Exome sequencing revealed a novel splice site variant in the ALX1 gene underlying frontonasal dysplasia.
Ullah, Clinical genetics 2017 (PubMed)- GeneRIF: Our study concludes that the splice site variant identified in the ALX1 gene causes mild form of Frontonasal dysplasia.
- [Knockdown of CART1 induces S phase arrest and inhibits invasion and migration of MDA-MB-231 breast cancer cells].
Guan, Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology 2016 (PubMed)- GeneRIF: Knockdown of the CART1 gene significantly inhibited cell invasion and proliferation and induce cell cycle arrest in S phase.
- Depletion of ALX1 causes inhibition of migration and induction of apoptosis in human osteosarcoma.
Yang, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2015 (PubMed)- GeneRIF: we found that depletion of ALX1 caused a dramatic cell cycle arrest, followed by massive apoptotic cell death, and eventually resulted in a significant decrease in migration and invasion of the osteosarcoma cell line studied.
- ALX1 promotes migration and invasion of lung cancer cells through increasing snail expression.
Yao, International journal of clinical and experimental pathology 2015 - GeneRIF: we identify critical roles of ALX1 in lung cancer development and progression
- ALX1 induces snail expression to promote epithelial-to-mesenchymal transition and invasion of ovarian cancer cells.
Yuan, Cancer research 2013 (PubMed)- GeneRIF: ALX1 upregulated expression of the key EMT regulator Snail (SNAI1) and that it mediated EMT activation and cell invasion by ALX1.
- A prognostic DNA methylation signature for stage I non-small-cell lung cancer.
Sandoval, Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2013 (PubMed)- GeneRIF: hypermethylation of HIST1H4F, PCDHGB6, NPBWR1, ALX1, and HOXA9 was significantly associated with shorter survival in stage 1 Non-small-cell lung cancer
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ALX1_RAT / Q63087 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Rattus norvegicus (Rat) (see 4 papers)
68% identity, 23% coverage
- function: Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes (PubMed:12929931). Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures (By similarity). Early on in development, it plays a role in forebrain mesenchyme survival (By similarity). May also induce epithelial to mesenchymal transition (EMT) through the expression of SNAI1 (By similarity).
subunit: Binds DNA as a homodimer; required for transcriptional activation (PubMed:12390248). Interacts (via homeobox domain) with EP300; acetylates ALX1 and stimulates its transcriptional activity (PubMed:12929931).
PAX3B_XENLA / Q0IH87 Paired box protein Pax-3-B; xPax3-B; Paired-domain transcription factor Pax3-B from Xenopus laevis (African clawed frog) (see 7 papers)
74% identity, 16% coverage
- function: Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.
XP_006245193 paired box protein Pax-3 isoform X1 from Rattus norvegicus
74% identity, 16% coverage
- PAX3 Promotes Cell Migration and CXCR4 Gene Expression in Neural Crest Cells.
Xu, Journal of molecular neuroscience : MN 2018 (PubMed)- GeneRIF: PAX3 promotes expression of CXCR4 and facilitates migration of neural crest cells.
- PAX3 inhibits β-Tubulin-III expression and neuronal differentiation of neural stem cell.
Cao, Biochemical and biophysical research communications 2017 (PubMed)- GeneRIF: PAX3 could inhibit the neuronal differentiation of neural stem celland the expression of TUBB3.
- Regulation of Schwann cell differentiation and proliferation by the Pax-3 transcription factor.
Doddrell, Glia 2012 - GeneRIF: These findings indicate new roles for the Pax-3 transcription factor in controlling the differentiation and proliferation of Schwann cells during development and after peripheral nerve injury.
- Pax3 gene expression is not altered during diaphragmatic development in nitrofen-induced congenital diaphragmatic hernia.
Gosemann, Journal of pediatric surgery 2012 (PubMed)- GeneRIF: Pax3 gene expression is unaltered in the pleuroperitoneal folds & developing diaphragm in the nitrofen congenital diaphragmatic hernia model.The diaphragmatic defect is not caused by disturbance of myogenesis & muscularization.
- Downregulation of Pax3 expression correlates with acquired GFAP expression during NSC differentiation towards astrocytes.
Liu, FEBS letters 2011 (PubMed)- GeneRIF: Pax3 negatively regulates GFAP expression during astrocyte differentiation in vitro
- Pax3 and Pax7 expression during myoblast differentiation in vitro and fast and slow muscle regeneration in vivo.
Brzóska, Cell biology international 2009 (PubMed)- GeneRIF: Pax3 and Pax7, both in vitro and in vivo, participated in the differentiation and regeneration events of muscle
- PAX3/7 expression coincides with MyoD during chronic skeletal muscle overload.
Hyatt, Muscle & nerve 2008 - GeneRIF: Pax3 and 7 coordinate the recapitulation of developmental-like regulatory mechanisms in response to growth-inducing stimuli in adult skeletal muscle
- Pax3 mRNA is decreased in the hearts of rats with experimental diaphragmatic hernia.
Gonzalez-Reyes, Pediatric surgery international 2005 (PubMed)- GeneRIF: Pax3 is underexpressed in the hearts of nitrofen-exposed embryonal rats before the end of gestation.
NP_001120838 paired box protein Pax-3 isoform PAX3i from Homo sapiens
74% identity, 16% coverage
- PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/β-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
Li, Biochemical and biophysical research communications 2024 (PubMed)- GeneRIF: PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/beta-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
- Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
Pan, Cellular and molecular biology (Noisy-le-Grand, France) 2024 (PubMed)- GeneRIF: Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
- Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
Macaskill, Clinical dysmorphology 2024 (PubMed)- GeneRIF: Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
- Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
Muralidharan, Cell and tissue research 2023 (PubMed)- GeneRIF: Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
- Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
Xiao, Functional & integrative genomics 2023 (PubMed)- GeneRIF: Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
- PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
Searcy, Nature communications 2023 - GeneRIF: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
- 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.
- Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
Zhang, Molecular biology reports 2022 (PubMed)- GeneRIF: Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
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Q8BRF1 Paired box 3 from Mus musculus
NP_001152992 paired box protein Pax-3 isoform b from Mus musculus
74% identity, 15% coverage
- The expression and function of PAX3 in development and disease.
Boudjadi, Gene 2018 - “...483 53,336 PAX3-208 (PAX3a) ENST00000409828.7 5,117 4 1254 215 25,136 Mouse ENSMUSG00000004872 1 P24610 & Q8BRF1 Pax3-201 (PAX3b) ENSMUST00000004994.15 95,572 9 3078 484 53,445 Pax3-202 (PAX3a) ENSMUST00000087086.6 95,865 8 3863 479 52,948 Table 2. Representative PAX3 target genes. Symbol Biochemical Category Representative Functions PAX3 binding location...”
- Pax3 induces target-specific reinnervation through axon collateral expression of PSA-NCAM.
Jara, Progress in neurobiology 2024 (PubMed)- GeneRIF: Pax3 induces target-specific reinnervation through axon collateral expression of PSA-NCAM.
- Loss of Pax3 causes reduction of melanocytes in the developing mouse cochlea.
Udagawa, Scientific reports 2024 - GeneRIF: Loss of Pax3 causes reduction of melanocytes in the developing mouse cochlea.
- Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development.
Kim, Disease models & mechanisms 2023 - GeneRIF: Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development.
- PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
Searcy, Nature communications 2023 - GeneRIF: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
- iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.
Guo, eLife 2022 - GeneRIF: iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.
- RNA-Seq analysis of a Pax3-expressing myoblast clone in-vitro and effect of culture surface stiffness on differentiation.
Richardson, Scientific reports 2022 - GeneRIF: RNA-Seq analysis of a Pax3-expressing myoblast clone in-vitro and effect of culture surface stiffness on differentiation.
- Pax3 inhibits Neuro-2a cells proliferation and neurite outgrowth.
Huo, Journal of cellular and molecular medicine 2021 - GeneRIF: Pax3 inhibits Neuro-2a cells proliferation and neurite outgrowth.
- Altered sacral neural crest development in Pax3 spina bifida mutants underlies deficits of bladder innervation and function.
Deal, Developmental biology 2021 - GeneRIF: Altered sacral neural crest development in Pax3 spina bifida mutants underlies deficits of bladder innervation and function.
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PAX3A_XENLA / Q645N4 Paired box protein Pax-3-A; xPax3-A; Paired-domain transcription factor Pax3-A from Xenopus laevis (African clawed frog) (see 7 papers)
74% identity, 15% coverage
- function: Probable transcription factor. Promotes both hatching gland and neural crest cell fates, two of the cell populations that arise from the neural plate border. Acts downstream of msx1 to induce the neural crest, cooperating with zic1 and mediating signals from both the wnt and fgf8 signaling pathways. Induction of hatching gland cell fate is independent of zic1.
NP_571300 retinal homeobox protein Rx1 from Danio rerio
71% identity, 21% coverage
XP_001495022 paired box protein Pax-3 isoform X2 from Equus caballus
74% identity, 16% coverage
NP_001193747 paired box protein Pax-3 from Bos taurus
74% identity, 15% coverage
PAX3_HUMAN / P23760 Paired box protein Pax-3; HuP2 from Homo sapiens (Human) (see 26 papers)
NP_852122 paired box protein Pax-3 isoform PAX3 from Homo sapiens
74% identity, 16% coverage
- function: Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis. Transcriptional activator of MITF, acting synergistically with SOX10 (PubMed:21965087).
subunit: Can bind to DNA as a homodimer or a heterodimer with PAX7. Interacts with PAXBP1; the interaction links PAX3 to a WDR5-containing histone methyltransferase complex. Interacts with DAXX. Interacts with TBX18. Interacts with SOX10 (PubMed:21965087). - The role of HR-HPV integration in the progression of premalignant lesions into different cancer types.
Catalán-Castorena, Heliyon 2024 - “...( P24385) BCL2L1 (Q07817) TRIP12 ( Q14669 ) COL6A3 (P12111 IDH1 (O75874) ERBB4 (Q15303) PAX3 (P23760) FGFR1 (P11362) MGMT (P16455) EED (O75530) ATM (Q13315) NTRK3 (Q16288) SMAD4 (Q13485) ARID3A (Q99856) SERPINB11 (Q96P15) STK11 (Q15831) Penile cancer [ 163 ] HPV-positive squamous cell penile carcinoma biopsies: 16,...”
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...mutations in the human Pax3 gene belong to the latter examples. From the UniProt entry P23760 the homeobox sequence is Q(219)RRSRTTFT AEQLEEL(234)ER AF(238)ERTHYPD IYTREELAQRA KLT EARVQV(265)W(266)FSNR(270)R(271)AR(273)WRK QA(278) for human Pax3 (we underlined helices 1, 2, and 3). The substitution of residues V(265), W(266), R(270), R(271), and...”
- Evidence of pioneer factor activity of an oncogenic fusion transcription factor.
Sunkel, iScience 2021 - “...Blot Scanner running Image Studio v5.2. Amino acid primary sequence analysis Human PAX3 (Uniprot ID: P23760 ) and FOXO1 (Uniprot ID: Q12778 ) amino acid sequence conservation was analyzed on the ConSurf Server using default parameters ( Berezin etal., 2004 ). ConSurf output files were used...”
- 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 - “...Myoblast determination protein 1 Human P13349 MYF5 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...”
- The expression and function of PAX3 in development and disease.
Boudjadi, Gene 2018 - “...Ensembl ID Pre-spliced (nt) Exons Spliced (nt) UniProt Length (aa) Mass (Da) Human ENSG00000135903 2q36.1 P23760 PAX3-201 (PAX3b) ENST00000258387.5 5,230 5 958 206 22,743 PAX3-202 (PAX3h) ENST00000336840.10 98,209 9 2038 407 45,217 PAX3-203 (PAX3g) ENST00000344493.8 99,109 8 3109 403 44,822 PAX3-204 (PAX3c) ENST00000350526.8 98,862 8 3610...”
- CIB1 synergizes with EphrinA2 to regulate Kaposi's sarcoma-associated herpesvirus macropinocytic entry in human microvascular dermal endothelial cells.
Bandyopadhyay, PLoS pathogens 2014 - “...INTEGRIN V P18084 INTEGRIN 1 Q13153 INTEGRIN 3 Q9H4B4 INTEGRIN 5 Q9NYY3 MEK P49810 MOESIN P23760 MYOSIN P78527 NF-kB Q14573 NUCLEOLIN P60763 ORF4 Q02750 ORF50 Q05513 ORF73 P07355 PAK1 P60953 PAX3 Q00610 PDK1 P01106 PI3-K P08514 PKC- P27348 PLK2/SNK P98160 PLK3/FNK P08195 PRESINILIN2 Q9UPY5 PRX-1 P08393...”
- The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes
Wheat, Molecular and cellular biology 1999 - “...sapiens Pax-1 (EMBL/GenBank accession no. P15863), Pax-3 (P23760), Pax-5 (M96944), Pax-6 (M77844), Pax-7 (Z35141), Pax-8 (L19606), and Pax-9 (S36115); Mus...”
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...sapiens NP_006151; Mus musculus AAH58965. Pax3 : Danio rerio AAC41253; Gallus gallus BAB85652; Homo sapiens NP_852122; Mus musculus AAH48699 ; Scyliorhinus canicula ABM89502; Xenopus laevis AAI08574. Pax7 : Danio rerio NP_571400; Gallus gallus NP_990396; Homo sapiens CAA65522; Mus musculus AF254422; Xenopus laevis NP_001088995. Pax2 : Danio...”
PAX3_MOUSE / P24610 Paired box protein Pax-3 from Mus musculus (Mouse) (see 3 papers)
74% identity, 16% coverage
- function: Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis. Transcriptional activator of MITF, acting synergistically with SOX10 (By similarity).
subunit: Can bind to DNA as homodimer or a heterodimer with PAX7. Interacts with DAXX. Interacts with PAXBP1; the interaction links PAX3 to a WDR5-containing histone methyltransferase complex. Interacts with TBX18. Interacts with SOX10 (By similarity). - The expression and function of PAX3 in development and disease.
Boudjadi, Gene 2018 - “...9 1782 483 53,336 PAX3-208 (PAX3a) ENST00000409828.7 5,117 4 1254 215 25,136 Mouse ENSMUSG00000004872 1 P24610 & Q8BRF1 Pax3-201 (PAX3b) ENSMUST00000004994.15 95,572 9 3078 484 53,445 Pax3-202 (PAX3a) ENSMUST00000087086.6 95,865 8 3863 479 52,948 Table 2. Representative PAX3 target genes. Symbol Biochemical Category Representative Functions PAX3...”
NP_001014818 paired like homeobox 2Bb from Danio rerio
77% identity, 23% coverage
XP_695330 homeobox protein aristaless-like 3 isoform X2 from Danio rerio
69% identity, 20% coverage
ALX1_DANRE / Q1LVQ7 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_001038539 ALX homeobox protein 1 from Danio rerio
69% identity, 23% coverage
- function: Sequence-specific DNA-binding transcription factor that binds palindromic sequences within promoters and may activate or repress the transcription of a subset of genes. Most probably regulates the expression of genes involved in the development of mesenchyme-derived craniofacial structures (By similarity). Required for proper neural crest cell migration into the frontonasal primordia during development (PubMed:23059813).
subunit: Binds DNA as a homodimer; required for transcriptional activation.
disruption phenotype: Morpholino-mediated knockdown causes severe craniofacial alterations including small, misshapen head, microphthalmia and loss of the jaw. It is associated with a more or less severe loss of the cartilaginous facial skeleton. Pericardial edema is also detected. - Defective neural crest migration revealed by a Zebrafish model of Alx1-related frontonasal dysplasia.
Dee, Human molecular genetics 2013 (PubMed)- GeneRIF: Alx1 plays a crucial role in regulating the migration of cranial neural crest (CNC) cells into the frontonasal primordia.
NP_996953 paired mesoderm homeobox protein 2A from Danio rerio
77% identity, 23% coverage
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...Mus musculus CAA40725 ; Takifugu rubripes AAC31810 ; Xenopus laevis NP_001081941. Phox2a : Danio rerio NP_996953; Homo sapiens NP_005160; Mus musculus Q62066; Xenopus laevis AAI24892. Phox2b : Danio rerio NP_001014818; Homo sapiens NP_003915; Mus musculus CAA74833; Scyliorhinus canicula ABM89504; Xenopus laevis NP_001084383. Sox1 : Gallus gallus...”
- Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Abril, BMC genomics 2010 - “...AAF34717 2,00E-15 90_6339 Nk1 protein [Platynereis dumerilii] CAJ38797 1,00E-11 F6AJIXP02G077U paired-like homeobox 2a [Danio rerio] NP_996953 5,00E-16 90_6703 phtf [Drosophila melanogaster] NP_610232 2,00E-55 90_25126 PLOX2-Dj [Dugesia japonica] BAA77402 2,00E-42 90_21567 PLOX4-Dj [Dugesia japonica] BAA77404 2,00E-21 90_23010 PLOX5-Dj [Dugesia japonica] BAA77405 6,00E-22 F6AJIXP02IVOTI PLOX5-Dj [Dugesia japonica] BAA77405...”
NP_446321 paired mesoderm homeobox protein 2A from Rattus norvegicus
77% identity, 23% coverage
NP_032913 paired mesoderm homeobox protein 2A from Mus musculus
Q62066 Paired mesoderm homeobox protein 2A from Mus musculus
77% identity, 23% coverage
- Characterisation of lamina I anterolateral system neurons that express Cre in a Phox2a-Cre mouse line.
Alsulaiman, Scientific reports 2021 - GeneRIF: Characterisation of lamina I anterolateral system neurons that express Cre in a Phox2a-Cre mouse line.
- Rnf220/Zc4h2-mediated monoubiquitylation of Phox2 is required for noradrenergic neuron development.
Song, Development (Cambridge, England) 2020 (PubMed)- GeneRIF: Rnf220/Zc4h2-mediated monoubiquitylation of Phox2 is required for noradrenergic neuron development.
- Functional Diversification of Motor Neuron-specific Isl1 Enhancers during Evolution.
Kim, PLoS genetics 2015 - GeneRIF: All E1 sequences from lamprey to mouse responded equally well to Phox2a and the Isl1-Lhx3 complex. Conversely, E2, the enhancer for limb-innervating motor neurons, was only found in tetrapod animals
- Specific and integrated roles of Lmx1a, Lmx1b and Phox2a in ventral midbrain development.
Deng, Development (Cambridge, England) 2011 (PubMed)- GeneRIF: reveal an unanticipated role for Lmx1b in regulating Phox2a expression and the sequential specification of ocular motor neurons (OMNs) and red nucleus neurons (RNNs) from progenitors located lateral to dopamine neurons in the midbrain
- Ongoing roles of Phox2 homeodomain transcription factors during neuronal differentiation.
Coppola, Development (Cambridge, England) 2010 (PubMed)- GeneRIF: Maintenance of noradrenergic differentiation during embryogenesis requires ongoing expression of Phox2b in sympathetic ganglia, and of Phox2a in the main noradrenergic center, the locus coeruleus.
- Abnormal inspiratory depth in Phox2a haploinsufficient mice.
Wrobel, Neuroscience 2007 (PubMed)- GeneRIF: These data indicate that Phox2a plays a critical role in the ontogeny of the reflex control of inspiration.
- Reciprocal gene replacements reveal unique functions for Phox2 genes during neural differentiation.
Coppola, The EMBO journal 2005 - GeneRIF: Phox2 genes have roles in neural differentiation
- Phox2a gene, A6 neurons, and noradrenaline are essential for development of normal respiratory rhythm in mice.
Viemari, The Journal of neuroscience : the official journal of the Society for Neuroscience 2004 - GeneRIF: Noradrenaline, A6 neurons, and the Phox2a gene, which is crucial for the generation of A6 neurons, are essential for development of normal respiratory rhythm in neonatal mice
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- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...AAC31810 ; Xenopus laevis NP_001081941. Phox2a : Danio rerio NP_996953; Homo sapiens NP_005160; Mus musculus Q62066; Xenopus laevis AAI24892. Phox2b : Danio rerio NP_001014818; Homo sapiens NP_003915; Mus musculus CAA74833; Scyliorhinus canicula ABM89504; Xenopus laevis NP_001084383. Sox1 : Gallus gallus BAA25092; Homo sapiens NP_005977; Mus musculus...”
CEH17_CAEEL / G5EC89 Homeobox protein ceh-17 from Caenorhabditis elegans (see 2 papers)
78% identity, 27% coverage
- function: Probable transcription factor involved in postembryonic differentiation of the ALA neuron, and regulation of genes that contribute to behavioral quiescence, a sleep-like behavior mediated by ALA (PubMed:20501595). Regulates its own expression and also that of homeodomain ceh-14, together forming an autoregulatory loop in the ALA neuron (PubMed:20501595). Involved in fasciculation-independent longitudinal axonal navigation in many neurons (PubMed:10887091).
disruption phenotype: ALA and SIA axons exhibit outgrowth abnormalities, failing to run along the lateral cord to the tail (PubMed:10887091). ALA axons are shortened further in a vab-8 mutant background (PubMed:10887091). Drastically reduced expression of let- 23/EGFR and plc-3/PLCgamma in ALA neurons (PubMed:20501595). RNAi- mediated knockdown causes severe defects in the ALA neuron in young adults (PubMed:20501595).
O35602 Retinal homeobox protein Rx from Mus musculus
NP_038861 retinal homeobox protein Rx from Mus musculus
70% identity, 20% coverage
- Functional, proteomic and bioinformatic analyses of Nrf2- and Keap1- null skeletal muscle
Gao, The Journal of physiology 2020 - “...1.88 Psma2 P49722 Proteasome subunit alpha type-2 0.03 2.43 Sept7 O55131 Septin-7 0.03 142.77 Rax O35602 Retinal homeobox protein Rx 0.03 1.95 Ak1 Q9R0Y5 Adenylate kinase isoenzyme 1 0.04 2.37 Idh3g P70404 Isocitrate dehydrogenase [NAD] subunit gamma 1, mitochondrial 0.04 3.57 Vcl Q64727 Vinculin 0.04 2.44...”
- Identification of an Alternative Splicing Product of the Otx2 Gene Expressed in the Neural Retina and Retinal Pigmented Epithelial Cells
Kole, PloS one 2016 - “...Alternate 3/5 + + New - Rax Mouse LA0AAA88YP21.CONTIG 3a - + - BC058757.1 * O35602 Mouse LA0AAA5YJ22.CONTIG 3b Alternate 3/5 - + New - Mouse LA0AAA89YO03.CONTIG 3c Alternate 3/5 + + New - Mouse LA0AAA80YH01.CONTIG 3d Exon skipping + + New - Mouse 3030000051432591 3e...”
- “...which in turn results in an alternate 3 splice site compared to the larger form, O35602. The clone 3d lacks coding for exon 2 resulting in exon skipping, 3b uses an alternate 3 splice site resulting in a shorter exon 3, encoding for shorter isoforms of...”
- Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...family 1 isoform P08553 Nefm neurofilament medium polypeptide 78 component of neurofilaments -- 1 isoform O35602 Rax retinal homeobox protein Rx 77 regulates initial specification of retinal cells and/or their subsequent proliferation -- 1 isoform Q02248 Ctnnb1 catenin beta-1 73 downstream component of canonical Wnt signaling...”
- The Rax homeoprotein in Müller glial cells is required for homeostasis maintenance of the postnatal mouse retina.
Yoshimoto, The Journal of biological chemistry 2023 - GeneRIF: The Rax homeoprotein in Muller glial cells is required for homeostasis maintenance of the postnatal mouse retina.
- The Rx transcription factor is required for determination of the retinal lineage and regulates the timing of neuronal differentiation.
Yamamoto, Development, growth & differentiation 2022 (PubMed)- GeneRIF: The Rx transcription factor is required for determination of the retinal lineage and regulates the timing of neuronal differentiation.
- Adult-born proopiomelanocortin neurons derived from Rax-expressing precursors mitigate the metabolic effects of congenital hypothalamic proopiomelanocortin deficiency.
Surbhi, Molecular metabolism 2021 - GeneRIF: Adult-born proopiomelanocortin neurons derived from Rax-expressing precursors mitigate the metabolic effects of congenital hypothalamic proopiomelanocortin deficiency.
- Truncating RAX Mutations: Anophthalmia, Hypopituitarism, Diabetes Insipidus, and Cleft Palate in Mice and Men.
Brachet, The Journal of clinical endocrinology and metabolism 2019 - GeneRIF: The mouse Rax knockout model showed defects in the anterior and posterior pituitary and absence of the palate and basisphenoid bone.
- The role of the Rx homeobox gene in retinal progenitor proliferation and cell fate specification.
Rodgers, Mechanisms of development 2018 - GeneRIF: Together these data demonstrate the importance of Rx for retinal progenitor proliferation and a specific requirement of Rx for cone formation in mice.
- A modulatory role of the Rax homeobox gene in mature pineal gland function: Investigating the photoneuroendocrine circadian system of a Rax conditional knockout mouse.
Rohde, Journal of neurochemistry 2017 (PubMed)- GeneRIF: Deletion of Rax in the eye generated loss of central visual pathways and the suprachiasmatic nucleus was absent.
- Essential function of the transcription factor Rax in the early patterning of the mammalian hypothalamus.
Orquera, Developmental biology 2016 - GeneRIF: the role of Rax in the early stages of hypothalamic development
- Rax Homeoprotein Regulates Photoreceptor Cell Maturation and Survival in Association with Crx in the Postnatal Mouse Retina.
Irie, Molecular and cellular biology 2015 - GeneRIF: Rax and Crx cooperatively transactivate Rhodopsin and cone opsin promoters and an optimum Rax expression level to transactivate photoreceptor gene expression exists.
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RXB_XENLA / O42567 Retinal homeobox protein Rx-B; Retina and anterior neural fold homeobox protein B; Rx2A; Xrx2 from Xenopus laevis (African clawed frog) (see paper)
73% identity, 20% coverage
- function: Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation.
RXA_XENLA / O42201 Retinal homeobox protein Rx-A; Rx1A; Xrx1; Retina and anterior neural fold homeobox protein A from Xenopus laevis (African clawed frog) (see 2 papers)
NP_001081687 retinal homeobox protein Rx-A from Xenopus laevis
73% identity, 20% coverage
NP_001084383 paired like homeobox 2B L homeolog from Xenopus laevis
77% identity, 22% coverage
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...: Danio rerio NP_001014818; Homo sapiens NP_003915; Mus musculus CAA74833; Scyliorhinus canicula ABM89504; Xenopus laevis NP_001084383. Sox1 : Gallus gallus BAA25092; Homo sapiens NP_005977; Mus musculus BAC75667; Xenopus laevis BAE72677. Sox2 : Danio rerio BAE48583; Gallus gallus BAC67545; Homo sapiens NP_003097; Mus musculus AAC31791; Takifugu rubripes...”
PHX2B_MOUSE / O35690 Paired mesoderm homeobox protein 2B; Neuroblastoma Phox; NBPhox; PHOX2B homeodomain protein; Paired-like homeobox 2B from Mus musculus (Mouse) (see paper)
PHX2B_HUMAN / Q99453 Paired mesoderm homeobox protein 2B; Neuroblastoma Phox; NBPhox; PHOX2B homeodomain protein; Paired-like homeobox 2B from Homo sapiens (Human) (see 3 papers)
NP_003915 paired mesoderm homeobox protein 2B from Homo sapiens
NP_032914 paired mesoderm homeobox protein 2B from Mus musculus
77% identity, 20% coverage
- subunit: Interacts with TRIM11.
- function: Involved in the development of several major noradrenergic neuron populations, including the locus coeruleus. Transcription factor which could determine a neurotransmitter phenotype in vertebrates. Enhances second-messenger-mediated activation of the dopamine beta- hydrolase and c-fos promoters, and of several enhancers including cAMP- response element and serum-response element
subunit: Interacts with TRIM11. - Proteomic Analysis of Protective Effects of Dl-3-n-Butylphthalide against mpp + -Induced Toxicity via downregulating P53 pathway in N2A Cells
Zhao, Proteome science 2023 - “...protein 1 0.007188 O35887 Calu Calumenin 0.000147 O35874 Slc1a4 Neutral amino acid transporter A 0.029691 O35690 Phox2b Paired mesoderm homeobox protein 2B 0.000918 O35639 Anxa3 Annexin A3 5.15E-05 O35601 Fyb1 FYN-binding protein 1 0.000189 O35075 Dscr3 Down syndrome critical region protein 3 homolog 0.000377 O09131 Gsto1...”
- [Study of GCN repeats of PHOX2B gene among individuals from southwest China and diagnosis of two patients with Congenital central hypoventilation syndrome].
Qin, Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2024 (PubMed)- GeneRIF: [Study of GCN repeats of PHOX2B gene among individuals from southwest China and diagnosis of two patients with Congenital central hypoventilation syndrome].
- Combined analysis of PHOX2B at two time points and its value for further risk stratification in high-risk neuroblastoma.
Yue, Pediatric blood & cancer 2023 (PubMed)- GeneRIF: Combined analysis of PHOX2B at two time points and its value for further risk stratification in high-risk neuroblastoma.
- The expression of PHOX2B in bone marrow and peripheral blood predicts adverse clinical outcome in non-high-risk neuroblastoma.
Fan, Pediatric hematology and oncology 2022 (PubMed)- GeneRIF: The expression of PHOX2B in bone marrow and peripheral blood predicts adverse clinical outcome in non-high-risk neuroblastoma.
- Spectrum of paired-like homeobox 2b immunoexpression in pediatric brain tumors with embryonal morphology.
Alturkustani, Pathology international 2022 - GeneRIF: Spectrum of paired-like homeobox 2b immunoexpression in pediatric brain tumors with embryonal morphology.
- Adult-onset congenital central hypoventilation syndrome due to PHOX2B mutation.
Meylemans, Acta neurologica Belgica 2021 (PubMed)- GeneRIF: Adult-onset congenital central hypoventilation syndrome due to PHOX2B mutation.
- NH2-terminal deletion of specific phosphorylation sites on PHOX2B disrupts the formation of enteric neurons in vivo.
Chang, American journal of physiology. Gastrointestinal and liver physiology 2021 (PubMed)- GeneRIF: NH2-terminal deletion of specific phosphorylation sites on PHOX2B disrupts the formation of enteric neurons in vivo.
- Paired-like homeobox gene (PHOX2B) nonpolyalanine repeat expansion mutations (NPARMs): genotype-phenotype correlation in congenital central hypoventilation syndrome (CCHS).
Zhou, Genetics in medicine : official journal of the American College of Medical Genetics 2021 (PubMed)- GeneRIF: Paired-like homeobox gene (PHOX2B) nonpolyalanine repeat expansion mutations (NPARMs): genotype-phenotype correlation in congenital central hypoventilation syndrome (CCHS).
- Variable phenotypes in congenital central hypoventilation syndrome with PHOX2B nonpolyalanine repeat mutations.
Kasi, Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine 2021 - GeneRIF: Variable phenotypes in congenital central hypoventilation syndrome with PHOX2B nonpolyalanine repeat mutations.
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- The Molecular Circadian Clock of Phox2b-expressing Cells Drives Daily Variation of the Hypoxic but Not Hypercapnic Ventilatory Response in Mice.
Jones, Function (Oxford, England) 2023 - GeneRIF: The Molecular Circadian Clock of Phox2b-expressing Cells Drives Daily Variation of the Hypoxic but Not Hypercapnic Ventilatory Response in Mice.
- Phox2b-expressing neurons contribute to breathing problems in Kcnq2 loss- and gain-of-function encephalopathy models.
Soto-Perez, Nature communications 2023 - GeneRIF: Phox2b-expressing neurons contribute to breathing problems in Kcnq2 loss- and gain-of-function encephalopathy models.
- Phox2b mutation mediated by Atoh1 expression impaired respiratory rhythm and ventilatory responses to hypoxia and hypercapnia.
Ferreira, eLife 2022 - GeneRIF: Phox2b mutation mediated by Atoh1 expression impaired respiratory rhythm and ventilatory responses to hypoxia and hypercapnia.
- Respiratory Control by Phox2b-expressing Neurons in a Locus Coeruleus-preBötzinger Complex Circuit.
Liu, Neuroscience bulletin 2021 - GeneRIF: Respiratory Control by Phox2b-expressing Neurons in a Locus Coeruleus-preBotzinger Complex Circuit.
- Ultrahigh-Frequency Echocardiography of Autonomic Devoid Phox2B Homozygous Embryos Does Not Reveal a Significant Cardiac Phenotype before Embryo Death.
Mokshagundam, Ultrasound in medicine & biology 2021 - GeneRIF: Ultrahigh-Frequency Echocardiography of Autonomic Devoid Phox2B Homozygous Embryos Does Not Reveal a Significant Cardiac Phenotype before Embryo Death.
- Disordered breathing in a Pitt-Hopkins syndrome model involves Phox2b-expressing parafacial neurons and aberrant Nav1.8 expression.
Cleary, Nature communications 2021 - GeneRIF: Disordered breathing in a Pitt-Hopkins syndrome model involves Phox2b-expressing parafacial neurons and aberrant Nav1.8 expression.
- A medullary centre for lapping in mice.
Dempsey, Nature communications 2021 - GeneRIF: A medullary centre for lapping in mice.
- Rnf220/Zc4h2-mediated monoubiquitylation of Phox2 is required for noradrenergic neuron development.
Song, Development (Cambridge, England) 2020 (PubMed)- GeneRIF: Rnf220/Zc4h2-mediated monoubiquitylation of Phox2 is required for noradrenergic neuron development.
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- Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions
Antón, Nature communications 2024 - “...cellular protection is indeed fascinating. Methods Sample preparation All the different human PHOX2B (UniProt KB Q99453, Origene) cDNA constructs were subcloned into modified pET28a vectors (Novagen) containing Thioredoxin (TXA) as a fusion protein followed by a six-histidine tag for Ni 2+ affinity purification and a Tobacco...”
- Identification of Candidate Biomarkers of Alzheimer's Disease via Multiplex Cerebrospinal Fluid and Serum Proteomics
Liu, International journal of molecular sciences 2023 - “...OTUD4 OTUD4 8.57 10 5 Q8TF62 Probable phospholipid-transporting ATPase IM AT8B4 ATP8B4 3.41 10 25 Q99453 Paired mesoderm homeobox protein 2B PHX2B PHOX2B 1.17 10 57 Q9BXR6 Complement factor H-related protein 5 FHR5 CFHR5 1.5 10 105 Q9NTU7 Cerebellin-4 CBLN4 CBLN4 3.24 10 26 Q9UBF6 RING-box...”
- Structure analysis of the proteins associated with polyA repeat expansion disorders.
Hernandez, Journal of biomolecular structure & dynamics 2022 - “...(Tract 3) P31271 18 24 PABPN1 Q86U42 10 12 OPMD; (OMIM #164300) PHOX2B (Tract 1) Q99453 9 25 CCHS; (OMIM #209880) PHOX2B (Tract 2) Q99453 20 33 RUNX2 Q13950 17 27 Brachydactyly and minor clinical features CCD; (OMIM #119600) SOX3 (Tract 1) P41225 15 22 XH;...”
- An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks.
Kim, Biomedicines 2020 - “...Coagulation factor XIII B chain 6 0.17 P02765 3.75 10 -2 AHSG Alpha-2-HS-glycoprotein 2 0.20 Q99453 3.85 10 -2 PHOX2B Paired mesoderm homeobox protein 2B 2 0.12 O43157 4.01 10 -2 PLXNB1 Plexin-B1 5 0.01 P06396 4.26 10 -2 GSN Gelsolin 6 0.04 O43866 4.41 10...”
- Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells.
Yamamoto, Oncotarget 2018 - “...Q06830 2.43 2 53 ILF3 Q12906 2.40 2 54 H3F3A P84243 2.00 10 55 PHOX2B Q99453 2.00 2 Only proteins with Peptides (95%) 2 and Unused ProtScore 2 are shown. Unused ProtScore for a particular protein was calculated from the sum of all peptide evidence for...”
- Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions
Darling, Molecules (Basel, Switzerland) 2017 - “...stem cells [ 244 ]. Paired mesoderm homeobox protein 2B (PHOX2B homeodomain protein, UniProt ID: Q99453) is expected to have 54.14% disordered residues (as evaluated by the MobiDB-based consensus disorder content). In agreement with these MobiDB predictions, Figure 2 E and Figure S1E show high levels...”
- “...protein ZIC2 (UniProt ID: O95409); ( E ) Paired mesoderm homeobox protein 2B (UniProt ID: Q99453); ( F ) Transcription factor SOX3 (UniProt ID: P41225); ( G ) Homeobox protein ARX (UniProt ID: Q96QS3); ( H ) Human FOXL2 (UniProt ID: P58012); ( I ) PABP2/PABPN1...”
- Novel Mechanisms for Heme-dependent Degradation of ALAS1 Protein as a Component of Negative Feedback Regulation of Heme Biosynthesis
Kubota, The Journal of biological chemistry 2016 - “...O60814 A0M8Q6 Q14974 Q9Y6Y0 Q9NZI8 Q9UHB6 P49006 O00264 Q99453 P30044 Q13310 Q9Y2S7 Q92841 Q15185 Q9P258 Q14257 P49458 O60749 Q9NYL9 Q13509 Q8NFA0 P62987 P16989...”
- Novel mutation-deletion in the PHOX2B gene of the patient diagnosed with Neuroblastoma, Hirschsprung's Disease, and Congenital Central Hypoventilation Syndrome (NB-HSCR-CCHS) Cluster.
Szymońska, Journal of genetic syndromes & gene therapy 2015 - “...CCDS set: CCDS3463.1 UniProtKB: This gene has proteins that correspond to the following Uniprot identifiers: Q99453 RefSeq: Overlapping RefSeq Gene ID 8929 matches and has similar biotype of protein coding LRG: LRG_513 provides a stable genomic reference framework for describing sequence variations for this gene Ensembl...”
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NP_989600 paired box protein Pax-3 isoform a from Gallus gallus
74% identity, 15% 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.
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PHX2A_HUMAN / O14813 Paired mesoderm homeobox protein 2A; ARIX1 homeodomain protein; Aristaless homeobox protein homolog; Paired-like homeobox 2A from Homo sapiens (Human) (see paper)
NP_005160 paired mesoderm homeobox protein 2A isoform 1 from Homo sapiens
77% identity, 23% coverage
- function: May be involved in regulating the specificity of expression of the catecholamine biosynthetic genes. Acts as a transcription activator/factor. Could maintain the noradrenergic phenotype
- Outcomes of strabismus surgery in genetically confirmed congenital fibrosis of the extraocular muscles.
Heidary, Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus 2019 - GeneRIF: Outcomes of strabismus surgery in genetically confirmed congenital fibrosis of the extraocular muscles.
- PHOX2A and PHOX2B are differentially regulated during retinoic acid-driven differentiation of SK-N-BE(2)C neuroblastoma cell line.
Di, Experimental cell research 2016 - GeneRIF: PHOX2A expression is finely controlled during retinoic acid differentiation and this, together with PHOX2B down-regulation.
- Phenotype-phenotype and genotype-phenotype correlations in patients with idiopathic superior oblique muscle palsy.
Ohkubo, Journal of human genetics 2012 (PubMed)- GeneRIF: Patients with ARIX and/or PHOX2B polymorphisms had less hypoplastic superior oblique muscles.
- [Identification of a novel PHOX2A gene mutation in a Chinese family with congenital fibrosis of extraocular muscles type 2].
Dong, Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2012 (PubMed)- GeneRIF: Genetic linkage was found at 11q13 between D11S4151 and D11S1320 and the PHOX2A gene.
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...; Takifugu rubripes AAC31810 ; Xenopus laevis NP_001081941. Phox2a : Danio rerio NP_996953; Homo sapiens NP_005160; Mus musculus Q62066; Xenopus laevis AAI24892. Phox2b : Danio rerio NP_001014818; Homo sapiens NP_003915; Mus musculus CAA74833; Scyliorhinus canicula ABM89504; Xenopus laevis NP_001084383. Sox1 : Gallus gallus BAA25092; Homo sapiens...”
- The Phox2 pathway is differentially expressed in neuroblastoma tumors, but no mutations were found in the candidate tumor suppressor gene PHOX2A.
Wilzén, International journal of oncology 2009 (PubMed)- GeneRIF: PHOX2A gene, localized in a tumor suppressor candidate region at 11q, weas screened for mutations by DNA sequencing in 47 tumors of different stages.
- Effects of transcription factors Phox2 on expression of norepinephrine transporter and dopamine beta-hydroxylase in SK-N-BE(2)C cells.
Fan, Journal of neurochemistry 2009 - GeneRIF: Transfection of Phox2a cDNA significantly increases mRNA and protein levels of norepinephrine transporter and dopamine beta-hydroxylase.
- Mutations in KIF21A and PHOX2A are absent in 16 patients with congenital vertical incomitant strabismus.
Khan, Ophthalmic genetics 2009 (PubMed)- GeneRIF: Our 16-patient sample suggests that KIF21A and PHOX2A sequence variation does not have a role in common forms of congenital incomitant vertical strabismus.
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XP_015140956 paired mesoderm homeobox protein 2B from Gallus gallus
77% identity, 22% coverage
XP_011607069 paired box protein Pax-3 isoform X1 from Takifugu rubripes
73% identity, 15% coverage
NP_571400 paired box protein Pax-7a isoform PAX7C from Danio rerio
71% identity, 15% coverage
- Activation of Pax7-positive cells in a non-contractile tissue contributes to regeneration of myogenic tissues in the electric fish S. macrurus
Weber, PloS one 2012 - “...GKKDDDDDC (antisense primer) domains were designed using alignments from protein sequences of Danio rerio (GenBank: NP_571400), Salmo salar (GenBank: CAF02090.1), Tetraodon nigroviridis (GenBank: CAG07040.1), and two sequences from Salvelinus alpinus (GenBank: CAG25716.1; CAG25714.1). To clone partial Pax7 cDNAs from S. macrurus , we carried out reverse...”
- “...NP_035169.1; Figure 2A ), and other teleosts including zebrafish ( D. rerio ; accession number NP_571400), Atlantic salmon ( S. salar ; accession number CAF02090.1), and arctic char ( S. alpinus ; accession number CAG25716.1) ( Figure 2B ) revealed a high degree of conservation among...”
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...NP_852122; Mus musculus AAH48699 ; Scyliorhinus canicula ABM89502; Xenopus laevis AAI08574. Pax7 : Danio rerio NP_571400; Gallus gallus NP_990396; Homo sapiens CAA65522; Mus musculus AF254422; Xenopus laevis NP_001088995. Pax2 : Danio rerio 2a NP571259; Danio rerio 2b NP571715; Gallus gallus NP_990124; Homo sapiens AAC63385 ; Mus...”
XP_009304561 paired box protein Pax-7a isoform X1 from Danio rerio
71% identity, 15% coverage
NP_001088995 paired box 7 L homeolog from Xenopus laevis
65% identity, 17% coverage
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...: Danio rerio NP_571400; Gallus gallus NP_990396; Homo sapiens CAA65522; Mus musculus AF254422; Xenopus laevis NP_001088995. Pax2 : Danio rerio 2a NP571259; Danio rerio 2b NP571715; Gallus gallus NP_990124; Homo sapiens AAC63385 ; Mus musculus CAA39302 ; Oryzias latipes CAB09696 ; Scyliorhinus canicula ABM89503 ; Xenopus...”
- Sequential actions of Pax3 and Pax7 drive xanthophore development in zebrafish neural crest
Minchin, Developmental biology 2008 - “...G. gallus (GG) Pax3: NP_989600; GG Pax7: NP_990396; X. tropicalis (XT) Pax3: CAJ82363; XT Pax7: NP_001088995; G. aculeatus (GA) Pax3: ENSGACG00000014017; GA Pax7: ENSGACG00000012890; GA Pax7 (2/2): ENSGACG00000001703; O. latipes (OL) Pax3: ENSORLG00000015932; OL Pax3b: ENSORLG00000009031; OL Pax7: ENSORLG00000004269; T. rubripes (TR) Pax3: SINFRUG00000132501; TR Pax3b:...”
PAX7_MOUSE / P47239 Paired box protein Pax-7 from Mus musculus (Mouse) (see 3 papers)
71% identity, 15% 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 DAXX (By similarity). Interacts with PAXBP1; the interaction links PAX7 to a WDR5-containing histone methyltransferase complex (PubMed:22862948). - Activation of Pax7-positive cells in a non-contractile tissue contributes to regeneration of myogenic tissues in the electric fish S. macrurus.
Weber, PloS one 2012 - “...are within the range in Pax7 protein sizes found in mouse (55 kDa; accession number P47239), and other teleosts including zebrafish (56 kDa; accession number NP_571400.1), arctic char (55 kDa; accession number Q5ZNB2), and Atlantic salmon (56 kDa; accession number Q683Y9). Western blots using S. macrurus...”
- Niche-independent symmetrical self-renewal of a mammalian tissue stem cell
Conti, PLoS biology 2005 - “...(P15655), Gad1 (Gad67) (P48318), Gfap (P03995), Nanog (Q7TN85), Nestin (Q6P5H2), Olig2 (Q9EQW6), Pax6 (P63015), Pax7 (P47239), Pou5f1 (Oct4, Oct3/4) (P20263), Slc1a3 (Glast) (P56564), Sox1 (P53783), Sox2 (P48432), Sox3 (P53784), and Vim (P20152). We are indebted to Helen Mardon, Barbara Evans, and Janet Carver at the University...”
XP_006538694 paired box protein Pax-7 isoform X3 from Mus musculus
71% identity, 15% coverage
XP_006239325 paired box protein Pax-7 isoform X1 from Rattus norvegicus
71% identity, 15% coverage
- Regulation of skeletal myogenesis in C2C12 cells through modulation of Pax7, MyoD, and myogenin via different low-frequency electromagnetic field energies.
Bi, Technology and health care : official journal of the European Society for Engineering and Medicine 2022 - GeneRIF: Regulation of skeletal myogenesis in C2C12 cells through modulation of Pax7, MyoD, and myogenin via different low-frequency electromagnetic field energies.
- The expression patterns of Pax7 in satellite cells during overload-induced rat adult skeletal muscle hypertrophy.
Ishido, Acta physiologica (Oxford, England) 2009 (PubMed)- GeneRIF: Pax7-regulated self-renewal of satellite cells(SC) may be induced during early stage of functional overload and may contribute to modulating SC population in hypertrophied muscles.
- Pax3 and Pax7 expression during myoblast differentiation in vitro and fast and slow muscle regeneration in vivo.
Brzóska, Cell biology international 2009 (PubMed)- GeneRIF: Pax3 and Pax7, both in vitro and in vivo, participated in the differentiation and regeneration events of muscle
- [Pax7 and depletion of satellite cell pool in prolonged denervated skeletal muscles of adult rats].
Liao, Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery 2009 (PubMed)- GeneRIF: One possible reason of the depletion of satellite cell pool in prolonged denervated muscle is the down-regulation of Pax7.
- PAX3/7 expression coincides with MyoD during chronic skeletal muscle overload.
Hyatt, Muscle & nerve 2008 - GeneRIF: Pax3 and 7 coordinate the recapitulation of developmental-like regulatory mechanisms in response to growth-inducing stimuli in adult skeletal muscle
- Pax7 expression in the adult rat superior colliculus following optic nerve injury.
Thomas, Neuroreport 2007 (PubMed)- GeneRIF: findings show that after optic nerve transection, the number of Pax7-expressing cells increased to re-establish the developmental rostral-caudal gradient and that these Pax7-expressing superior colliculus cells were neurons [Pax7]
XP_018080096 paired box 7 L homeolog isoform X1 from Xenopus laevis
65% identity, 17% coverage
3a01F / Q06453 Crystal structure of aristaless and clawless homeodomains bound to dna (see paper)
82% identity, 71% coverage
NP_446130 retinal homeobox protein Rx from Rattus norvegicus
70% identity, 20% coverage
XP_066838118 paired box protein Pax-7 isoform X1 from Anser cygnoides
71% identity, 14% coverage
RX_HUMAN / Q9Y2V3 Retinal homeobox protein Rx; Retina and anterior neural fold homeobox protein from Homo sapiens (Human) (see 2 papers)
NP_038463 retinal homeobox protein Rx from Homo sapiens
70% identity, 20% coverage
- function: Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE- 1/Ret 1) in the photoreceptor cell-specific arrestin promoter
- Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity.
Atefi, BMC molecular and cell biology 2021 - GeneRIF: Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity.
- Unraveling the genetic cause of a consanguineous family with unilateral coloboma and retinoschisis: expanding the phenotypic variability of RAX mutations.
Huang, Scientific reports 2017 - GeneRIF: combination of WES and homozygosity mapping identified a novel homozygous RAX mutation in a consanguineous family segregating with rarely reported asymmetrical coloboma. Clinical findings and genetic results support that RAX mutation is responsible for eye malformations.
- Derivation of human differential photoreceptor-like cells from the iris by defined combinations of CRX, RX and NEUROD.
Seko, PloS one 2012 - GeneRIF: Photosensitive photoreceptor cells can be generated by combinations of transcription factors. The combination of CRX and RX generate immature photoreceptors: and additional NEUROD promotes maturation.
- RAX and anophthalmia in humans: evidence of brain anomalies.
Abouzeid, Molecular vision 2012 - GeneRIF: The three consanguineous Egyptian anophthalmia patients carry a novel homozygous c.543+3A>G mutation (IVS2+3A>G) in RAX.
- Mutational screening of CHX10, GDF6, OTX2, RAX and SOX2 genes in 50 unrelated microphthalmia-anophthalmia-coloboma (MAC) spectrum cases.
Gonzalez-Rodriguez, The British journal of ophthalmology 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Sequence alterations in RX in patients with microphthalmia, anophthalmia, and coloboma.
London, Molecular vision 2009 - GeneRIF: A missense mutation in RX was observed in a patient with a small, typical chorioretinal coloboma, and postulate that the mutation is responsible for the patient's phenotype.
- Mutations in the newly identified RAX regulatory sequence are not a frequent cause of micro/anophthalmia.
Chassaing, Genetic testing and molecular biomarkers 2009 (PubMed)- GeneRIF: Mutations in the newly identified RAX regulatory sequence are not a frequent cause of micro/anophthalmia.
- Mutational screening of 10 genes in Chinese patients with microphthalmia and/or coloboma.
Zhang, Molecular vision 2009 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- More
- Unraveling the genetic cause of a consanguineous family with unilateral coloboma and retinoschisis: expanding the phenotypic variability of RAX mutations.
Huang, Scientific reports 2017 - “...damaging (PolyPhen2 score: 0.873) to the protein, retina and anterior neural fold homeobox (Protein Accession: Q9Y2V3). Subdomain identification was performed using SMART, indicating this mutation neither located in homeobox nor paired box. The potential effect on RAX function was further analyzed using the RaptorX service, visualized...”
- Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
Hou, PLoS computational biology 2006 - “...AT19 (Q8TE59), CABL2_human (NP_665850), DYN2 (P50570), EVL (Q9UI08), P73_human (O15350), PRL3 (P02814), RBMG (Q9UPN6), RX (Q9Y2V3), SCA3 (O14828), SEM6A (Q9H2E6), SEM6D (Q76KF3), SEM6D_mouse (NP_954711), SEP4 (O43236), TACT (P40200), WASF1 (Q92558), and WASF4 (Q8IV90). The MD simulations were performed on the Linux cluster in the Center for...”
A0A0B7A551 Uncharacterized protein (Fragment) from Arion vulgaris
71% identity, 16% 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_001098373 retinal homeobox protein Rx2 from Oryzias latipes
65% identity, 24% coverage
NP_001139621 paired box protein Pax-7b from Danio rerio
71% identity, 15% coverage
LOC536229, XP_015316176 paired box protein Pax-7 from Bos taurus
71% identity, 18% coverage
- Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle
Liu, Frontiers in genetics 2022 - “...dual luciferase reporter assay system using the psiCHECK-2 vector (Promega, Madison, WI). The LOC104975788 and LOC536229 ( Pax7 ) sequences were separately cloned into the reporter gene vector (psiCHECK-2) to synthesize the predicted miRNA mimics and control. The potential binding target of each miRNA was cloned...”
- “...binding site prediction software (RNA22 and RNAhybird) predicted potential interaction of miR-133a with LOC104975788 and LOC536229 ( Pax7 ). The results showed that both LOC104975788 and LOC536229 ( Pax7 ) contained miR-133a binding sites. Verification of Sequencing Results Nine differentially expressed LncRNAs and five differentially expressed...”
- MicroRNA bta-miR-365-3p inhibits proliferation but promotes differentiation of primary bovine myoblasts by targeting the activin A receptor type I
Hao, Journal of animal science and biotechnology 2021 - “...cell myogenic differentiation 26424132 bta-miR-206 HDAC4 517,559 Skeletal muscle satellite cell myogenic differentiation 26424132 bta-miR-1 LOC536229 536,229 Skeletal muscle satellite cell myogenic differentiation 26424132 bta-miR-206 LOC536229 536,229 Skeletal muscle satellite cell myogenic differentiation 26424132 bta-miR-23a ZNF423 508,025 Adipogeneses in skeletal muscle 28255176 bta-miR-27b MSTN 281,187 Skeletal...”
- A novel PAX7 10-bp indel variant modulates promoter activity, gene expression and contributes to different phenotypes of Chinese cattle.
Xu, Scientific reports 2018 - GeneRIF: The authors detected a novel 10-bp insertion/deletion (indel) polymorphism in the bovine PAX7 promoter and revealed that the indel altered the binding of the transcriptional factor ZNF219.
- Consistent effects of single and combined SNP(s) within bovine paired box 7 gene (Pax7) on growth traits.
Xu, Journal of genetics 2011 (PubMed)- GeneRIF: four novel polymorphisms were identified in the Pax7 gene; the association analysis of genotypes in the single and combined SNP(s) revealed consistent effects on growth traits in NY cattle
Ci-Rx / CAC34833.1 Ci-Rx protein from Ciona intestinalis (see paper)
63% identity, 9% coverage
XP_018669748 prx1 protein isoform X1 from Ciona intestinalis
63% identity, 10% coverage
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
65% identity, 17% 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...”
XP_020951119 paired box protein Pax-7 isoform X3 from Sus scrofa
65% identity, 17% coverage
- Tributyrin, a Butyrate Pro-Drug, Primes Satellite Cells for Differentiation by Altering the Epigenetic Landscape.
Murray, Cells 2021 - GeneRIF: Tributyrin, a Butyrate Pro-Drug, Primes Satellite Cells for Differentiation by Altering the Epigenetic Landscape.
- Porcine skeletal muscle-derived multipotent PW1pos/Pax7neg interstitial cells: isolation, characterization, and long-term culture.
Lewis, Stem cells translational medicine 2014 - GeneRIF: Porcine skeletal muscle-derived PW1(pos)/Pax7(neg) interstitial cells are a source of stem/progenitor cells.
- Expression of the paired box domain Pax7 protein in myogenic cells isolated from the porcine semitendinosus muscle after birth.
Patruno, Tissue & cell 2008 (PubMed)- GeneRIF: Pax7 might be one of the molecules involved in controlling the proliferation/differentiation ratio in the pool of satellite cells present in post-natal porcine skeletal muscles.
- The expression pattern of myogenic regulatory factors MyoD, Myf6 and Pax7 in postnatal porcine skeletal muscles.
Ropka-Molik, Gene expression patterns : GEP (PubMed)- GeneRIF: The total expression profile of MyoD and Pax7 genes suggests that higher muscularity in Pietrain pigs is associated with the presence of a greater number of active satellite stem cells compared to other breeds.
8osbE / Q9H161 Twist1-tcf4-alx4 complex on specific DNA (see paper)
84% identity, 71% coverage
Q5ZNB2 Paired box protein 7 from Salvelinus alpinus
65% identity, 17% coverage
NP_990396 paired box protein Pax-7 from Gallus gallus
65% identity, 16% coverage
- Molecular analysis of neurogenic placode development in a basal ray-finned fish
Modrell, Genesis (New York, N.Y. : 2000) 2011 - “...AAH48699 ; Scyliorhinus canicula ABM89502; Xenopus laevis AAI08574. Pax7 : Danio rerio NP_571400; Gallus gallus NP_990396; Homo sapiens CAA65522; Mus musculus AF254422; Xenopus laevis NP_001088995. Pax2 : Danio rerio 2a NP571259; Danio rerio 2b NP571715; Gallus gallus NP_990124; Homo sapiens AAC63385 ; Mus musculus CAA39302 ;...”
- Sequential actions of Pax3 and Pax7 drive xanthophore development in zebrafish neural crest
Minchin, Developmental biology 2008 - “...M. musculus (MM) Pax3: NP_032807; MM Pax7: NP_035169; G. gallus (GG) Pax3: NP_989600; GG Pax7: NP_990396; X. tropicalis (XT) Pax3: CAJ82363; XT Pax7: NP_001088995; G. aculeatus (GA) Pax3: ENSGACG00000014017; GA Pax7: ENSGACG00000012890; GA Pax7 (2/2): ENSGACG00000001703; O. latipes (OL) Pax3: ENSORLG00000015932; OL Pax3b: ENSORLG00000009031; OL Pax7:...”
NP_001245266 paired box protein Pax-7a from Oncorhynchus mykiss
65% identity, 17% coverage
Q683Y9 Paired box protein 7 from Salmo salar
71% identity, 15% coverage
UNC4_MOUSE / O08934 Homeobox protein unc-4 homolog; Homeobox protein Uncx4.1 from Mus musculus (Mouse) (see 11 papers)
NP_038730 homeobox protein unc-4 homolog from Mus musculus
66% identity, 14% coverage
- function: Transcription factor involved in somitogenesis and neurogenesis. Required for the maintenance and differentiation of particular elements of the axial skeleton. May act upstream of PAX9. Plays a role in controlling the development of connections of hypothalamic neurons to pituitary elements, allowing central neurons to reach the peripheral blood circulation and to deliver hormones for control of peripheral functions.
disruption phenotype: Mice die perinatally and exhibit severe malformations of the axial skeleton. Pedicles of the neural arches and proximal ribs are not formed. In addition, dorsal root ganglia are disorganized. In the hypothalamo-neurohypophysial system, neurons are viable and able to express neuropeptides; however, the connectivity of magnocellular neurons with posterior pituitary elements is compromised. - The transcription factor Uncx4.1 acts in a short window of midbrain dopaminergic neuron differentiation.
Rabe, Neural development 2012 - GeneRIF: Uncx4.1 might play an important role during glutamatergic neuronal differentiation in the mouse midbrain.
- Uncx regulates proliferation of neural progenitor cells and neuronal survival in the olfactory epithelium.
Sammeta, Molecular and cellular neurosciences 2010 - GeneRIF: Uncx acts downstream of neural determination factors to broadly control transcriptional mechanisms used by progenitor cells to specify the phenotype of the olfactory sensory neuron.
- GeneRIF: UNCX acts downstream of neural determination factors to broadly control transcriptional mechanisms used by neural progenitor cells to specify neural phenotypes
- Examination of the Lunatic fringe and Uncx4.1 expression by whole-mount in situ hybridization in the embryo of the CKH-Jsr (jumbled spine and ribs) mouse.
Okano, The Japanese journal of veterinary research 2005 (PubMed)- GeneRIF: We examined Lunatic Fringe (Lfng) and Uncx4.1 expression in the presomitic mesoderm (PSM) and somites of Jsr-mutant (CKH-Jsr/+) embryos to elucidate pathogenesis of the Jsr mutation.
NP_001245265 paired box gene 7b from Oncorhynchus mykiss
65% identity, 17% coverage
A6NJT0 Homeobox protein unc-4 homolog from Homo sapiens
NP_001073930 homeobox protein unc-4 homolog from Homo sapiens
73% identity, 12% coverage
NP_571302 retinal homeobox protein Rx3 from Danio rerio
64% identity, 25% coverage
- Holoprosencephaly with a Special Form of Anophthalmia Result from Experimental Induction of bmp4, Oversaturating BMP Antagonists in Zebrafish.
Bulk, International journal of molecular sciences 2023 - GeneRIF: Holoprosencephaly with a Special Form of Anophthalmia Result from Experimental Induction of bmp4, Oversaturating BMP Antagonists in Zebrafish.
- Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus.
Muthu, Development (Cambridge, England) 2016 - GeneRIF: Shh and Rx3 govern formation of a distinct progenitor domain that elaborates patterning through its anisotropic growth and differentiation.
- A zebrafish LMO4 ortholog limits the size of the forebrain and eyes through negative regulation of six3b and rx3.
McCollum, Developmental biology 2007 - GeneRIF: lmo4b has an essential role in forebrain development as a modulator of six3 and rx3 expression, and thus indirectly influences neural cell fate commitment, cell proliferation and tissue growth in the anterior CNS.
- Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3.
Stigloher, Development (Cambridge, England) 2006 (PubMed)- GeneRIF: The process segregating the telencephalic and eye fields is isolated from diencephalic patterning, and is mediated by Rx3.
- chokh/rx3 specifies the retinal pigment epithelium fate independently of eye morphogenesis.
Rojas-Muñoz, Developmental biology 2005 (PubMed)- GeneRIF: In addition to controlling optic lobe evagination and proliferation, chk/rx3 also determines cellular fate.
- Zebrafish rx3 and mab21l2 are required during eye morphogenesis.
Kennedy, Developmental biology 2004 (PubMed)- GeneRIF: rx3 mutation leads to microphthalmia, incomplete eye maturation, and dramatic increases in apoptotic eye progenitors
XP_002936715 retinal homeobox protein Rx from Xenopus tropicalis
73% identity, 20% coverage
UNC4_RAT / P97830 Homeobox protein unc-4 homolog; Homeobox protein Uncx4.1; Paired-type homeodomain transcription factor 1 from Rattus norvegicus (Rat) (see paper)
66% identity, 14% coverage
- function: Transcription factor involved in somitogenesis and neurogenesis. Required for the maintenance and differentiation of particular elements of the axial skeleton. May act upstream of PAX9. Plays a role in controlling the development of connections of hypothalamic neurons to pituitary elements, allowing central neurons to reach the peripheral blood circulation and to deliver hormones for control of peripheral functions (By similarity).
VSX1_DANRE / O42250 Visual system homeobox 1; Transcription factor VSX1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_571408 visual system homeobox 1 from Danio rerio
71% identity, 19% coverage
XP_015149815 homeobox protein unc-4 homolog isoform X1 from Gallus gallus
73% identity, 13% coverage
VSX1_CARAU / Q90277 Visual system homeobox 1; Homeobox protein VSX-1; Transcription factor VSX1 from Carassius auratus (Goldfish) (see paper)
71% identity, 19% coverage
- function: May stabilize the differentiated state of a subset of cells in the inner nuclear layer and may be involved in cellular differentiation during retinal development and regeneration
subunit: Interacts with UBE2I.
UNC4_CAEEL / P29506 Homeobox protein unc-4; Homeobox protein ceh-4; Uncoordinated protein 4 from Caenorhabditis elegans (see 8 papers)
NP_496138 Homeobox protein unc-4 from Caenorhabditis elegans
68% identity, 28% coverage
- function: Transcription factor (PubMed:1347150, PubMed:28056346, PubMed:7904971). Involved in motor neuron fate determination and maintenance (PubMed:28056346, PubMed:34388088). In concert with unc-37, represses the expression of VB-specific genes such as ceh-12, thereby preventing the adoption of VB motor neuron fate (PubMed:10557206, PubMed:11245684, PubMed:17289921, PubMed:7904971, PubMed:9165118). Regulates synaptic specificity and the pattern of synaptic input to VA motor neurons, and, depending on context, acting in opposition to, or supported by, Wnt signaling (PubMed:1347150, PubMed:22619391, PubMed:7555714, PubMed:7904971). Required in patterning of the synaptic outputs of the postmitotic DA class cholinergic motor neurons (PubMed:34388088). Acts as a transcriptional repressor to counteract gene activation by transcription factor unc-3 in a subset of motor neurons, probably by binding to specific promoter elements (PubMed:28056346). Has no role in axonal guidance or outgrowth (PubMed:1347150).
subunit: Interacts with unc-37.
disruption phenotype: Worms are unable to crawl backwards because VA motor neurons are miswired with synaptic connections normally reserved for their sister cells, the VB motor neurons. - Sustained expression of unc-4 homeobox gene and unc-37/Groucho in postmitotic neurons specifies the spatial organization of the cholinergic synapses in C. elegans.
Kurashina, eLife 2021 - GeneRIF: Sustained expression of unc-4 homeobox gene and unc-37/Groucho in postmitotic neurons specifies the spatial organization of the cholinergic synapses in C. elegans.
- UNC-4 antagonizes Wnt signaling to regulate synaptic choice in the C. elegans motor circuit.
Schneider, Development (Cambridge, England) 2012 - GeneRIF: UNC-4 prevents VA motor neurons from responding to a local EGL-20 cue by disabling a canonical Wnt signaling cascade.
- UNC-4 represses CEH-12/HB9 to specify synaptic inputs to VA motor neurons in C. elegans.
Von, Genes & development 2007 - GeneRIF: UNC-4 represses CEH-12/HB9 to specify synaptic inputs to VA motor neurons.
NP_001315326 paired box protein Pax-3b from Danio rerio
76% identity, 14% coverage
VSX1_HUMAN / Q9NZR4 Visual system homeobox 1; Homeodomain protein RINX; Retinal inner nuclear layer homeobox protein; Transcription factor VSX1 from Homo sapiens (Human) (see 10 papers)
68% identity, 18% coverage
- function: Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster (PubMed:10903837). May regulate the activity of the LCR and the cone opsin genes at earlier stages of development (PubMed:10903837). Dispensable in early retinal development (By similarity).
- Priorities and trends in the study of proteins in eye research, 1924-2014
Semba, Proteomics. Clinical applications 2015 - “...monosaturated very long chain fatty acids Stargardt disease 3 1 isoform 1 PTM 38 variants Q9NZR4 VSX1 visual system homeobox 1 31 binds to the locus core region of the red/green visual pigment gene cluster corneal dystrophy, posterior polymorphous, 1; keratoconus 1; craniofacial anomalies and anterior...”
R7TKD0 Transcription factor Pax3/7 (Fragment) from Capitella teleta
68% identity, 28% 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...”
RAX2_HUMAN / Q96IS3 Retina and anterior neural fold homeobox protein 2; Q50-type retinal homeobox protein; Retina and anterior neural fold homeobox-like protein 1 from Homo sapiens (Human) (see 2 papers)
NP_116142 retina and anterior neural fold homeobox protein 2 from Homo sapiens
59% identity, 41% coverage
- function: May be involved in modulating the expression of photoreceptor specific genes. Binds to the Ret-1 and Bat-1 element within the rhodopsin promoter.
subunit: Interacts with CRX. - Quantitative bile and serum proteomics for the screening and differential diagnosis of primary sclerosing cholangitis.
Holm, PloS one 2022 - “...8,4 5,15E-05 1,000 2,7 MORC family CW-type zinc finger protein 2 MORC2 0,795 0,683 0,890 Q96IS3 2 2 6,9 6,62E-08 1,000 -2,7 Retina and anterior neural fold homeobox protein 2 RAX2 0,900 0,830 0,958 P01034 7 5 34,9 2,73E-09 1,000 -2,3 Cystatin-C CST3 0,942 0,885 0,985...”
- Autosomal Dominant Retinal Dystrophy With Electronegative Waveform Associated With a Novel RAX2 Mutation.
Yang, JAMA ophthalmology 2015 - GeneRIF: A frameshift heterozygous mutation in RAX2 inherited in an autosomal dominant fashion was associated with mixed cone and rod dysfunction.
- New genetic associations detected in a host response study to hepatitis B vaccine.
Davila, Genes and immunity 2010 (PubMed)- GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
VSX1_MOUSE / Q91V10 Visual system homeobox 1; Homeodomain protein RINX; Retinal inner nuclear layer homeobox protein; Transcription factor VSX1 from Mus musculus (Mouse) (see 2 papers)
NP_473409 visual system homeobox 1 from Mus musculus
68% identity, 18% coverage
- function: Binds to the 37-bp core of the locus control region (LCR) of the red/green visual pigment gene cluster (By similarity). May regulate the activity of the LCR and the cone opsin genes at earlier stages of development (By similarity). Dispensable in early retinal development (PubMed:17919464).
disruption phenotype: At embryonic day 14.5 ocular morphology is normal as is expression and localization of retinal transcription and cell cycle regulatory proteins. - Vsx1 and Chx10 paralogs sequentially secure V2 interneuron identity during spinal cord development.
Debrulle, Cellular and molecular life sciences : CMLS 2020 - GeneRIF: Vsx1 and Chx10 paralogs sequentially secure V2 interneuron identity during spinal cord development.
- Investigating the Pathogenicity of VSX1 Missense Mutations and Their Association With Corneal Disease.
Litke, Investigative ophthalmology & visual science 2018 (PubMed)- GeneRIF: Our results indicate that although VSX1 sequence variants can alter transcriptional activity, in the context of a mouse genetic model, at least one of these changes does not lead to corneal abnormalities. While we cannot exclude a role for VSX1 as a risk factor for corneal disease, on its own, it does not appear to play a major causative role.
- Requirement for the paired-like homeodomain transcription factor VSX1 in type 3a mouse retinal bipolar cell terminal differentiation.
Shi, The Journal of comparative neurology 2012 (PubMed)- GeneRIF: These findings reveal a role for Vsx1 in type 3a bipolar cells and suggest that Vsx1 function is required transiently in this cell type during the postnatal period.
- Vsx1 regulates terminal differentiation of type 7 ON bipolar cells.
Shi, The Journal of neuroscience : the official journal of the Society for Neuroscience 2011 - GeneRIF: findings indicate that Vsx1 regulates terminal gene expression in Type 7 bipolar cells and is necessary for proper ON visual signaling within a directionally selective circuit.
- Negative regulation of Vsx1 by its paralog Chx10/Vsx2 is conserved in the vertebrate retina.
Clark, Brain research 2008 - GeneRIF: Although Vsx1 mRNA is upregulated in Chx10/Vsx2 deficient RPCs, Vsx1 does not genetically compensate for loss of Chx10/Vsx2, demonstrating that Prd-L:CVC genes, although important, are not absolutely required to initiate retinal development.
- Genetic control of circuit function: Vsx1 and Irx5 transcription factors regulate contrast adaptation in the mouse retina.
Kerschensteiner, The Journal of neuroscience : the official journal of the Society for Neuroscience 2008 - GeneRIF: Transcription factor visual system homeobox 1 homolog (Vsx1) controls specific aspects of visual function in the neural circuitry of the mammalian retina.
- Control of late off-center cone bipolar cell differentiation and visual signaling by the homeobox gene Vsx1.
Chow, Proceedings of the National Academy of Sciences of the United States of America 2004 - GeneRIF: role in late differentiation and function of OFF-CB cells and is associated with a heritable OFF visual pathway-specific retinal defect
- Regulation of retinal cone bipolar cell differentiation and photopic vision by the CVC homeobox gene Vsx1.
Ohtoshi, Current biology : CB 2004 (PubMed)- GeneRIF: Vsx1 is required for cone bipolar cell differentiation and regulates photopic vision perception.
NP_990100 visual system homeobox 1 from Gallus gallus
67% identity, 19% coverage
XP_012818027 visual system homeobox 1 isoform X1 from Xenopus tropicalis
68% identity, 19% coverage
RAX2_BOVIN / Q7YRX0 Retina and anterior neural fold homeobox protein 2; Q50-type retinal homeobox protein; Retina and anterior neural fold homeobox-like protein 1 from Bos taurus (Bovine) (see paper)
59% identity, 41% coverage
- function: May be involved in modulating the expression of photoreceptor specific genes. Binds to the Ret-1 and Bat-1 element within the rhodopsin promoter (By similarity).
subunit: Interacts with CRX.
NP_723721 paired, isoform B from Drosophila melanogaster
P06601 Segmentation protein paired from Drosophila melanogaster
64% identity, 12% coverage
Bm8528 Uncharacterized protein from Brugia malayi
73% identity, 35% coverage
- Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting
Grote, PLoS neglected tropical diseases 2020 - “...5 [Bm2802, OVOC9504], [Bm7179, OVOC394] M5* <L3,L3D6> 93.3 1.23 2.9*10 4 M5348_1.02 (CIS-BP Brugia inferred) Bm8528 Retinal homeobox protein Rx3 [Bm1938, OVOC2080], [Bm8228, C27D6.4], [Bm1559, OVOC7210], [Bm4184, OVOC3386] M6* <L3,L3D6> 33.3 2.03 3.0*10 5 M5221_1.02 (CIS-BP Brugia inferred) Bm4429 Involved in regulation of transcription, DNA-templated and...”
- “...[ 43 ]. Motifs M4.1, M4.2, and M4.3 matched blmp-1. M5 matched a homeobox protein, Bm8528, and M6 matched a nuclear receptor, Bm4429. The 12 motifs are conserved in either C . elegans or O . volvulus ( Table 2 , last column; S4 Table )....”
NP_001079212 pituitary homeobox 3 from Xenopus laevis
65% identity, 25% coverage
PITX3_HUMAN / O75364 Pituitary homeobox 3; Homeobox protein PITX3; Paired-like homeodomain transcription factor 3 from Homo sapiens (Human) (see 2 papers)
NP_005020 pituitary homeobox 3 from Homo sapiens
64% identity, 25% coverage
- function: Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons during development. In addition to its importance during development, it also has roles in the long-term survival and maintenance of the mdDA neurons. Activates NR4A2/NURR1-mediated transcription of genes such as SLC6A3, SLC18A2, TH and DRD2 which are essential for development of mdDA neurons. Acts by decreasing the interaction of NR4A2/NURR1 with the corepressor NCOR2/SMRT which acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state. Essential for the normal lens development and differentiation. Plays a critical role in the maintenance of mitotic activity of lens epithelial cells, fiber cell differentiation and in the control of the temporal and spatial activation of fiber cell-specific crystallins. Positively regulates FOXE3 expression and negatively regulates PROX1 in the anterior lens epithelium, preventing activation of CDKN1B/P27Kip1 and CDKN1C/P57Kip2 and thus maintains lens epithelial cells in cell cycle (By similarity).
subunit: Interacts with SFPQ. - Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts.
Berry, Eye (London, England) 2022 - GeneRIF: Variants in PAX6, PITX3 and HSF4 causing autosomal dominant congenital cataracts.
- Complementation of dopaminergic signaling by Pitx3-GDNF synergy induces dopamine secretion by multipotent Ntera2 cells.
Eskandarian, Journal of cellular biochemistry 2020 (PubMed)- GeneRIF: Complementation of dopaminergic signaling by Pitx3-GDNF synergy induces dopamine secretion by multipotent Ntera2 cells.
- PITX3 mutations associated with autosomal dominant congenital cataract in the Chinese population.
Wu, Molecular medicine reports 2019 - GeneRIF: The functional analysis of these 2 PITX3 mutations in the in vitro functional studies is an important complement and extension, which provides a potential interpretation for the pathogenesis and molecular mechanism of PITX3 mutations associated with CC.
- A novel mutation in the OAR domain of PITX3 associated with congenital posterior subcapsular cataract.
Fan, BMC medical genetics 2019 - GeneRIF: The mutation c.797_814del, p.Ser266_Ala271del is a novel mutation in the conserved DNA-binding OAR domain of PITX3 that causes congenital cataract.
- Identification of PITX3 mutations in individuals with various ocular developmental defects.
Zazo, Ophthalmic genetics 2018 (PubMed)- GeneRIF: Heterozygous mutation in the PITX3 gene is associated with ocular developmental defects.
- Genetic analysis of PITX3 variants in patients with essential tremor.
Chen, Acta neurologica Scandinavica 2017 (PubMed)- GeneRIF: PITX3 variants rs3758549 and rs4919621 are not associated with ET in Chinese Han population.
- PITX3 DNA methylation is an independent predictor of overall survival in patients with head and neck squamous cell carcinoma.
Sailer, Clinical epigenetics 2017 - GeneRIF: Study showed that PITX3 methylation was significantly methylated in head and neck squamous cell carcinoma (HNSCC) tumor compared to normal adjacent tissue and correlated with lymph node status. These results provide evidence that PITX3 DNA methylation is an independent prognostic biomarker for overall survival in patients with HNSCC and might aid in the process of risk stratification for individualized treatment.
- Whole Exome Sequencing Identifies a Novel Mutation in the PITX3 Gene, Causing Autosomal Dominant Congenital Cataracts in a Chinese Family.
Liu, Annals of clinical and laboratory science 2017 (PubMed)- GeneRIF: These findings suggest that p.A203fs in PITX3 is the cause of cataracts in the recruited family.
- More
PITX3_MOUSE / O35160 Pituitary homeobox 3; Homeobox protein PITX3; Paired-like homeodomain transcription factor 3 from Mus musculus (Mouse) (see 6 papers)
NP_032878 pituitary homeobox 3 from Mus musculus
64% identity, 25% coverage
- function: Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons during development. In addition to its importance during development, it also has roles in the long-term survival and maintenance of the mdDA neurons. Activates NR4A2/NURR1-mediated transcription of genes such as SLC6A3, SLC18A2, TH and DRD2 which are essential for development of mdDA neurons. Acts by decreasing the interaction of NR4A2/NURR1 with the corepressor NCOR2/SMRT which acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state. Essential for the normal lens development and differentiation. Plays a critical role in the maintenance of mitotic activity of lens epithelial cells, fiber cell differentiation and in the control of the temporal and spatial activation of fiber cell-specific crystallins. Positively regulates FOXE3 expression and negatively regulates PROX1 in the anterior lens epithelium, preventing activation of CDKN1B/P27Kip1 and CDKN1C/P57Kip2 and thus maintains lens epithelial cells in cell cycle.
subunit: Interacts with SFPQ.
disruption phenotype: Mice show loss of nascent substantia nigra dopaminergic neurons at the beginning of their final differentiation and a loss of tyrosine hydroxylase (TH) expression specifically in the substantia nigra neurons. - Expression of truncated PITX3 in the developing lens leads to microphthalmia and aphakia in mice
Wada, PloS one 2014 - “...acids (aa) is according to the PITX3 aa sequence of the wild-type and miak mice (NP_032878 and AB971349). PITX3 possesses homeodomain (HD, black box) and otp, aristaless, and rax (OAR, light gray box) as major functional domains near the N- and C-termini, respectively. The nonsense mutation...”
PITX3_RAT / P81062 Pituitary homeobox 3; Homeobox protein PITX3; Paired-like homeodomain transcription factor 3 from Rattus norvegicus (Rat) (see paper)
XP_006231540 pituitary homeobox 3 isoform X1 from Rattus norvegicus
64% identity, 25% coverage
- function: Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons during development. In addition to its importance during development, it also has roles in the long-term survival and maintenance of the mdDA neurons. Activates NR4A2/NURR1-mediated transcription of genes such as SLC6A3, SLC18A2, TH and DRD2 which are essential for development of mdDA neurons. Acts by decreasing the interaction of NR4A2/NURR1 with the corepressor NCOR2/SMRT which acts through histone deacetylases (HDACs) to keep promoters of NR4A2/NURR1 target genes in a repressed deacetylated state. Essential for the normal lens development and differentiation. Plays a critical role in the maintenance of mitotic activity of lens epithelial cells, fiber cell differentiation and in the control of the temporal and spatial activation of fiber cell-specific crystallins. Positively regulates FOXE3 expression and negatively regulates PROX1 in the anterior lens epithelium, preventing activation of CDKN1B/P27Kip1 and CDKN1C/P57Kip2 and thus maintains lens epithelial cells in cell cycle (By similarity).
subunit: Interacts with SFPQ. - A homeodomain gene Ptx3 has highly restricted brain expression in mesencephalic dopaminergic neurons.
Smidt, Proceedings of the National Academy of Sciences of the United States of America 1997 - Dysregulation of Dopaminergic Regulatory Factors TH, Nurr1, and Pitx3 in the Ventral Tegmental Area Associated with Neuronal Injury Induced by Chronic Morphine Dependence.
Shi, International journal of molecular sciences 2019 - GeneRIF: a significant reduction in expression of the dopaminergic regulation factors Nurr1 and Pitx3 could not effectively regulate TH in the VTA during chronic morphine dependence, which affects the survival of dopaminergic neurons and ultimately leads to neuronal pathology.
- FoxP1 promotes midbrain identity in embryonic stem cell-derived dopamine neurons by regulating Pitx3.
Konstantoulas, Journal of neurochemistry 2010 (PubMed)- GeneRIF: Thus, this study demonstrates for the first time a transcription regulatory role for FoxP1 on the Pitx3 gene in mammalian stem cells.
- Immunocytochemical expression of dopamine-related transcription factors Pitx3 and Nurr1 in prenatally stressed adult rats.
Katunar, Journal of neuroscience research 2009 (PubMed)- GeneRIF: results show that the expression of both Nurr1 and Pitx3 increased in prenatally stressed adult offspring in the ventral tegmental area, whereas no changes were observed in the substantia nigra area
- Pitx3-transfected astrocytes secrete brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor and protect dopamine neurons in mesencephalon cultures.
Yang, Journal of neuroscience research 2008 (PubMed)- GeneRIF: Pitx3-transfection in astrocytes can up-regulate brain-derived neurotrophic factor and glial cell line-derived neurotrophic factor expression and produce protective benefit to dopamine neurons
- Differential expression of the homeobox gene Pitx3 in midbrain dopaminergic neurons.
Korotkova, The European journal of neuroscience 2005 (PubMed)- GeneRIF: higher Pitx3 expression levels in ventral tegmental area than in substantia nigra neurons may contribute to the different vulnerability of these dopaminergic nuclei to neurodegeneration
XP_006526827 pituitary homeobox 3 isoform X1 from Mus musculus
64% identity, 19% coverage
- The Crucial Roles of Pitx3 in Midbrain Dopaminergic Neuron Development and Parkinson's Disease-Associated Neurodegeneration.
Wang, International journal of molecular sciences 2023 - GeneRIF: The Crucial Roles of Pitx3 in Midbrain Dopaminergic Neuron Development and Parkinson's Disease-Associated Neurodegeneration.
- Activation of CB2R with AM1241 ameliorates neurodegeneration via the Xist/miR-133b-3p/Pitx3 axis.
He, Journal of cellular physiology 2020 (PubMed)- GeneRIF: Activation of CB2R with AM1241 ameliorates neurodegeneration via the Xist/miR-133b-3p/Pitx3 axis.
- Hypomorphic Expression of Pitx3 Disrupts Circadian Clocks and Prevents Metabolic Entrainment of Energy Expenditure.
Del, Cell reports 2019 (PubMed)- GeneRIF: Hypomorphic Expression of Pitx3 Disrupts Circadian Clocks and Prevents Metabolic Entrainment of Energy Expenditure.
- The role of Pitx2 and Pitx3 in muscle stem cells gives new insights into P38α MAP kinase and redox regulation of muscle regeneration.
L'honoré, eLife 2018 - GeneRIF: Using Pitx2/3 single and double mutant mice that provide genetic models of deregulated redox states, we demonstrate that moderate overproduction of ROS results in premature differentiation of satellite cells while high levels lead to their senescence and regenerative failure
- Specificity of Pitx3-Dependent Gene Regulatory Networks in Subsets of Midbrain Dopamine Neurons.
Bifsha, Molecular neurobiology 2017 (PubMed)- GeneRIF: that Pitx3 is co-recruited to regions that foster the formation of GATA-bHLH-BRN complexes, which usually involve Lmo co-regulatory proteins
- Pitx3 and En1 determine the size and molecular programming of the dopaminergic neuronal pool.
Kouwenhoven, PloS one 2017 - GeneRIF: in absence of En1 and Pitx3, only a limited number of Mesodiencephalic dopaminergic neurons are present in mouse embryo.
- Differences in the spatiotemporal expression and epistatic gene regulation of the mesodiencephalic dopaminergic precursor marker PITX3 during chicken and mouse development.
Klafke, Development (Cambridge, England) 2016 (PubMed)- GeneRIF: the sonic hedgehog signaling pathway is both necessary and sufficient for the induction of ectopic PITX3 expression in chick mesencephalon downstream of WNT9A-induced LMX1a transcription.
- Pitx3 deficiency produces decreased dopamine signaling and induces motor deficits in Pitx3(-/-) mice.
Le, Neurobiology of aging 2015 - GeneRIF: Pitx3 is specifically required for DA-related function and, if impaired, Pitx3 could contribute during the pathogenesis of Parkinson's disease.
- More
XP_005164261 homeobox protein unc-4 homolog from Danio rerio
66% identity, 15% coverage
NP_001082023 paired like homeodomain 3 L homeolog from Xenopus laevis
65% identity, 25% coverage
NP_001014693 eyeless, isoform D from Drosophila melanogaster
54% identity, 9% coverage
- Whole exome sequence analysis of Peters anomaly
Weh, Human genetics 2014 - “...(NP_001245391), mouse Pax6-5a (NP_001231127), chicken pax6-5a (NP_990397), zebrafish pax6a (NP_571379), zebrafish pax6b (NP_571716), Drosophila ey (NP_001014693) and Drosophila toy (NP_524638) sequences were used for the alignment; the position of p.(C52Y) is shown with red arrow Fig. 2 a Patient 2: Pedigree and TFAP2A genotypes. DNA chromatograms...”
XP_421631 pituitary homeobox 3 isoform X1 from Gallus gallus
65% identity, 25% coverage
PITX3_DANRE / Q6QU75 Pituitary homeobox 3; Bicoid-like homeodomain transcription factor Pitx3; Homeobox protein PITX3; Paired-like homeodomain transcription factor 3 from Danio rerio (Zebrafish) (Brachydanio rerio) (see 3 papers)
NP_991238 pituitary homeobox 3 from Danio rerio
65% identity, 25% coverage
- function: Transcriptional regulator which may play a role in the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons (By similarity). Required for lens and retinal development and for pituitary pre-placode formation and cell specification.
- Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene
Becker, PloS one 2010 - “...XP_589431 (cattle), XP_001499185 (horse), EDL41981 (mouse), NP_062120 (rat), XP_421631 (chicken), NP_001082023 ( Xenopus laevis ), NP_991238 ( Danio rerio ). Mutation Analysis We designed PCR primers for the amplification of a 14.5 kb segment containing the entire PITX3 gene and determined the genomic sequence of four...”
- Expression and function of nr4a2, lmx1b, and pitx3 in zebrafish dopaminergic and noradrenergic neuronal development.
Filippi, BMC developmental biology 2007 - GeneRIF: while lmx1b paralogues may contribute to the generation of diencephalic dopaminergic precursors. Conversely, knock-down of pitx3 does not specifically affect any diencephalic dopamine cluster
- Zebrafish foxe3: roles in ocular lens morphogenesis through interaction with pitx3.
Shi, Mechanisms of development 2006 (PubMed)- GeneRIF: Data demonstrate that Foxe3 is necessary for lens development in zebrafish and that foxe3 lies genetically downstream of pitx3 in a zebrafish lens development pathway.
- Modulation of zebrafish pitx3 expression in the primordia of the pituitary, lens, olfactory epithelium and cranial ganglia by hedgehog and nodal signaling.
Zilinski, Genesis (New York, N.Y. : 2000) 2005 (PubMed)- GeneRIF: pitx3 expression in the primordia of the pituitary, lens, olfactory mucosa, and cranial ganglia is modulated by hedgehog and nodal proteins' signaling.
- pitx3 defines an equivalence domain for lens and anterior pituitary placode.
Dutta, Development (Cambridge, England) 2005 (PubMed)- GeneRIF: expressing cells constitute an equivalence domain of cells that can form either pituitary or lens
- Zebrafish pitx3 is necessary for normal lens and retinal development.
Shi, Mechanisms of development 2005 (PubMed)- GeneRIF: results demonstrate zebrafish pitx3 represents a true ortholog of the human PITX3 gene and the general function of the Pitx3 protein in lens development is conserved between mammals and the teleost fish
NP_726607 eyeless, isoform B from Drosophila melanogaster
54% identity, 13% coverage
- A multi-gene knockdown approach reveals a new role for Pax6 in controlling organ number in Drosophila.
Ordway, Development (Cambridge, England) 2021 - GeneRIF: A multi-gene knockdown approach reveals a new role for Pax6 in controlling organ number in Drosophila.
- Temporal identity establishes columnar neuron morphology, connectivity, and function in a Drosophila navigation circuit.
Sullivan, eLife 2019 - GeneRIF: We conclude that neurons with similar developmental origin have similar connectivity, that Eyeless maintains equal E-PG and P-EN neuron number, and that Eyeless is required for the development of circuits that control adult navigation.
- Altering the Temporal Regulation of One Transcription Factor Drives Evolutionary Trade-Offs between Head Sensory Organs.
Ramaekers, Developmental cell 2019 (PubMed)- GeneRIF: changes in the temporal regulation of the highly conserved eyeless/Pax6 gene expression during development is a conserved mechanism for sensory trade-offs within and between Drosophila species.
- Homeodomain-interacting protein kinase phosphorylates the Drosophila Paired box protein 6 (Pax6) homologues Twin of eyeless and Eyeless.
Steinmetz, Insect molecular biology 2018 (PubMed)- GeneRIF: This study set Hipk and the master regulators Toy and Ey in an enzyme-substrate relationship. The interaction and phosphorylation of the master regulator Toy by Hipk may be important for precise tuning of signalling within the retinal determination gene network and therefore for Drosophila eye development.
- Polycomb group (PcG) proteins and Pax6 cooperate to inhibit in vivo reprogramming of the developing Drosophila eye.
Zhu, Development (Cambridge, England) 2018 - GeneRIF: The loss of Pax6, but not of Eya, is required for Sfmbt dependent eye-to-wing transformation.
- Eyeless/Pax6 initiates eye formation non-autonomously from the peripodial epithelium.
Baker, Development (Cambridge, England) 2018 - GeneRIF: Loss of Ey within the peripodial epithelium leads to the loss of dpp expression within the eye, failure of the furrow to initiate, and abrogation of retinal development. These findings reveal an unexpected mechanism for how Pax6 controls eye development in Drosophila.
- Integrative genomic analysis reveals novel regulatory mechanisms of eyeless during Drosophila eye development.
Yeung, Nucleic acids research 2018 - GeneRIF: Ey could use multiple molecular mechanisms to regulate target gene expression and pathway function, which might enable Ey to exhibit a greater flexibility in controlling different processes during eye development
- Drosophila Pax6 promotes development of the entire eye-antennal disc, thereby ensuring proper adult head formation.
Zhu, Proceedings of the National Academy of Sciences of the United States of America 2017 - GeneRIF: Pax6 initiates both eye specification and proliferation
- More
PAX6_DROME / O18381 Paired box protein Pax-6; Protein eyeless from Drosophila melanogaster (Fruit fly) (see paper)
54% identity, 9% coverage
- function: Involved in eye morphogenesis.
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “..., 56 , 57 , 58 ]. Identical hexadecapeptide penetratin analog is present in Drosophila O18381, mouse P63015, and human P26367 Pax-6 parent proteins. It is the arginine-rich AR I QV WF S NRR A KW RR sequence (residues identical to Drosophila pAntp penetratin are in...”
- XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis
Sczyrba, BMC genomics 2005 - “...7.10E-49 1 18 36 2636 2 YES NP_729075 CG10625- 1.70E-28 16 1185 37 8386 YES O18381 Eyeless protein 3.90E-70 7 75 38 11614 1 YES P00528 Tyrosine-protein kinase Src64B 4.30E-152 3 150 39 4073 1 NO P10181 Homeobox protein rough 3.10E-14 13 165 40 919 NO...”
Q25411 Pax6-like protein from Lineus sanguineus
61% identity, 20% coverage
- The Pax gene family: Highlights from cephalopods.
Navet, PloS one 2017 - “...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 protein Pax6 Lineus_sanguineus Nemertea_Anopla O96756 DtPax-6 protein Pax6B Girardia_tigrina Platyhelminthes_Rhabditophora Accession: accession number or genome reference. Submitted name: name found in databases. Proposed name: our interpretation (grey background if...”
NP_001158383 paired box 6 from Saccoglossus kowalevskii
66% identity, 14% coverage
T1F6U6 Paired box protein Pax-6 from Helobdella robusta
61% identity, 10% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...Pax2/5/8(f) Helobdella_robusta Annelida_Clitellata T1FMW8 Uncharacterized protein Pax3/7A Helobdella_robusta Annelida_Clitellata T1G8F8 Uncharacterized protein Pax3/7B(f) Helobdella_robusta Annelida_Clitellata T1F6U6 Uncharacterized protein Pax6A Helobdella_robusta Annelida_Clitellata T1G400 Uncharacterized protein Pax6B(f) Helobdella_robusta Annelida_Clitellata T1EHA5 Uncharacterized protein Pax1(f) Helobdella_robusta Annelida_Clitellata T1G182 Uncharacterized protein Pax2(f) Helobdella_robusta Annelida_Clitellata R7VKC0 Uncharacterized protein Pax1/9(f) Capitella_teleta Annelida_Polychaeta R7T7W6...”
VSX1_XENLA / Q0P031 Visual system homeobox 1; Transcription factor vsx1; Xvsx1 from Xenopus laevis (African clawed frog) (see 2 papers)
66% identity, 19% coverage
- function: Involved in the differentiation of bipolar cells, the last neurons of the retina to form. Together with other retinal homeobox proteins, acts as an effector of a cellular clock which, depending on cell cycle progression, establishes the generation of distinct retinal neuronal cell types.
NP_001290114 paired box protein Pax-7 from Meleagris gallopavo
58% identity, 15% coverage
UNC4_DANRE / Q50D79 Homeobox protein unc-4 homolog; Homeobox protein Uncx4.1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_001018616 homeobox protein unc-4 homolog from Danio rerio
58% identity, 18% coverage
ISX_MOUSE / A1A546 Intestine-specific homeobox from Mus musculus (Mouse) (see 2 papers)
NP_082113 intestine-specific homeobox isoform 2 from Mus musculus
59% identity, 30% coverage
XP_018111896 paired box 6 L homeolog isoform X1 from Xenopus laevis
60% identity, 16% coverage
NP_001020793 short stature homeobox protein from Canis lupus familiaris
67% identity, 25% coverage
Q5IGV4 Homeodomain transcription factor PaxC from Nematostella vectensis
64% identity, 15% coverage
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...sequence is present in the Nematostella vectensis (sea anemone) PaxC homeodomain from the transcription factor Q5IGV4. That cnidarian has a variable number of neurons (several hundred at most [ 75 ]) in decentralized nerve nets and poorly understood eyeless photodetection [ 76 ]). Another cnidarian, the...”
- “...of the moonlight [ 77 ]. It is unknown whether the penetratin analog ARIQVWFSNRRAKWRK from Q5IGV4 protein, with a conservative Arg to Lys substitution, plays a role in light sensing by coral larva or not. It would not be surprising that more ancient eyeless vision needed...”
GSBN_DROME / P09083 Protein gooseberry-neuro; BSH4; Protein gooseberry proximal from Drosophila melanogaster (Fruit fly) (see paper)
NP_523862 gooseberry-neuro from Drosophila melanogaster
69% identity, 15% coverage
- function: Expressed in a segmentally repeating pattern to define the polarity of embryonic segments.
- Expression of the Lhx genes apterous and lim1 in an errant polychaete: implications for bilaterian appendage evolution, neural development, and muscle diversification
Winchell, EvoDevo 2013 - “...XP_001626470, XP_971202, NP_523907, NP_001004015, NP_001015899, CAA04012, AAV84105, XP_392622, NP_001139341, NP_001158443, XP_002592485, XP_001635417, AEN75257, NP_001014434, NP_001035099, NP_523862, ACN66454, AAV85467, ABD37012. Expression of Nar - ap At the hatchling stage, Nar - ap mRNAs are distributed widely in the head (Figure 2 A; compare with Figure 2 B)....”
- Differential and redundant functions of gooseberry and gooseberry neuro in the central nervous system and segmentation of the Drosophila embryo.
He, Developmental biology 2013 (PubMed)- GeneRIF: gsb and gsbn share overlapping functions in segmentation and the central nervous system.
- Formation and specification of a Drosophila dopaminergic precursor cell.
Watson, Development (Cambridge, England) 2012 - GeneRIF: Data show that the gooseberry/gooseberry-neuro (gsb/gsb-n) transcription factor genes act to specify MP3 cell fate.
- The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes
Wheat, Molecular and cellular biology 1999 - “...melanogaster Paired (P06601), Gooseberry proximal (Gsb-p; P09083), Gooseberry distal (Gsb-d; P09082), Sparkling (AF010256), Eyeless (X79492), Pox-meso (P23757),...”
V3ZQV3 Uncharacterized protein (Fragment) from Lottia gigantea
XP_009066032 hypothetical protein from Lottia gigantea
62% identity, 18% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...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 protein Pax6 Lineus_sanguineus Nemertea_Anopla O96756 DtPax-6...”
- Cloning and Functional Analysis of Pax6 from the Hydrothermal Vent Tubeworm Ridgeia piscesae
Yuan, PloS one 2016 - “...): CAJ40659; Terebratalia transversa Pax6 ( TtPax6 ): ADZ24784; Lottia gigantea Pax6 ( LgPax6 ): XP_009066032; Cupiennius salei Pax6 ( CsPax6 ): CEH19758; Saccoglossus kowalevskii Pax6 ( SkPax6 ): NP_001158383; Limulus polyphemus Pax6 ( LpPax6 ): XP_013778820; Drosophila melanogaster eyeless ( DmEy ): AAF59318; Mus musculus...”
SHOX_HUMAN / O15266 Short stature homeobox protein; Pseudoautosomal homeobox-containing osteogenic protein; Short stature homeobox-containing protein from Homo sapiens (Human) (see 4 papers)
67% identity, 25% coverage
- function: Controls fundamental aspects of growth and development
- Network Pharmacology Identifies the Mechanisms of Action of Shaoyao Gancao Decoction in the Treatment of Osteoarthritis
Zhu, Medical science monitor : international medical journal of experimental and clinical research 2019 - “...1 Homo sapiens Genecards Q9Y2R2 PTPN22 Protein Tyrosine Phosphatase, Non-Receptor Type 22 Homo sapiens Genecards O15266 SHOX Short Stature Homeobox Homo sapiens Genecards Q93099 HGD Homogentisate 1,2-Dioxygenase Homo sapiens Genecards Supplementary Table 3. SGD compound targets. Gene symbol Herb ABCC2 GC APOB GC ATAD5 GC BAZ2B...”
V4AMZ8 Uncharacterized protein (Fragment) from Lottia gigantea
70% identity, 23% 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...”
XP_012818036 short stature homeobox protein 2 isoform X1 from Xenopus tropicalis
71% identity, 23% coverage
T1G400 Uncharacterized protein from Helobdella robusta
68% identity, 16% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...Pax3/7A Helobdella_robusta Annelida_Clitellata T1G8F8 Uncharacterized protein Pax3/7B(f) Helobdella_robusta Annelida_Clitellata T1F6U6 Uncharacterized protein Pax6A Helobdella_robusta Annelida_Clitellata T1G400 Uncharacterized protein Pax6B(f) Helobdella_robusta Annelida_Clitellata T1EHA5 Uncharacterized protein Pax1(f) Helobdella_robusta Annelida_Clitellata T1G182 Uncharacterized protein 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...”
NP_006874 short stature homeobox protein isoform SHOXb from Homo sapiens
67% identity, 32% coverage
- SHOX Variations in Idiopathic Short Stature in North India and a Review of Cases from Asian Countries
Srivastava, Journal of clinical research in pediatric endocrinology 2024 - GeneRIF: SHOX Variations in Idiopathic Short Stature in North India and a Review of Cases from Asian Countries.
- Expression levels and DNA methylation profiles of the growth gene SHOX in cartilage tissues and chondrocytes.
Hattori, Scientific reports 2024 - GeneRIF: Expression levels and DNA methylation profiles of the growth gene SHOX in cartilage tissues and chondrocytes.
- Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
Li, Genes 2023 - GeneRIF: Genetic Analysis and Sonography Characteristics in Fetus with SHOX Haploinsufficiency.
- Leri-Weill Dyschondrosteosis Caused by a Leaky Homozygous SHOX Splice-Site Variant.
Vodopiutz, Genes 2023 - GeneRIF: Leri-Weill Dyschondrosteosis Caused by a Leaky Homozygous SHOX Splice-Site Variant.
- Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability.
Dantas, European journal of endocrinology 2023 (PubMed)- GeneRIF: Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability.
- Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis.
Fanelli, Molecular genetics & genomic medicine 2022 - GeneRIF: Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Leri-Weill dyschondrosteosis.
- Adult Height of Patients with SHOX Haploinsufficiency with or without GH Therapy: A Real-World Single-Center Study.
Dantas, Hormone research in paediatrics 2022 (PubMed)- GeneRIF: Adult Height of Patients with SHOX Haploinsufficiency with or without GH Therapy: A Real-World Single-Center Study.
- Evidence of intrauterine growth restriction and growth hormone deficiency in 49,XXXXY syndrome.
Counts, American journal of medical genetics. Part A 2021 (PubMed)- GeneRIF: Evidence of intrauterine growth restriction and growth hormone deficiency in 49,XXXXY syndrome.
- More
PAX6_CHICK / P47237 Paired box protein Pax-6 from Gallus gallus (Chicken) (see paper)
65% identity, 30% coverage
- function: May be a transcription factor with important functions in eye and nasal development
subunit: Interacts with MAF.
NP_001091013 paired box gene 6 from Canis lupus familiaris
60% identity, 17% coverage
NP_001231127 paired box protein Pax-6 isoform 1 from Mus musculus
NP_001231129 paired box protein Pax-6 isoform 1 from Mus musculus
60% identity, 17% coverage
- Characterization of neural damage and neuroinflammation in Pax6 small-eye mice.
Cole, Experimental eye research 2024 - GeneRIF: Characterization of neural damage and neuroinflammation in Pax6 small-eye mice.
- A positive feedback inhibition of isocitrate dehydrogenase 3β on paired-box gene 6 promotes Alzheimer-like pathology.
Wang, Signal transduction and targeted therapy 2024 - GeneRIF: A positive feedback inhibition of isocitrate dehydrogenase 3beta on paired-box gene 6 promotes Alzheimer-like pathology.
- IGF2BP2 Maintains Retinal Pigment Epithelium Homeostasis by Stabilizing PAX6 and OTX2.
Wu, Investigative ophthalmology & visual science 2024 - GeneRIF: IGF2BP2 Maintains Retinal Pigment Epithelium Homeostasis by Stabilizing PAX6 and OTX2.
- Effects of miR-204-5p modulation on PAX6 regulation and corneal inflammation.
Abbasi, Scientific reports 2024 - GeneRIF: Effects of miR-204-5p modulation on PAX6 regulation and corneal inflammation.
- Long noncoding RNA MALAT1 inhibition attenuates sepsis-induced acute lung injury through modulating the miR-129-5p/PAX6/ZEB2 axis.
Li, Microbiology and immunology 2023 (PubMed)- GeneRIF: Long noncoding RNA MALAT1 inhibition attenuates sepsis-induced acute lung injury through modulating the miR-129-5p/PAX6/ZEB2 axis.
- Pregnenolone enhances the proliferation of mouse neural stem cells and promotes oligodendrogenesis, together with Sox10, and neurogenesis, along with Notch1 and Pax6.
Negintaji, Neurochemistry international 2023 (PubMed)- GeneRIF: Pregnenolone enhances the proliferation of mouse neural stem cells and promotes oligodendrogenesis, together with Sox10, and neurogenesis, along with Notch1 and Pax6.
- Pax6 affects Ras-Raf-ERK1/2 in mouse aging brain.
Srivastava, Biogerontology 2023 (PubMed)- GeneRIF: Pax6 affects Ras-Raf-ERK1/2 in mouse aging brain.
- Autoregulation of Pax6 in neuronal cells is mediated by Pax6(5a), Pax6(ΔPD), SPARC, and p53.
Shukla, Molecular biology reports 2022 (PubMed)- GeneRIF: Autoregulation of Pax6 in neuronal cells is mediated by Pax6(5a), Pax6(DeltaPD), SPARC, and p53.
- More
- Proteomic and microRNA-omic profiles and potential mechanisms of dysfunction in pancreatic islet cells primed by inflammation
Ding, Experimental and therapeutic medicine 2021 - “...Forward: CCCCAGTTTACAAGCTCGCT 177 Reverse: CTCGGTTCCATTCGGGAAAGG Mouse Gcg NP_032126 Forward: TTACTTTGTGGCTGGATTGCTT 149 Reverse: AGTGGCGTTTGTCTTCATTCA Mouse Pax-6 NP_001231129 Forward: GCAGATGCAAAAGTCCAGGTG 285 Reverse: CAGGTTGCGAAGAACTCTGTTT Mouse Snap25 NP_035558 Forward: CAACTGGAACGCATTGAGGAA 177 Reverse: GGCCACTACTCCATCCTGATTAT Mouse Mafa NP_919331 Forward: AGGAGGGTCATCCGACTG 113 Reverse: CTTCTCGCTCCAGAATGTG Mouse Ins2 NP_001172013 Forward: GCTTCTTCTACACACCCATGTC 147 Reverse: AGCACTGATCTACAATGCCAC Mouse...”
O60902 Short stature homeobox protein 2 from Homo sapiens
68% identity, 21% coverage
- Dysregulated Tear Film Proteins in Macular Edema Due to the Neovascular Age-Related Macular Degeneration Are Involved in the Regulation of Protein Clearance, Inflammation, and Neovascularization.
Winiarczyk, Journal of clinical medicine 2021 - “...12 124,925 96,246 5.52 6.41 16 12 0.560 0.037 32 Short stature homeobox protein 2 O60902 H. sapiens 65 5 35,160 8.99 12 0.529 0.041 Abbreviations: MWmolecular weight; pIisoelectric point; Seq. Covsequence coverage; Rtratio. jcm-10-03060-t002_Table 2 Table 2 AMD group up- and downregulated proteins. Identified Protein...”
- A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.
Yao, BMC genomics 2007 - “...-1 5.99E-06 Hs.432862 MARCH-VI: O60337 RING-CH protein VI 2091 4245 2.03 -1 4.97E-09 Hs.55967 SHOX2: O60902 Short stature homeobox 2 58 137 2.38 -1 1.13E-12 Hs.443625 COL3A1: P02461 Collagen, type III, alpha 1 638 1538 2.41 -1 2.06E-04 Hs.252418 ELN: P15502 Elastin 35 117 3.34 -1...”
- An unappreciated role for RNA surveillance.
Hillman, Genome biology 2004 - “...NM_015833 O15126 SCA1_HUMAN 2 SCAMP1; SCAMP NM_052822 Q13243 SFR5_HUMAN SRP40 2 SFRS5; SRP40; HRS NM_006925 O60902 SHX2_HUMAN MAJOR SHOX2; SHOT; OG12X NM_006884 Q13425 SNB2_HUMAN 2 SNTB2; SNT2B2 NM_130845 Q9Y5W8 SNXD_HUMAN 2 SNX13; KIAA0713 NM_015132 P18583 SON_HUMAN E SON; NREBP; DBP5; C21ORF50; KIAA1019 NM_058183 C NM_138926 Q15528...”
NP_037160 short stature homeobox protein 2 from Rattus norvegicus
68% identity, 21% coverage
HM08_CAEEL / Q94398 Homeobox protein ceh-8 from Caenorhabditis elegans (see paper)
60% identity, 26% coverage
- function: Required for cell specification of the RIA interneurons.
SHOX2_MOUSE / P70390 Short stature homeobox protein 2; Homeobox protein Og12X; OG-12; Paired family homeodomain protein Prx3 from Mus musculus (Mouse) (see paper)
P70390 glutaredoxin-dependent peroxiredoxin (EC 1.11.1.25) from Mus musculus (see paper)
68% identity, 21% coverage
XP_012307699 paired box protein Pax-6 isoform X2 from Aotus nancymaae
60% identity, 17% coverage
VSX2_MOUSE / Q61412 Visual system homeobox 2; Ceh-10 homeodomain-containing homolog; Homeobox protein CHX10 from Mus musculus (Mouse) (see 8 papers)
72% identity, 16% coverage
- function: Acts as a transcriptional regulator through binding to DNA at the consensus sequence 5'-[TC]TAATT[AG][AG]-3' upstream of gene promoters (PubMed:17919464, PubMed:18539116). Plays a significant role in the specification and morphogenesis of the sensory retina (PubMed:8630490). May play a role in specification of V2a interneurons during spinal cord development (PubMed:18539116). Mediates differentiation of V2a interneurons by repression of motor neuron gene transcription, via competitively binding to response elements that are activated by the ISL1-LHX3 complex, such as VSX1 and MNX1 (PubMed:17919464, PubMed:18539116, PubMed:27477290). Acts as a positive transcriptional regulator of NXNL1; regulation is significantly increased in synergy with VSX1 (PubMed:19843539). Acts as a negative transcriptional regulator of MITF (PubMed:23028343). Represses SAG transcription by competitive inhibition of ISL1-LHX3 response elements (By similarity). Binds to the photoreceptor conserved element-1 (PCE-1) in the promoter of rod photoreceptor arrestin SAG and acts as a transcriptional repressor (PubMed:16236706). Involved in the development of retinal ganglion cells (RGCs) which leads to release of SHH by RGCs, promoting Hedgehog signaling and subsequent proliferation of retinal progenitor cells (PubMed:18417110). Participates in the development of the cells of the inner nuclear layer, by promoting postnatal differentiation of bipolar cells with a comparable inhibition of rod cell differentiation (PubMed:16547132, PubMed:8630490). May play a role in the maintenance of neural retina identity during development by regulation of canonical Wnt genes and CTNNB1 localization, suggesting a role in the regulation of canonical Wnt signaling (By similarity).
subunit: Interacts with MITF.
disruption phenotype: RNAi-mediated knockdown in the retina of newborn mice results in an increase in the number of photoreceptor cells as a result of a decrease in the number of bipolar cells and a comparable increase in rod cells at postnatal day 21. - Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...P15409 Rho rhodopsin 244 photoreceptor required for vision at low light intensity -- 1 isoform Q61412 Vsx2 visual system homeobox 2 162 role in specification and morphogenesis of sensory retina defects in Vsx2 are cause of ocular retardation (OR(J)), a disease with microphthalmia, retinal destruction, and...”
NP_571537 visual system homeobox 2 from Danio rerio
72% identity, 15% coverage
- Mutual antagonism of the paired-type homeobox genes, vsx2 and dmbx1, regulates retinal progenitor cell cycle exit upstream of ccnd1 expression.
Wong, Developmental biology 2015 (PubMed)- GeneRIF: Mutual antagonism of the paired-type homeobox genes, vsx2 and dmbx1, regulates retinal progenitor cell cycle exit upstream of ccnd1 expression.
- Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis.
Gago-Rodrigues, Nature communications 2015 (PubMed)- GeneRIF: These data support a model by which vsx2, operating through the effector gene opo, acts as a central transcriptional node that coordinates neural retina patterning and optic cup invagination in zebrafish.
- Vsx2 in the zebrafish retina: restricted lineages through derepression.
Vitorino, Neural development 2009 - GeneRIF: Vsx2-positive RPCs are fully multipotent retinal progenitors and that when Vsx2 is downregulated, Vsx2-negative progenitors escape Vsx2 repression and so are able to express factors that restrict lineage potential.
PAX6_HUMAN / P26367 Paired box protein Pax-6; Aniridia type II protein; Oculorhombin from Homo sapiens (Human) (see 26 papers)
PAX6_MOUSE / P63015 Paired box protein Pax-6; Oculorhombin from Mus musculus (Mouse) (see 6 papers)
NP_001121084 paired box protein Pax-6 isoform a from Homo sapiens
NP_000271 paired box protein Pax-6 isoform a from Homo sapiens
NP_001253186 paired box protein Pax-6 from Macaca mulatta
60% identity, 17% coverage
- function: Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells (By similarity). Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Acts as a transcriptional repressor of NFATC1- mediated gene expression (By similarity).
subunit: Interacts with MAF and MAFB (By similarity). Interacts with TRIM11; this interaction leads to ubiquitination and proteasomal degradation, as well as inhibition of transactivation, possibly in part by preventing PAX6 binding to consensus DNA sequences (By similarity). Interacts with TLE6/GRG6 (By similarity). - function: Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells (PubMed:9163426). Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains (By similarity). Acts as a transcriptional repressor of NFATC1-mediated gene expression (PubMed:23990468).
subunit: Interacts with MAF and MAFB (PubMed:17901057). Interacts with TRIM11; this interaction leads to ubiquitination and proteasomal degradation, as well as inhibition of transactivation, possibly in part by preventing PAX6 binding to consensus DNA sequences (PubMed:18628401). Interacts with TLE6/GRG6 (PubMed:23990468). - Reduction of lens size in PAX6-related aniridia.
Duncan, Experimental eye research 2024 - GeneRIF: Reduction of lens size in PAX6-related aniridia.
- Novel and recurrent variants in PAX6 in four patients with ocular phenotypes from Southeast Asia.
Goh, Clinical dysmorphology 2024 (PubMed)- GeneRIF: Novel and recurrent variants in PAX6 in four patients with ocular phenotypes from Southeast Asia.
- PAX6 gene promoter methylation is correlated with myopia in Chinese adolescents: a pilot sutdy.
Jiang, Ophthalmic genetics 2024 (PubMed)- GeneRIF: PAX6 gene promoter methylation is correlated with myopia in Chinese adolescents: a pilot sutdy.
- A positive feedback inhibition of isocitrate dehydrogenase 3β on paired-box gene 6 promotes Alzheimer-like pathology.
Wang, Signal transduction and targeted therapy 2024 - GeneRIF: A positive feedback inhibition of isocitrate dehydrogenase 3beta on paired-box gene 6 promotes Alzheimer-like pathology.
- PAX6 promotes neuroendocrine phenotypes of prostate cancer via enhancing MET/STAT5A-mediated chromatin accessibility.
Jing, Journal of experimental & clinical cancer research : CR 2024 - GeneRIF: PAX6 promotes neuroendocrine phenotypes of prostate cancer via enhancing MET/STAT5A-mediated chromatin accessibility.
- Analysis of Phenotypes Associated with Deficiency of PAX6 Haplotypes in Chinese Aniridia Families.
Hao, Current medical science 2024 (PubMed)- GeneRIF: Analysis of Phenotypes Associated with Deficiency of PAX6 Haplotypes in Chinese Aniridia Families.
- The Systemic Genotype-Phenotype Characterization of PAX6-Related Eye Disease in 164 Chinese Families.
Jiang, Investigative ophthalmology & visual science 2024 - GeneRIF: The Systemic Genotype-Phenotype Characterization of PAX6-Related Eye Disease in 164 Chinese Families.
- PAX6-WNK2 Axis Governs Corneal Epithelial Homeostasis.
Zhu, Investigative ophthalmology & visual science 2024 - GeneRIF: PAX6-WNK2 Axis Governs Corneal Epithelial Homeostasis.
- More
- Cloning and Functional Analysis of Pax6 from the Hydrothermal Vent Tubeworm Ridgeia piscesae
Yuan, PloS one 2016 - “...): XP_012307699; Xenopus laevis Pax6 ( XlPax6 ): AF154555; Homo sapiens Pax6 ( HsPax6 ): NP_000271; Platynereis dumerilii Pax6 ( PdPax6 ): CAJ40659; Terebratalia transversa Pax6 ( TtPax6 ): ADZ24784; Lottia gigantea Pax6 ( LgPax6 ): XP_009066032; Cupiennius salei Pax6 ( CsPax6 ): CEH19758; Saccoglossus kowalevskii...”
- Mutation analysis of paired box 6 gene in inherited aniridia in northern China
Chen, Molecular vision 2013 - “...species included Rattus norvegicus ( NP_037133.1 ), Bos taurus ( NP_001035735.1 ), Macaca mulatta ( NP_001253186 ), Xenopus (Silurana) tropicalis ( NP_001006763.1 ), Sus scrofa ( NP_001231102.1 ), Cricetulus griseus ( XP_003497614.1 ), and Anolis carolinensis ( XP_003214735.1 ). Paired box 6 gene messenger ribonucleic acid...”
- Variant effect predictor correlation with functional assays is reflective of clinical classification performance.
Livesey, Genome biology 2025 - Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...58 ]. Identical hexadecapeptide penetratin analog is present in Drosophila O18381, mouse P63015, and human P26367 Pax-6 parent proteins. It is the arginine-rich AR I QV WF S NRR A KW RR sequence (residues identical to Drosophila pAntp penetratin are in a bold font). We can...”
- Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA-protein interaction.
Williamson, Genetics in medicine : official journal of the American College of Medical Genetics 2020 - “...of the pathogenic and putatively benign (gnomAD) variants in the primary PAX6 isoform (Uniprot ID: P26367). The predicted properties of all variants are provided in Table S2 . To assess evolutionary conservation of PAX6 residues among orthologous proteins, 124 sequences from Ensembl Compara were used (...”
- 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 - “...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, particularly eye 5449 POU1F1 Y N P28069 POU hsa_V$POU1F1_Q6 Brain and pituitary development 6667 SP1 N Y P08047 zfC2H2 hsa_GGGCGGR_V$SP1_Q6, hsa_V$SP1_Q6, hsa_V$SP1_Q6_01 Cell cycle 6736...”
- Priorities and trends in the study of proteins in eye research, 1924-2014
Semba, Proteomics. Clinical applications 2015 - “...1 , 2 UniProt ID Gene Protein name Citations Functions Associated diseases Isoforms, PTMs, variants P26367 PAX6 paired box protein PAX-6 204 transcription factor aniridia; Peters anomaly; foveal hypoplasia 1; keratitis hereditary; coloboma of iris, choroid, and retina; coloboma of optic nerve; bilateral optic nerve hypoplasia;...”
- DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors.
Narasimhan, Nucleic acids research 2015 - “...Pax paralogs marking secondary structure elements above the alignment. Numbering corresponds to human PAX6 uniprot-ID P26367 for easier reference to eye diseases mutations. Red bars mark the Asn17 and Gly18 di-peptide binding to the di-nucleotide switch and residues previously shown to provide discriminatory sequence recognition between...”
- Explorative search of distributed bio-data to answer complex biomedical questions.
Masseroli, BMC bioinformatics 2014 - “...setting input parameter values with the human Paired box protein Pax-6 isoform a protein [UniProt: P26367 ] ID as amino acid sequence X , tumor as pathological biological condition Y , and regulation of apoptotic process as biological process Z . Unpredictably, in the bio-data then...”
- The Diabetes-Linked Transcription Factor PAX4: From Gene to Functional Consequences.
Lorenzo, Genes 2017 - “...homeodomain (HD). ( B ) Alignment of mouse PAX4 (UniProtKB P32115) and mouse PAX6 (UniProtKB P63015) protein sequences using Clustal Omega Analysis Tool Web Services from the EMBL-EBI. Conservation code: {*} fully conserved residue {:} conservation between groups of strongly similar properties and {.} conservation between...”
- Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...1 , 2 UniProt ID Gene Protein name Citations Functions Associated diseases in mice Isoforms P63015 Pax6 paired box protein Pax-6 653 transcription factor involved in development of eye and other organs defects in Pax6 cause condition of small eye (Sey) with lack of eyes and...”
- The pathologic effect of a novel neomorphic Fgf9(Y162C) allele is restricted to decreased vision and retarded lens growth.
Puk, PloS one 2011 - “...expression of p27 kip1 (UniProt: P46414), p57 kip2 (UniProt: P49919), Prox1 (UniProt: P48437), Pax6 (UniProt: P63015), c-Maf (UniProt: P54843), E-cadherin (UniProt: P09803), and crystallins (UniProt: P24622, P02525, and P04345) [41] . In conlcusion, the Fgf9 Y162 mouse line described here provides a novel Fgf9 allele with...”
- Niche-independent symmetrical self-renewal of a mammalian tissue stem cell
Conti, PLoS biology 2005 - “...Fgf2 (bFGF) (P15655), Gad1 (Gad67) (P48318), Gfap (P03995), Nanog (Q7TN85), Nestin (Q6P5H2), Olig2 (Q9EQW6), Pax6 (P63015), Pax7 (P47239), Pou5f1 (Oct4, Oct3/4) (P20263), Slc1a3 (Glast) (P56564), Sox1 (P53783), Sox2 (P48432), Sox3 (P53784), and Vim (P20152). We are indebted to Helen Mardon, Barbara Evans, and Janet Carver at...”
NP_001289286 short stature homeobox protein 2 isoform 2 from Mus musculus
69% identity, 21% coverage
- A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
Abassah-Oppong, Nature communications 2024 - GeneRIF: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
- The Transcription Factor Shox2 Shapes Neuron Firing Properties and Suppresses Seizures by Regulation of Key Ion Channels in Thalamocortical Neurons.
Yu, Cerebral cortex (New York, N.Y. : 1991) 2021 - GeneRIF: The Transcription Factor Shox2 Shapes Neuron Firing Properties and Suppresses Seizures by Regulation of Key Ion Channels in Thalamocortical Neurons.
- Conjugated activation of myocardial-specific transcription of Gja5 by a pair of Nkx2-5-Shox2 co-responsive elements.
Yang, Developmental biology 2020 - GeneRIF: Conjugated activation of myocardial-specific transcription of Gja5 by a pair of Nkx2-5-Shox2 co-responsive elements.
- Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice.
Fahrner, JCI insight 2019 - GeneRIF: Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice.
- Shox2 regulates osteogenic differentiation and pattern formation during hard palate development in mice.
Xu, The Journal of biological chemistry 2019 - GeneRIF: Data suggest that short stature homeobox 2 (Shox2) controls osteogenesis of a cell lineage and contributes to the palatine process of the maxilla by regulate skeletogenic gene expression and to pattern the hard palate.
- Spinal Shox2 interneuron interconnectivity related to function and development.
Ha, eLife 2018 - GeneRIF: gap junctional coupling promotes synchronization of Shox2 interneurons, and may be implicated in locomotor rhythmicity in developing mice.
- Comparative expression analysis of Shox2-deficient embryonic stem cell-derived sinoatrial node-like cells.
Hoffmann, Stem cell research 2017 (PubMed)- GeneRIF: Shox2(+/+) and Shox2(-/-) embryonic stem cell clones were isolated and differentiated according to five different protocols in order to evaluate the most efficient enrichment of sinoatrial node-like cells. .
- A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.
Ye, Development (Cambridge, England) 2016 - GeneRIF: Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.
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NP_001157150 short stature homeobox protein 2 isoform c from Homo sapiens
69% identity, 21% coverage
- Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Abril, BMC genomics 2010 - “...protein [Schistosoma mansoni] XP_002578694 4,00E-25 F6AJIXP02HZIDG short stature 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...”
VSX2_DANRE / O42477 Visual system homeobox 2; Ceh-10 homeodomain-containing homolog; Homeobox protein ALX; Homeobox protein CHX10; Transcription factor VSX2 from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
72% identity, 15% coverage
- function: Acts as a transcriptional regulator (By similarity). Mediates the differentiation of V2a interneurons (By similarity). Plays a role in eye development and organization of the neuroretina (PubMed:17919464, PubMed:9203137).
disruption phenotype: Morpholino knockdown causes a decrease in eye size and an increase in expression of vsx1 and ccnd1 at 24 hours post- fertilization.
VSX2_CHICK / Q9IAL1 Visual system homeobox 2; Ceh-10 homeodomain-containing homolog; Homeobox protein CHX10 from Gallus gallus (Chicken) (see paper)
NP_990099 visual system homeobox 2 from Gallus gallus
72% identity, 15% coverage
VSX2_HUMAN / P58304 Visual system homeobox 2; Ceh-10 homeodomain-containing homolog; Homeobox protein CHX10 from Homo sapiens (Human) (see 8 papers)
NP_878314 visual system homeobox 2 from Homo sapiens
72% identity, 16% coverage
- function: Acts as a transcriptional regulator through binding to DNA at the consensus sequence 5'-[TC]TAATT[AG][AG]-3' upstream of gene promoters (PubMed:27301076). Plays a significant role in the specification and morphogenesis of the sensory retina (By similarity). May play a role in specification of V2a interneurons during spinal cord development (By similarity). Mediates differentiation of V2a interneurons by repression of motor neuron gene transcription, via competitively binding to response elements that are activated by the ISL1-LHX3 complex, such as VSX1 (PubMed:17919464, PubMed:27477290). Acts as a positive transcriptional regulator of NXNL1; regulation is significantly increased in synergy with VSX1 (By similarity). Acts as a negative transcriptional regulator of MITF (By similarity). Represses SAG transcription by competitive inhibition of ISL1-LHX3 response elements (PubMed:16236706, PubMed:27477290). Binds to the photoreceptor conserved element-1 (PCE-1) in the promoter of rod photoreceptor arrestin SAG and acts as a transcriptional repressor (By similarity). Involved in the development of retinal ganglion cells (RGCs) which leads to release of SHH by RGCs, promoting Hedgehog signaling and subsequent proliferation of retinal progenitor cells (By similarity). Participates in the development of the cells of the inner nuclear layer, by promoting postnatal differentiation of bipolar cells with a comparable inhibition of rod cell differentiation (By similarity). May play a role in the maintenance of neural retina identity during development by regulation of canonical Wnt genes and CTNNB1 localization, suggesting a role in the regulation of canonical Wnt signaling (PubMed:27301076).
subunit: Interacts with MITF. - Identification of perioperative neurocognitive dysfunction biomarkers in cerebrospinal fluid with quantitative proteomic approach in patients undergoing transurethral resection of prostate with combined spinal and epidural analgesia
Luo, Medicine 2022 - “...0.38 60kDa heat shock protein, mitochondrial P07237 26 P07237 Down 1037 0.39 0.49 Protein disulfide-isomerase P58304 27 P58304 Down 453 0.26 0.29 Visual system homeobox 2 Q93088 28 Q93088 Down 839 0.46 0.60 Betaine--homocysteine S-methyltransferase 1 P02647 29 P02647 Down 0.76 0.69 Apolipoprotein A-I P05787 30...”
- Dog Tear Film Proteome In-Depth Analysis.
Winiarczyk, PloS one 2015 - “...sequence-binding protein 2-like Q93073 34 4 SECISBP2L RNA binding unclassified 3 Visual system homeobox 2 P58304 51 6 VSX2 DNA binding transcription 4 Tensin-1 Q9HBL0 61 11 TNS1 RNA binding unclassified 5 Zinc finger protein 780A O75290 34 4 ZNF780A DNA binding transcription 6 Putative homeodomain...”
- Evolutionary conservation of VSX2 super-enhancer modules in retinal development.
Honnell, Development (Cambridge, England) 2024 - GeneRIF: Evolutionary conservation of VSX2 super-enhancer modules in retinal development.
- Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis.
Bian, Development (Cambridge, England) 2022 - GeneRIF: Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis.
- Association of Missense Variants in VSX2 With a Peculiar Form of Congenital Stationary Night Blindness Affecting All Bipolar Cells.
Smirnov, JAMA ophthalmology 2022 - GeneRIF: Association of Missense Variants in VSX2 With a Peculiar Form of Congenital Stationary Night Blindness Affecting All Bipolar Cells.
- Sequence characterization of RET in 117 Chinese Hirschsprung disease families identifies a large burden of de novo and parental mosaic mutations.
Jiang, Orphanet journal of rare diseases 2019 - GeneRIF: These findings expand the clinical and molecular spectrum of RET variants in Hirschsprung disease and reveal a high frequency of RET DNVs in the Chinese population.
- Regulation of WNT Signaling by VSX2 During Optic Vesicle Patterning in Human Induced Pluripotent Stem Cells.
Capowski, Stem cells (Dayton, Ohio) 2016 - GeneRIF: Regulation of WNT signaling by VSX2 during optic vesicle patterning in human induced pluripotent stem cells has been described.
- Lens subluxation and retinal dysfunction in a girl with homozygous VSX2 mutation.
Khan, Ophthalmic genetics 2015 (PubMed)- GeneRIF: The phenotype of this girl is unique and suggests a normal regulatory role for VSX2 in iris, zonule, and cone-rod development.
- VSX2 and ASCL1 Are Indicators of Neurogenic Competence in Human Retinal Progenitor Cultures.
Wright, PloS one 2015 - GeneRIF: marker for neurogenic potential in cultured retinal progenitor cells
- Modeling human retinal development with patient-specific induced pluripotent stem cells reveals multiple roles for visual system homeobox 2.
Phillips, Stem cells (Dayton, Ohio) 2014 - GeneRIF: The role of visual system homeobox 2 (VSX2), using human induced pluripotent stem cells derived from a patient with microphthalmia caused by an R200Q mutation in the VSX2 homeodomain region, is reported.
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UNC4_DROME / O77215 Homeobox protein unc-4; Paired-like homeodomain protein unc-4; DPHD-1 from Drosophila melanogaster (Fruit fly) (see paper)
74% identity, 10% coverage
- function: Transcription factor that regulates synaptic specificity.
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
Jarnot, Briefings in bioinformatics 2022 - “...QLQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAHAQ AQAQAQAQAQAQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQLQPLPRQ QLQQ P14922 * 2 GAGGGGGGGGGGGGSGGGGGGGGAGGAGGAAAAAAGAGAVAAQAQAQAA AAAAAAAAAAAGGGGGGGYGSSSSGYGV E9Q4N7 * 201(301 cluster) AAAAAAAAAAAAAAA P35453 GGGGGGGGGTGGGGGGG O77215 3 QQQQQQQEQKQQLQQQQQQQQQLQQQQQQQQQQ P04725 3 (233 cluster) LQQLQQQQQLQQQQQLQQQQQQQLQQQQQLQQQQLQQQQQQQQLQQQQQ QQLQQQQQQLQQQQQQQQQQFQQQQQQQQ O14686 * LQRQRQQQQLQQQQQQQLQQQQ P52288 4 LQQQLSQQQQQLSQQQQQQQQLSQQQQQQLSQQQQQQLSQQQQQQLSQQ QQQQ Q9ZTX8 * 1 (743 cluster) 5 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS Q8BTI8 119 (11 cluster) SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS...”
PAX6_RAT / P63016 Paired box protein Pax-6; Oculorhombin from Rattus norvegicus (Rat) (see 4 papers)
60% identity, 17% coverage
- function: Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells. Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters (By similarity). Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains. Acts as a transcriptional repressor of NFATC1-mediated gene expression (By similarity).
subunit: Interacts with MAF and MAFB (By similarity). Interacts with TRIM11; this interaction leads to ubiquitination and proteasomal degradation, as well as inhibition of transactivation, possibly in part by preventing PAX6 binding to consensus DNA sequences (By similarity). Interacts with TLE6/GRG6 (By similarity).
XP_006713790 short stature homeobox protein 2 isoform X1 from Homo sapiens
69% identity, 20% coverage
- Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma.
Zhao, BMC cancer 2024 - GeneRIF: Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma.
- A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
Abassah-Oppong, Nature communications 2024 - GeneRIF: A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival.
- Downregulation of short-stature homeobox protein 2 suppresses gastric cancer cell growth and stemness in vitro and in vivo via inactivating wnt/β-catenin signaling.
Chen, Drug development research 2024 (PubMed)- GeneRIF: Downregulation of short-stature homeobox protein 2 suppresses gastric cancer cell growth and stemness in vitro and in vivo via inactivating wnt/beta-catenin signaling.
- lncRNA SNHG11 promotes the development of colorectal cancer by mediating miR-339-3p/SHOX2.
Yang, Minerva medica 2022 (PubMed)- GeneRIF: lncRNA SNHG11 promotes the development of colorectal cancer by mediating miR-339-3p/SHOX2.
- SHOX2 methylation in Vietnamese patients with lung cancer.
Vo, Molecular biology reports 2022 (PubMed)- GeneRIF: SHOX2 methylation in Vietnamese patients with lung cancer.
- [Diagnostic Efficacy of SHOX2 Gene Hypermethylation for Lung Cancer: A Meta-Analysis].
Liu, Zhongguo fei ai za zhi = Chinese journal of lung cancer 2021 - GeneRIF: [Diagnostic Efficacy of SHOX2 Gene Hypermethylation for Lung Cancer: A Meta-Analysis].
- [SHOX2 promotes migration, invasion and stemness of bladder cancer cells in vitro].
Zhi, Nan fang yi ke da xue xue bao = Journal of Southern Medical University 2021 - GeneRIF: [SHOX2 promotes migration, invasion and stemness of bladder cancer cells in vitro].
- SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3.
Teng, Journal of experimental & clinical cancer research : CR 2021 - GeneRIF: SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3.
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NP_001288356 visual system homeobox 2 isoform 1 from Mus musculus
72% identity, 15% coverage
- Evolutionary conservation of VSX2 super-enhancer modules in retinal development.
Honnell, Development (Cambridge, England) 2024 - GeneRIF: Evolutionary conservation of VSX2 super-enhancer modules in retinal development.
- A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 ocular retardation J mice.
Leung, Developmental dynamics : an official publication of the American Association of Anatomists 2023 - GeneRIF: A framework to identify functional interactors that contribute to disrupted early retinal development in Vsx2 ocular retardation J mice.
- Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis.
Bian, Development (Cambridge, England) 2022 - GeneRIF: Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis.
- Vsx1 and Chx10 paralogs sequentially secure V2 interneuron identity during spinal cord development.
Debrulle, Cellular and molecular life sciences : CMLS 2020 - GeneRIF: Vsx1 and Chx10 paralogs sequentially secure V2 interneuron identity during spinal cord development.
- Genetic chimeras reveal the autonomy requirements for Vsx2 in embryonic retinal progenitor cells.
Sigulinsky, Neural development 2015 - GeneRIF: Vsx2 represses Mitf in a cell-autonomous way. It also uses cell-nonautonomous mechanisms to regulate progenitor properties in the embryonic retina. Vsx2's role in regulating Mitf is in part separable from its role in promoting proliferation.
- Lhx3-Chx10 reticulospinal neurons in locomotor circuits.
Bretzner, The Journal of neuroscience : the official journal of the Society for Neuroscience 2013 - GeneRIF: The results of this study suggested that Lhx3/Chx10 medullary reticular formation neurons are involved in locomotion.
- Restoration of retinal development in Vsx2 deficient mice by reduction of Gdf11 levels.
Santos, Advances in experimental medicine and biology 2012 - GeneRIF: Reducing GDF11 levels might promote restoration of retinal development in the microophthalmic Vsx2 mutant mouse.
- Regulatory role for a conserved motif adjacent to the homeodomain of Hox10 proteins.
Guerreiro, Development (Cambridge, England) 2012 (PubMed)- GeneRIF: analysis of the regulatory role of a conserved motif adjacent to the homeodomain of Hox10 proteins
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XP_017449515 visual system homeobox 2 isoform X1 from Rattus norvegicus
72% identity, 15% coverage
HM10_CAEEL / P41935 Homeobox protein ceh-10 from Caenorhabditis elegans (see 7 papers)
61% identity, 20% coverage
- function: Transcription factor (PubMed:15177025). Binds to a sequence motif, 5'-TTATTGGCTTCGTTAA-3', which may be involved in AIY interneuron function, in the regulatory elements of target genes; binding is more efficient, in vitro, together with LIM/homeobox protein ttx-3 (PubMed:15177025). Required for larval development and for cell fate specification and migration of CAN neurons (PubMed:11493519, PubMed:2361334, PubMed:9475729). Required for generation, or placement, and differentiation of the ALA neuron, and may play a role in ALA axon migration (PubMed:20501595). Involved in development and function of the AIY interneurons, acting by regulating expression of LIM/homeobox protein ttx-3 (PubMed:11493519, PubMed:15177025, PubMed:19386265). Also acts in an autoregulatory feedback loop to maintain its own expression (PubMed:19386265). Modulates lifespan, perhaps acting in the AIY interneurons (PubMed:21055415). Plays a role in fertility and egg- laying behavior (PubMed:21055415).
disruption phenotype: RNAi-mediated knockdown causes severe defects in the ALA neuron in young adults, and when RNAi is begun embryonically, some individuals lack a detectable ALA neuron.
DMBX1_MOUSE / Q91ZK4 Diencephalon/mesencephalon homeobox protein 1; Diencephalon/mesencephalon-expressed brain homeobox gene 1 protein; Orthodenticle homolog 3; Paired-like homeobox protein DMBX1; Paired-type homeobox Atx from Mus musculus (Mouse) (see 8 papers)
XP_017175447 diencephalon/mesencephalon homeobox protein 1 isoform X3 from Mus musculus
65% identity, 18% coverage
- function: Functions as a transcriptional repressor. May repress OTX2- mediated transactivation by forming a heterodimer with OTX2 on the P3C (5'-TAATCCGATTA-3') sequence. Required for brain development, neonatal survival, postnatal growth, and nursing ability.
subunit: Homodimer or heterodimer. Forms heterodimers with OTX2. - Genetic deletion of Autotaxin from CD11b+ cells decreases the severity of experimental autoimmune encephalomyelitis.
Ninou, PloS one 2020 - GeneRIF: ATX genetic deletion from CD11b+ cells attenuated the severity of experimental autoimmune encephalomyelitis (EAE), thus proposing a pathogenic role for the ATX/LPA axis in neuroinflammatory disorders.
- Importance of Adult Dmbx1 in Long-Lasting Orexigenic Effect of Agouti-Related Peptide.
Hirono, Endocrinology 2016 (PubMed)- GeneRIF: Data (including data from studies in transgenic/knockout mice) suggest that expression in adult brain neurons (especially in parabrachial nucleus) of both Dmbx1 and AgRP (agouti-related peptide) is important in appetite regulation leading to leanness.
- Structural basis for specific inhibition of Autotaxin by a DNA aptamer.
Kato, Nature structural & molecular biology 2016 (PubMed)- GeneRIF: The crystal structure of mouse ATX in complex with an anti-ATX aptamer.
- Dmbx1 is essential in agouti-related protein action.
Fujimoto, Proceedings of the National Academy of Sciences of the United States of America 2007 - GeneRIF: Dmbx1 is essential for various actions of agouti-related protein and plays a role in normal regulation of energy homeostasis and behavior
- Functional analysis of transcriptional repressor Otx3/Dmbx1.
Kimura, FEBS letters 2005 (PubMed)- GeneRIF: Otx3/Dmbx1 represses Otx2-mediated transcription in the developing brain
- Neonatal lethality, dwarfism, and abnormal brain development in Dmbx1 mutant mice.
Ohtoshi, Molecular and cellular biology 2004 - GeneRIF: Results demonstrate that Dmbx1 is required for postnatal survival, growth, and brain development.
- Dmbx1, a novel evolutionarily conserved paired-like homeobox gene expressed in the brain of mouse embryos.
Ohtoshi, Mechanisms of development 2002 (PubMed)- GeneRIF: Dmbx1, a novel evolutionarily conserved paired-like homeobox gene is expressed in the brain of mouse embryos. Linkage analysis mapped mouse Dmbx1 to the mid-portion of chromosome 4.
- Mbx, a novel mouse homeobox gene.
Miyamoto, Development genes and evolution 2002 (PubMed)- GeneRIF: provides a useful molecular marker for early mouse midbrain development and may play a critical role in brain development
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DMX1B_DANRE / Q566X8 Diencephalon/mesencephalon homeobox protein 1-B from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_001017625 diencephalon/mesencephalon homeobox protein 1-B from Danio rerio
65% identity, 18% coverage
LOC107439785 diencephalon/mesencephalon homeobox protein 1-A from Parasteatoda tepidariorum
58% identity, 31% coverage
NP_001139175 paired like homeobox 2Ba from Danio rerio
67% identity, 43% coverage
3cmyA / P23760 Structure of a homeodomain in complex with DNA (see paper)
78% identity, 67% coverage
XP_005168876 paired box protein Pax-6b isoform X1 from Danio rerio
60% identity, 16% coverage
- Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
Takamiya, PLoS genetics 2020 - GeneRIF: Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
- Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes.
Lavergne, BMC biology 2020 - GeneRIF: Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes.
- Molecular description of eye defects in the zebrafish Pax6b mutant, sunrise, reveals a Pax6b-dependent genetic network in the developing anterior chamber.
Takamiya, PloS one 2015 - GeneRIF: Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme
- The Pax6b homeodomain is dispensable for pancreatic endocrine cell differentiation in zebrafish.
Verbruggen, The Journal of biological chemistry 2010 - GeneRIF: The Pax6b homeodomain is dispensable for pancreatic endocrine cell differentiation in zebrafish.
- Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence.
Kleinjan, PLoS genetics 2008 - GeneRIF: following a postulated whole-genome duplication event in an ancestral teleost, duplicates pax6a and pax6b encode transcription factors required for eye, brain, olfactory system, and pancreas development
- Expression of zebrafish pax6b in pancreas is regulated by two enhancers containing highly conserved cis-elements bound by PDX1, PBX and PREP factors.
Delporte, BMC developmental biology 2008 - GeneRIF: data indicate a conserved role of enhancers A and C in the pancreatic expression of pax6b and emphasize the importance of the homeoproteins PBX and PREP cooperating with PDX1, in activating pax6b expression in endocrine pancreatic cells
NP_001290437 intestine-specific homeobox from Homo sapiens
62% identity, 27% coverage
- Interaction between retinol intake and ISX rs5755368 polymorphism in colorectal cancer risk: a case-control study in a Korean population.
Bui, Scientific reports 2023 - GeneRIF: Interaction between retinol intake and ISX rs5755368 polymorphism in colorectal cancer risk: a case-control study in a Korean population.
- Impact of bromodomain-containing protein 4 (BRD4) and intestine-specific homeobox (ISX) expression on the prognosis of patients with hepatocellular carcinoma' for better clarity.
Chuang, Cancer medicine 2021 - GeneRIF: Impact of bromodomain-containing protein 4 (BRD4) and intestine-specific homeobox (ISX) expression on the prognosis of patients with hepatocellular carcinoma' for better clarity.
- Phosphorylation of intestine-specific homeobox by ERK1 modulates oncogenic activity and sorafenib resistance.
Wang, Cancer letters 2021 (PubMed)- GeneRIF: Phosphorylation of intestine-specific homeobox by ERK1 modulates oncogenic activity and sorafenib resistance.
- Aryl hydrocarbon receptor promotes hepatocellular carcinoma tumorigenesis by targeting intestine-specific homeobox expression.
Hsu, Molecular carcinogenesis 2017 (PubMed)- GeneRIF: Results show that ISX expression mediated AHR-induced tumorigenesis in hepatocellular carcinoma.
- Intestine-Specific Homeobox Gene ISX Integrates IL6 Signaling, Tryptophan Catabolism, and Immune Suppression.
Wang, Cancer research 2017 (PubMed)- GeneRIF: Overall, our results identified a feed-forward mechanism of immune suppression in hepatocellular carcinoma organized by ISX, which involves kynurenine-AHR signaling and PD-L1, offering insights into immune escape by hepatocellular carcinoma
- Intestine-specific homeobox (ISX) induces intestinal metaplasia and cell proliferation to contribute to gastric carcinogenesis.
Sue, Journal of gastroenterology 2016 (PubMed)- GeneRIF: ISX expression induced by H. pylori infection may lead to intestinal metaplasia and hyperproliferation of gastric mucosa through CDX1/2 and cyclinD1 expression, contributing to gastric carcinogenesis.
- Intestine-specific homeobox (ISX) upregulates E2F1 expression and related oncogenic activities in HCC.
Wang, Oncotarget 2016 - GeneRIF: our results indicate that E2F1 is an important downstream gene of ISX in hepatoma progression.
- Proinflammatory homeobox gene, ISX, regulates tumor growth and survival in hepatocellular carcinoma.
Hsu, Cancer research 2013 (PubMed)- GeneRIF: our results highlight ISX as an important regulator in hepatoma progression with significant potential as a prognostic and therapeutic target in HCCs.
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XP_065401022 paired mesoderm homeobox protein 2B from Macaca fascicularis
53% identity, 19% coverage
DMBX1_CHICK / F1NEA7 Diencephalon/mesencephalon homeobox protein 1 from Gallus gallus (Chicken) (see 2 papers)
65% identity, 19% coverage
- function: Functions as a transcriptional repressor. Required for brain development.
subunit: Homodimer.
XP_005167911 short stature homeobox protein isoform X1 from Danio rerio
65% identity, 24% coverage
DMX1A_DANRE / Q8JI10 Diencephalon/mesencephalon homeobox protein 1-A; Paired homeobox protein 1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
65% identity, 18% coverage
- function: Required for eye and tectum development. May act as a transcriptional repressor.
DMBX1_HUMAN / Q8NFW5 Diencephalon/mesencephalon homeobox protein 1; Orthodenticle homolog 3; Paired-like homeobox protein DMBX1 from Homo sapiens (Human) (see 2 papers)
65% identity, 18% coverage
- function: Functions as a transcriptional repressor. May repress OTX2- mediated transactivation by forming a heterodimer with OTX2 on the P3C (5'-TAATCCGATTA-3') sequence. Required for brain development (By similarity).
subunit: Homodimer or heterodimer. Forms heterodimers with OTX2 (By similarity).
NP_571379 paired box protein Pax-6 from Danio rerio
60% identity, 16% coverage
- Unique activities of two overlapping PAX6 retinal enhancers.
Uttley, Life science alliance 2023 - GeneRIF: Unique activities of two overlapping PAX6 retinal enhancers.
- Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
Takamiya, PLoS genetics 2020 - GeneRIF: Pax6 organizes the anterior eye segment by guiding two distinct neural crest waves.
- Pax6 regulates the formation of the habenular nuclei by controlling the temporospatial expression of Shh in the diencephalon in vertebrates.
Chatterjee, BMC biology 2014 - GeneRIF: Pax6 has an evolutionarily conserved function in establishing the temporospatial expression of Shh in the mid-diencephalic organizer in vertebrates.
- Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences.
Ravi, PLoS genetics 2013 - GeneRIF: morpholino depletion of zebrafish Pax6.2 resulted in a "small eye" phenotype, supporting a role in retinal development.
- Characterization and regulation of the hb9/mnx1 beta-cell progenitor specific enhancer in zebrafish.
Arkhipova, Developmental biology 2012 - GeneRIF: loss of Pax6b or Hb9 independently results in the loss of insulin expression, the data reveal a novel cross-talk between the two essential regulators of early beta-cell differentiation.
- Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence.
Kleinjan, PLoS genetics 2008 - GeneRIF: following a postulated whole-genome duplication event in an ancestral teleost, duplicates pax6a and pax6b encode transcription factors required for eye, brain, olfactory system, and pancreas development
- Direct non-cell autonomous Pax6 activity regulates eye development in the zebrafish.
Lesaffre, Neural development 2007 - GeneRIF: This study supports the hypothesis that the Pax6 transcription factor is also a signaling molecule with direct non-cell autonomous activity.
- Changing Pax6 expression correlates with axon outgrowth and restoration of topography during optic nerve regeneration.
Rodger, Neuroscience 2006 (PubMed)- GeneRIF: The results suggest that decreased Pax6 expression is permissive for axon regeneration and extensive searching, while higher levels of Pax6 are associated with restoration of topography.
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NP_996314 Ptx1, isoform C from Drosophila melanogaster
57% identity, 14% coverage
PITX_DROME / O18400 Pituitary homeobox homolog Ptx1; D-PTX1 from Drosophila melanogaster (Fruit fly) (see paper)
57% identity, 15% coverage
- function: Appears to control physiological cell functions rather than pattern formation during embryogenesis.
LOC101486458 visual system homeobox 2 from Maylandia zebra
70% identity, 15% coverage
- Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes
Vernaz, Nature communications 2021 - “...embryonic and developmental processes. Namely, in the genes coding for visual system homeobox 2 vsx2 (LOC101486458), growth-associated protein 43 gap43 (LOC101472990) and teneurin transmembrane protein 2 tenm2 (LOC101470261). Liver and muscle methylome profiles shownin green and purple, respectively (averaged mCG/CG levels [%] in 50bp bins for...”
T1G8F8 Uncharacterized protein from Helobdella robusta
64% identity, 25% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...Pax2/5/8?(f) Helobdella_robusta Annelida_Clitellata T1EH18 Uncharacterized protein Pax2/5/8(f) Helobdella_robusta Annelida_Clitellata T1FMW8 Uncharacterized protein Pax3/7A Helobdella_robusta Annelida_Clitellata T1G8F8 Uncharacterized protein Pax3/7B(f) Helobdella_robusta Annelida_Clitellata T1F6U6 Uncharacterized protein Pax6A Helobdella_robusta Annelida_Clitellata T1G400 Uncharacterized protein Pax6B(f) Helobdella_robusta Annelida_Clitellata T1EHA5 Uncharacterized protein Pax1(f) Helobdella_robusta Annelida_Clitellata T1G182 Uncharacterized protein Pax2(f) Helobdella_robusta Annelida_Clitellata R7VKC0...”
VAB3_CAEEL / G5EDS1 Paired box protein 6 homolog; Homeobox and paired domain-containing protein vab-3; Protein male abnormal 18; Variable abnormal morphology protein 3 from Caenorhabditis elegans (see 14 papers)
NP_001024570 Paired box protein 6 homolog from Caenorhabditis elegans
63% identity, 14% coverage
- function: Transcription factor that binds a motif with the core sequence 5'-GCGTA-3' in the promoter of various genes (PubMed:11476572, PubMed:30890567). During development, required for cell fate specification probably by promoting or repressing expression of genes involved in specific cell fate (PubMed:11476572, PubMed:30890567, PubMed:7649393). Involved in head epidermal morphogenesis (PubMed:7659159). Involved in gonadal distal tip cell (DTC) migration, during which modulates expression of the integrin alpha genes, pat-2 and ina-1 (PubMed:10388818, PubMed:15579687, PubMed:17606640). Regulates ventral and dorsal cephalic sheath (CEPsh) glia differentiation and expression of transcription factor hlh-17 in CEPsh glia (PubMed:18508862). Plays a role in establishing unequal cytokinesis and cell fate specification in male-specific postembryonic blast cell B (PubMed:7649393). May cooperate with the phosphatase eya-1 and transcription factor ceh-32 to regulate the transcription factor ets-5 (PubMed:30890567).
function: [Isoform a]: Transcription factor involved in head epidermal morphogenesis and required for normal cell fate in anterior lateral epidermal blast (seam) cells (PubMed:15579687, PubMed:7659159). Required for the generation or differentiation of neurons of the anterior ganglion, probably acting upstream of unc-86 (PubMed:8647436). Represses BAG sensory neuron fate in non-BAG cells, probably through cooperation with the phosphatase eya-1 and transcription factor ceh-32 (PubMed:30890567). May be involved in regulating the generation of dopaminergic neurons (PubMed:21079745). May cooperate with hlh-17 to preferentially regulate expression of hlh-17 in ventral CEPsh glia (PubMed:18508862).
function: [Isoform b]: Transcription factor that acts within the male- specific genital sensilla (simple sense organs) known as rays to determine their identity (PubMed:15579687, PubMed:1782863, PubMed:7659160). Promotes BAG sensory neuron fate in a cell-autonomous manner (PubMed:30890567). Required for function of chemosensory BAG neurons (PubMed:30890567).
disruption phenotype: RNAi-mediated knockdown causes defects in gonadal distal tip cell migration (PubMed:17606640). RNAi-mediated knockdown reduces expression of the integrin alpha pat-2 in gonadal DTCs in about 70% of individuals and in 90% on a vab-3 mutant background (PubMed:17606640). RNAi-mediated knockdown increases expression of the integrin alpha ina-1 in gonadal DTCs in hermaphrodites (PubMed:17606640). RNAi-mediated knockdown induces generation of additional dopaminergic neurons (PubMed:21079745). BAG sensory neuron- specific RNAi-mediated knockdown reduces expression of receptor-type guanylyl cyclase gcy-9 (PubMed:30890567). - mls-2 and vab-3 Control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegans.
Yoshimura, Development (Cambridge, England) 2008 (PubMed)- GeneRIF: demonstrate ventral- and dorsal-restricted roles for the mls-2/Nkx/Hmx and vab-3/Pax6/Pax7 genes, respectively, in CEPsh glia differentiation and expression of the genes hlh-17/Olig and ptr-10/Patched-related
- Control of C. elegans hermaphrodite gonad size and shape by vab-3/Pax6-mediated regulation of integrin receptors.
Meighan, Genes & development 2007 - GeneRIF: Transcriptional control of migration termination provides a new mechanism for regulation of morphogenesis and organ size by vab-3.
- The homeoproteins MAB-18 and CEH-14 insulate the dauer collagen gene col-43 from activation by the adjacent promoter of the Spermatheca gene sth-1 in Caenorhabditis elegans.
Bando, Journal of molecular biology 2005 (PubMed)- GeneRIF: Results indicate that MAB-18 and CEH-14 interact to repress col-43 expression in sth-1-expressing tissues.
- The C. elegans eyes absent ortholog EYA-1 is required for tissue differentiation and plays partially redundant roles with PAX-6.
Furuya, Developmental biology 2005 (PubMed)- GeneRIF: eya-1 and pax-6/Pax6 mutants showed a strong genetic interaction for larval viability and embryonic anterior morphogenesis.
- Positive and negative regulatory inputs restrict pax-6/vab-3 transcription to sensory organ precursors in Caenorhabditis elegans.
Johnson, Mechanisms of development (PubMed)- GeneRIF: analysis of multiple genetic pathways that act to restrict pax-6/vab-3 gene expression to the sensory organ precursor cells
CG9876 uncharacterized protein from Drosophila melanogaster
62% identity, 25% coverage
- Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries
Balasubramanian, Nucleic acids research 2024 - “...and two genes located in the same TAD as the+51 kb insertion ( CG9877 and CG9876 ) showing a significant upregulation compared to the wild-type control ( Supplementary Figure S15 ). Of note, a similar pattern was observed in the E3(+39kb) line ( Supplementary Figure S15...”
- A modERN resource: identification of Drosophila transcription factor candidate target genes using RNAi
Fisher, Genetics 2023 - “...profiling embryonic dataset ( Graveley et al . 2011 ). For two TFs, Hr51 and CG9876 we selected secondary peak stages because the normal expression exhibited two distinct expression peaks. In parallel experiments, we assessed whether the RNAi cross resulted in lethality or other phenotype at...”
- “...0.49 0.91 CG32006 1214 2.35 2.12 Embryonic CG33557 68 1.57 0.45 CG34376 1012 0.05 0.02 CG9876 a 68; 1214 0.31; 0.68 1.58 dac 68 0.52 0.74 dmrt99B 68 0.20 0.42 E5 1012 0.15 0.16 ERR 1012 1.23 1.14 Larval esn 1416 0.86 0.98 Ets65A 1214 0.65...”
- Lpt, trr, and Hcf regulate histone mono- and dimethylation that are essential for Drosophila heart development
Huang, Developmental biology 2022 - “...Transcription factor Zfpm1 Ush 6 1 0.45 0.55 0.0418 0.51 0.0296 Heart development, transcription Prrx2 CG9876 6 1 0.51 0.34 0.0016 0.42 0.0030 Homeodomain transcription factor Aff1 Lilli 7 1 0.32 0.24 0.0041 0.29 0.0052 Transcription factor GPCR Gpr146 CCKLR 1 1 0.56 0.12 0.0010 0.36...”
- Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers
Field, PloS one 2016 - “...y CG4328 y CG4328 y oc y CG7056 y CG7056 y otp y otp y CG9876 y CG9876 y prd y prd y Deaf1 n Deaf1 n repo y repo y Dfd y ro y ro y Dll y Dll y sd n E5 y E5...”
NP_477026 reversed polarity from Drosophila melanogaster
75% identity, 8% coverage
- The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.
Trébuchet, The Journal of neuroscience : the official journal of the Society for Neuroscience 2019 - GeneRIF: Repo expression inhibits the expression of hemocyte-specific genes in the nervous system
- Transcriptional Regulation of the Glutamate/GABA/Glutamine Cycle in Adult Glia Controls Motor Activity and Seizures in Drosophila.
Mazaud, The Journal of neuroscience : the official journal of the Society for Neuroscience 2019 - GeneRIF: Repo expression is continuously required in adult glia to transcriptionally regulate the highly conserved function of neurotransmitter recycling in both males and females.
- Developmental regulation of glial cell phagocytic function during Drosophila embryogenesis.
Shklyar, Developmental biology 2014 (PubMed)- GeneRIF: REPO directly regulates DRPR expression. gcm and repo have a critical role in controlling glial phagocytic function through regulation of SIMU and DRPR specific expression.
- Characterization of cis-regulatory elements controlling repo transcription in Drosophila melanogaster.
Johnson, Gene 2012 (PubMed)- GeneRIF: we characterized three cis-regulatory elements
- Ectopic Repo suppresses expression of castor gene in Drosophila central nervous system.
Park, Biochemical and biophysical research communications 2009 (PubMed)- GeneRIF: These results indicate that cas could be directly suppressed by Repo.
- The tumor suppressor, vitamin D3 up-regulated protein 1 (VDUP1), functions downstream of REPO during Drosophila gliogenesis.
Mandalaywala, Developmental biology 2008 (PubMed)- GeneRIF: novel role for the dVDUP1 tumor suppressor during nervous system development as a regulatory target for REPO during gliogenesis
- Transcriptional regulation of the Drosophila glial gene repo.
Lee, Mechanisms of development 2005 (PubMed)- GeneRIF: Gcm acts synergistically with other factors to control repo transcription in glial cells
- Drosophila homeodomain protein REPO controls glial differentiation by cooperating with ETS and BTB transcription factors.
Yuasa, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: REPO plays a key role in both glial development and diversification.
NP_957490 short stature homeobox protein 2 from Danio rerio
67% identity, 23% coverage
T1FMW8 Uncharacterized protein from Helobdella robusta
63% identity, 14% coverage
- The Pax gene family: Highlights from cephalopods
Navet, PloS one 2017 - “...Pax1/9(f) Helobdella_robusta Annelida_Clitellata T1EIE6 Uncharacterized protein Pax2/5/8?(f) Helobdella_robusta Annelida_Clitellata T1EH18 Uncharacterized protein Pax2/5/8(f) Helobdella_robusta Annelida_Clitellata T1FMW8 Uncharacterized protein Pax3/7A Helobdella_robusta Annelida_Clitellata T1G8F8 Uncharacterized protein Pax3/7B(f) Helobdella_robusta Annelida_Clitellata T1F6U6 Uncharacterized protein Pax6A Helobdella_robusta Annelida_Clitellata T1G400 Uncharacterized protein Pax6B(f) Helobdella_robusta Annelida_Clitellata T1EHA5 Uncharacterized protein Pax1(f) Helobdella_robusta Annelida_Clitellata T1G182...”
NP_524638 twin of eyeless, isoform A from Drosophila melanogaster
58% identity, 13% coverage
- Whole exome sequence analysis of Peters anomaly
Weh, Human genetics 2014 - “...chicken pax6-5a (NP_990397), zebrafish pax6a (NP_571379), zebrafish pax6b (NP_571716), Drosophila ey (NP_001014693) and Drosophila toy (NP_524638) sequences were used for the alignment; the position of p.(C52Y) is shown with red arrow Fig. 2 a Patient 2: Pedigree and TFAP2A genotypes. DNA chromatograms of the probands and...”
NP_001033832 visual system homeobox 2, isoform A from Drosophila melanogaster
64% identity, 10% coverage
NP_523389 Ods-site homeobox from Drosophila melanogaster
67% identity, 16% coverage
- A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH).
Nunes, G3 (Bethesda, Md.) 2024 - GeneRIF: A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH).
- Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.
Sun, G3 (Bethesda, Md.) 2024 - GeneRIF: Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila.
- Reduction of germ cells in the Odysseus null mutant causes male fertility defect in Drosophila melanogaster.
Cheng, Genes & genetic systems 2012 (PubMed)- GeneRIF: early developing germ cells, including spermatogonia and spermatocytes, are reduced in the OdsH mutant males.
- The normal function of a speciation gene, Odysseus, and its hybrid sterility effect.
Sun, Science (New York, N.Y.) 2004 (PubMed)- GeneRIF: normal function of OdsH identified as a modest enhancement of sperm production in young males
- Gene duplication and speciation in Drosophila: evidence from the Odysseus locus.
Ting, Proceedings of the National Academy of Sciences of the United States of America 2004 - GeneRIF: a hybrid-male sterility gene, Odysseus (OdsH), arose by gene duplication in the Drosophila genome
1fjlA / P06601 Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide (see paper)
71% identity, 69% coverage
Smp_126560 putative orthopedia homeobox protein from Schistosoma mansoni
73% identity, 5% coverage
OTX1B_DANRE / Q91994 Homeobox protein OTX1 B; zOtx1; Orthodenticle homolog 1 B from Danio rerio (Zebrafish) (Brachydanio rerio) (see 3 papers)
59% identity, 21% coverage
- function: May play a role in very early embryogenesis, gastrulation, and the development and subdivision of the diencephalon and the midbrain
NP_571325 homeobox protein OTX1 B from Danio rerio
59% identity, 21% coverage
XP_013834407 pituitary homeobox 2 isoform X1 from Sus scrofa
61% identity, 22% coverage
XP_005207658 pituitary homeobox 2 isoform X1 from Bos taurus
61% identity, 22% coverage
PITX2_XENLA / Q9PWR3 Pituitary homeobox 2; Homeobox protein PITX2; Paired-like homeodomain transcription factor 2; xPtx2 from Xenopus laevis (African clawed frog) (see 2 papers)
60% identity, 22% coverage
- function: Involved in left-right asymmetry of the developing embryo (PubMed:10585561). May play an important role in development and maintenance of anterior structures. Could play a role at the interface of lateral plate signaling and heart and gut morphogenesis.
PITX2_CHICK / O93385 Pituitary homeobox 2; Homeobox protein PITX2; cPITX2; Paired-like homeodomain transcription factor 2 from Gallus gallus (Chicken) (see paper)
62% identity, 21% coverage
- function: May play a role in myoblast differentiation. May be involved in the establishment of left-right asymmetry in the developing embryo (By similarity). May play a role in vasculogenesis during avian embryogenesis.
NP_990341 pituitary homeobox 2 from Gallus gallus
62% identity, 21% coverage
- The left-right Pitx2 pathway drives organ-specific arterial and lymphatic development in the intestine.
Mahadevan, Developmental cell 2014 - GeneRIF: Pitx2 pathway drives organ-specific arterial and lymphatic development in the intestine
- The transcription factor Pitx2 positions the embryonic axis and regulates twinning.
Torlopp, eLife 2014 - GeneRIF: Pitx2 is essential for axis formation, and that it acts as a direct regulator of cVg1 expression by binding to enhancers within neighbouring genes.
- Altered PITX2 and LEF1 gene expression in the cadmium-induced omphalocele in the chick model.
Doi, Pediatric surgery international 2011 (PubMed)- GeneRIF: Downregulation of PITX2 and LEF1 genes may interfere with ventral body wall formation in Cd chick model causing omphalocele by disrupting somite myogenesis.
- Wnt/Lef1 signaling acts via Pitx2 to regulate somite myogenesis.
Abu-Elmagd, Developmental biology 2010 (PubMed)- GeneRIF: Wnt/Lef1 signaling regulates epaxial myogenesis via Pitx2.
- The Pitx2c N-terminal domain is a critical interaction domain required for asymmetric morphogenesis.
Simard, Developmental dynamics : an official publication of the American Association of Anatomists 2009 - GeneRIF: Data suggest that the Pitx2c N-terminal domain competes with endogenous Pitx2c for binding to a protein interaction partner that is required for the activation of genes that direct asymmetric morphogenesis along the left-right axis.
- Expression patterns of Shh, Ptc2, Raldh3, Pitx2, Isl1, Lim3 and Pax6 in the developing chick hypophyseal placode and Rathke's pouch.
Sjödal, Gene expression patterns : GEP 2008 (PubMed)- GeneRIF: Pitx2 is together with Pax6 expressed in the entire domain of the Rathke's pouch.
- Pitx2 regulates gonad morphogenesis.
Rodríguez-León, Proceedings of the National Academy of Sciences of the United States of America 2008 - GeneRIF: Pitx2 activity directs asymmetrical gonad morphogenesis by controlling mitotic spindle orientation of the developing gonad cortex and how, by modulating cyclinD1 expression during asymmetric ovarian development
- PITX2 controls asymmetric gonadal development in both sexes of the chick and can rescue the degeneration of the right ovary.
Guioli, Development (Cambridge, England) 2007 (PubMed)- GeneRIF: Mechanism in females that actively promotes the underlying L-R asymmetry initiated by Pitx2 and the degeneration of the right gonad, and a mechanism in males that allows it to be ignored or overridden.
PITX2_MOUSE / P97474 Pituitary homeobox 2; ALL1-responsive protein ARP1; BRX1 homeoprotein; Bicoid-related homeobox protein 1; Homeobox protein PITX2; Orthodenticle-like homeobox 2; Paired-like homeodomain transcription factor 2; Solurshin from Mus musculus (Mouse) (see 8 papers)
NP_035228 pituitary homeobox 2 isoform b from Mus musculus
61% identity, 22% coverage
- function: May play a role in myoblast differentiation. When unphosphorylated, associates with an ELAVL1-containing complex, which stabilizes cyclin mRNA and ensuring cell proliferation. Phosphorylation by AKT2 impairs this association, leading to CCND1 mRNA destabilization and progression towards differentiation.
function: [Isoform Ptx2c]: Involved in the establishment of left-right asymmetry in the developing embryo.
subunit: Interacts with EFEMP2 (By similarity). Interacts (when unphosphorylated on Thr-90) with ELAVL1/HUR (PubMed:20019746).
disruption phenotype: [Isoform Ptx2c]: Knockout embryos exhibit cardiac and laterality defects. Embryos have defects in the aortic arch vessels, such as double-outlet right ventricle and right-sided or double aortic arches. Most have bilateral, left-sided or midline inferior caval veins, right atrial and pulmonary isomerism. None have abnormal ventricular topology, but some have malposition of the heart to the right and the hearts of the remaining embryos are in the midline rather than to the left. In addition, most embryos have ventricular septal defects with associated double-outlet right ventricle. Some embryos show right-sided aortic arches and some have right-sided stomachs or, in one case, a midline stomach. The spleen is absent or small. Unlike mice lacking all Pitx2 isoforms, Pitx2c-specific knockout embryos have no defects in ventral body wall closure. - Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...P15105 Glul glutamine synthetase 53 essential for proliferation of fetal skin fibroblasts -- 1 isoform P97474 Pitx2 pituitary homeobox 2 52 involved in cell proliferation and morphogenesis mice embryos lacking isoform Ptx2c show left-right patterning defects and severe development abnormalities 5 isoforms P28236 Gja8 gap junction...”
- Lefty blocks a subset of TGFbeta signals by antagonizing EGF-CFC coreceptors
Cheng, PLoS biology 2004 - “...Lefty1 (Q9W6I6), Lefty2 (P57785), mLefty1 (Q64280), Nodal (P43021), no tail (Q07998), one-eyed pinhead (O57516), Pitx2 (P97474), squint (O13144), VEGF-D (P97946), and Vg1 (P09534). We thank members of the Schier, Brivanlou, and Yelon laboratories for discussions; Gord Fishell, Kathy Joubin, Alvaro Sagasti, and Will Talbot for comments...”
- Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2.
Jiang, JCI insight 2024 - GeneRIF: Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2.
- Interplay between Pitx2 and Pax7 temporally governs specification of extraocular muscle stem cells.
Kuriki, PLoS genetics 2024 - GeneRIF: Interplay between Pitx2 and Pax7 temporally governs specification of extraocular muscle stem cells.
- Transcriptional programs of Pitx2 and Tfap2a/Tfap2b controlling lineage specification of mandibular epithelium during tooth initiation.
Shao, PLoS genetics 2024 - GeneRIF: Transcriptional programs of Pitx2 and Tfap2a/Tfap2b controlling lineage specification of mandibular epithelium during tooth initiation.
- Pitx2 patterns an accelerator-brake mechanical feedback through latent TGFβ to rotate the gut.
Sanketi, Science (New York, N.Y.) 2022 - GeneRIF: Pitx2 patterns an accelerator-brake mechanical feedback through latent TGFbeta to rotate the gut.
- PRRX1 deficiency induces mesenchymal-epithelial transition through PITX2/miR-200-dependent SLUG/CTNNB1 regulation in hepatocellular carcinoma.
Chen, Cancer science 2021 - GeneRIF: PRRX1 deficiency induces mesenchymal-epithelial transition through PITX2/miR-200-dependent SLUG/CTNNB1 regulation in hepatocellular carcinoma.
- Paired-like homeodomain transcription factor 2 affects endometrial cell function and embryo implantation through the Wnt/β-catenin pathway.
Zhang, Cell biology international 2021 (PubMed)- GeneRIF: Paired-like homeodomain transcription factor 2 affects endometrial cell function and embryo implantation through the Wnt/beta-catenin pathway.
- A missense mutation in Pitx2 leads to early-onset glaucoma via NRF2-YAP1 axis.
Yang, Cell death & disease 2021 - GeneRIF: A missense mutation in Pitx2 leads to early-onset glaucoma via NRF2-YAP1 axis.
- The asymmetric Pitx2 gene regulates gut muscular-lacteal development and protects against fatty liver disease.
Hu, Cell reports 2021 - GeneRIF: The asymmetric Pitx2 gene regulates gut muscular-lacteal development and protects against fatty liver disease.
- More
PITX2_HUMAN / Q99697 Pituitary homeobox 2; ALL1-responsive protein ARP1; Homeobox protein PITX2; Paired-like homeodomain transcription factor 2; RIEG bicoid-related homeobox transcription factor; Solurshin from Homo sapiens (Human) (see 12 papers)
61% identity, 22% coverage
- function: May play a role in myoblast differentiation. When unphosphorylated, associates with an ELAVL1-containing complex, which stabilizes cyclin mRNA and ensuring cell proliferation. Phosphorylation by AKT2 impairs this association, leading to CCND1 mRNA destabilization and progression towards differentiation.
function: [Isoform PTX2C]: Involved in the establishment of left-right asymmetry in the developing embryo.
subunit: Interacts with EFEMP2 (PubMed:22919265). Interacts (when unphosphorylated on Thr-90) with ELAVL1/HUR (By similarity). - A network analysis revealed the essential and common downstream proteins related to inguinal hernia.
Mao, PloS one 2020 - “...PDGFRA P11362 FGFR1 P01116 KRAS P35354 PTGS2 Q86XX4 FRAS1 Q8WW38 ZFPM2 P02458 COL2A1 P00797 REN Q99697 PITX2 P07951 TPM2 P13647 KRT5 O95259 KCNH1 Q9NQX1 PRDM5 Q01974 ROR2 Q16671 AMHR2 P61812 TGFB2 P27986 PIK3R1 P37058 HSD17B3 Q06124 PTPN11 Q07889 SOS1 Q16637 SMN1 P36897 TGFBR1 Q5SZK8 FREM2 P22888...”
- Shotgun proteomics coupled to nanoparticle-based biomarker enrichment reveals a novel panel of extracellular matrix proteins as candidate serum protein biomarkers for early-stage breast cancer detection.
Fredolini, Breast cancer research : BCR 2020 - “...4507651 P67936 TPM4 Tropomyosin 4 isoform 2 29 125 M 173 21 SPECIFIC 15 24234708 Q99697 PITX2 Paired-like homeodomain transcription factor 2 isoform b 35 N/A N 50 26 NOVEL 16 37550464 A6NMN3 FAM170B PREDICTED:family with sequence similarity 170,member B 36 3.16 M 67 21 17...”
- ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia.
Gregory, Proceedings of the National Academy of Sciences of the United States of America 2016 - Priorities and trends in the study of proteins in eye research, 1924-2014
Semba, Proteomics. Clinical applications 2015 - “...Prp31 46 involved in pre-mRNA splicing retinitis pigmentosa 11 3 isoforms 9 PTM 40 variants Q99697 PITX2 pituitary homeobox 2 46 involved in cell proliferation, morphogenesis Axenfeld-Rieger syndrome 1; iridogoniodysgenesis 2; Peters anomaly; ring dermoid of cornea 3 isoforms 1 PTM 47 variants P07320 CRYGD gamma-crystallin...”
- Protein interactions of the transcription factor Hoxa1
Lambert, BMC developmental biology 2012 - “...cytoplasmic Y PFKM phosphofructokinase, muscle 5213 P08237 Glycolysis / N PITX2 paired-like homeodomain 2 5308 Q99697 Transcription factor (homeodomain) Nuclear Y PLSCR4 phospholipid scramblase 4 57088 Q9NRQ2 Phospholipid scramblase, transcription factor Nuclear Y RAB33A member RAS oncogene family 9363 Q14088 Small GTPase, vesicular trafficking (Ras pathway)...”
- Blood biomarkers in cardioembolic stroke.
García-Berrocoso, Current cardiology reviews 2010 - “...P01303 Elevated in AF patients vs . controls. [ 50 ] 21 Paired-like homeodomain (PITX2) Q99697 Transcription factor associated with AF. Gene polymorphism associated with CE stroke. [ 36 , 37 ] 22 Platelet factor 4 (PF-4) P02776 Marker of platelet activation in AF patients. [...”
XP_005681362 pituitary homeobox 2 isoform X2 from Capra hircus
NP_001191328 pituitary homeobox 2 isoform a from Homo sapiens
XP_051676055 pituitary homeobox 2 isoform X2 from Oryctolagus cuniculus
61% identity, 26% coverage
- Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (PITX2) gene in dairy goats.
Zhao, Gene 2013 (PubMed)- GeneRIF: Genetic variations in the caprine PITX2 gene had significant effects on milk traits.
- Exploring the association between PITX2, third molars agenesis and sella turcica morphology : PITX2, third molars agenesis and sella turcica morphology.
Küchler, Head & face medicine 2024 - GeneRIF: Exploring the association between PITX2, third molars agenesis and sella turcica morphology : PITX2, third molars agenesis and sella turcica morphology.
- Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2.
Jiang, JCI insight 2024 - GeneRIF: Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2.
- PITX2 functions as a transcription factor for GPX4 and protects pancreatic cancer cells from ferroptosis.
Wang, Experimental cell research 2024 (PubMed)- GeneRIF: PITX2 functions as a transcription factor for GPX4 and protects pancreatic cancer cells from ferroptosis.
- Enamel defects of Axenfeld-Rieger syndrome and the role of PITX2 in its pathogenesis.
Yang, Oral diseases 2023 (PubMed)- GeneRIF: Enamel defects of Axenfeld-Rieger syndrome and the role of PITX2 in its pathogenesis.
- Genotype-phenotype association of PITX2 and FOXC1 in Axenfeld-Rieger syndrome.
Zhou, Experimental eye research 2023 (PubMed)- GeneRIF: Genotype-phenotype association of PITX2 and FOXC1 in Axenfeld-Rieger syndrome.
- PITX2 Knockout Induces Key Findings of Electrical Remodeling as Seen in Persistent Atrial Fibrillation.
Schulz, Circulation. Arrhythmia and electrophysiology 2023 (PubMed)- GeneRIF: PITX2 Knockout Induces Key Findings of Electrical Remodeling as Seen in Persistent Atrial Fibrillation.
- Association Between rs2200733 Polymorphism of PITX2 Gene and the Risk of Atrial Fibrillation.
Shen, Anatolian journal of cardiology 2023 - GeneRIF: Association Between rs2200733 Polymorphism of PITX2 Gene and the Risk of Atrial Fibrillation.
- PITX2 induction leads to impaired cardiomyocyte function in arrhythmogenic cardiomyopathy.
van, Stem cell reports 2023 - GeneRIF: PITX2 induction leads to impaired cardiomyocyte function in arrhythmogenic cardiomyopathy.
- More
- Pitx2 and nodal as conserved early markers of the anterior-posterior axis in the rabbit embryo.
Plöger, Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft 2018 (PubMed)- GeneRIF: In the anterior segment of the posterior pitx2 expression domain, the anterior streak domain is defined by nodal expression as a hypothetical progenitor region of the anterior half of the primitive streak
NP_062207 pituitary homeobox 2 isoform 2 from Rattus norvegicus
61% identity, 26% coverage
- Pitx2 suppression at meiotic stages associates with seasonal inhibition of testis development in Rattus norvegicus caraco.
Tian, Integrative zoology 2023 (PubMed)- GeneRIF: Pitx2 suppression at meiotic stages associates with seasonal inhibition of testis development in Rattus norvegicus caraco.
- Long-standing arterial hypertension is associated with Pitx2 down-regulation in a rat model of spontaneous atrial tachyarrhythmias.
Scridon, Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology 2015 (PubMed)- GeneRIF: The present study suggests the presence of age-dependent left atrial Pitx2 down-regulation in SHRs
- Pitx2 expression promotes p21 expression and cell cycle exit in neural stem cells.
Heldring, CNS & neurological disorders drug targets 2012 (PubMed)- GeneRIF: Data suggest that up-regulation of Pitx2 expression induces decrease in cell proliferation associated with an accumulation of neural stem cells in G1 phase; Pitx2 expression causes up-regulation in expression of cell cycle inhibitor p21 (Cdkn1a).
- Smad3 and Pitx2 cooperate in stimulation of FSHbeta gene transcription.
Suszko, Molecular and cellular endocrinology 2008 (PubMed)- GeneRIF: Smad3 and Pitx2 cooperate in stimulation of FSHbeta gene transcription.
- Involvement of Pitx2, a homeodomain transcription factor, in hypothyroidism associated reproductive disorders.
Ghosh, Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 2007 (PubMed)- GeneRIF: The present study reveals that the reduced Pitx2 expression in hypothyroid ovary could lead to ovarian dysfunction by modulating the Pitx2-Plod2 interaction.
- Pitx factors are involved in basal and hormone-regulated activity of the human prolactin promoter.
Quentien, The Journal of biological chemistry 2002 (PubMed)- GeneRIF: the paired-like homeobox transcription factors Pitx1 and Pitx2 are factors functionally activating the proximal human prolactin promoter (hPRL-164luc)
XP_015134823 paired mesoderm homeobox protein 2 isoform X1 from Gallus gallus
68% identity, 24% coverage
pax-6B / CAC85262.2 Pax-6B protein from Dugesia japonica (see paper)
49% identity, 13% coverage
PITX2_DANRE / Q9W5Z2 Pituitary homeobox 2; Homeobox protein PITX2; Paired-like homeodomain transcription factor 2 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
66% identity, 20% coverage
- function: [Isoform c]: Regulates mesendoderm formation and the establishment of left-right asymmetry in the developing embryo.
function: [Isoform a]: Regulates mesendoderm formation and the establishment of left-right asymmetry in the developing embryo, with a particularly strong effect on heart laterality.
OTX1_HUMAN / P32242 Homeobox protein OTX1; Orthodenticle homolog 1 from Homo sapiens (Human) (see paper)
NP_001186699 homeobox protein OTX1 from Homo sapiens
59% identity, 19% coverage
- function: Probably plays a role in the development of the brain and the sense organs. Can bind to the BCD target sequence (BTS): 5'-TCTAATCCC- 3'
- Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development
Karlin, Proceedings of the National Academy of Sciences of the United States of America 1996 - “...(Q03052) 398 G6, G6, G6, P6, H6 1 0, 0, 2 0, 0 OTX1 (P32242) 354 1,0, 1 3 +, n/a Ss, A6, H5, Hio SOX-4 (Q06945) 474 G7, G6, G6, A7, S7 +, ++ 0 0, 1, 1...”
- OTX1 regulates tumorigenesis and metastasis in glioma.
Cao, Pathology, research and practice 2024 (PubMed)- GeneRIF: OTX1 regulates tumorigenesis and metastasis in glioma.
- MiR-195-5p suppresses gastric adenocarcinoma cell progression via targeting OTX1.
Hu, Histology and histopathology 2023 (PubMed)- GeneRIF: MiR-195-5p suppresses gastric adenocarcinoma cell progression via targeting OTX1.
- Overexpression of OTX1 promotes tumorigenesis in patients with esophageal squamous cell carcinoma.
Chai, Pathology, research and practice 2022 (PubMed)- GeneRIF: Overexpression of OTX1 promotes tumorigenesis in patients with esophageal squamous cell carcinoma.
- Knockdown of circMYOF inhibits cell growth, metastasis, and glycolysis through miR-145-5p/OTX1 regulatory axis in laryngeal squamous cell carcinoma.
Li, Functional & integrative genomics 2022 (PubMed)- GeneRIF: Knockdown of circMYOF inhibits cell growth, metastasis, and glycolysis through miR-145-5p/OTX1 regulatory axis in laryngeal squamous cell carcinoma.
- OTX1 promotes tumorigenesis and progression of cervical cancer by regulating the Wnt signaling pathway.
Zhou, Oncology reports 2022 - GeneRIF: OTX1 promotes tumorigenesis and progression of cervical cancer by regulating the Wnt signaling pathway.
- Orthodenticle homeobox OTX1 is a potential prognostic biomarker for bladder cancer.
Jiang, Bioengineered 2021 - GeneRIF: Orthodenticle homeobox OTX1 is a potential prognostic biomarker for bladder cancer.
- Long non-coding RNA HNF1A-AS1 upregulates OTX1 to enhance angiogenesis in colon cancer via the binding of transcription factor PBX3.
Wu, Experimental cell research 2020 (PubMed)- GeneRIF: Long non-coding RNA HNF1A-AS1 upregulates OTX1 to enhance angiogenesis in colon cancer via the binding of transcription factor PBX3.
- MicroRNA-4516 suppresses pancreatic cancer development via negatively regulating orthodenticle homeobox 1.
Chen, International journal of biological sciences 2020 - GeneRIF: MicroRNA-4516 suppresses pancreatic cancer development via negatively regulating orthodenticle homeobox 1.
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PRRX2_HUMAN / Q99811 Paired mesoderm homeobox protein 2; Paired-related homeobox protein 2; PRX-2 from Homo sapiens (Human) (see paper)
NP_057391 paired mesoderm homeobox protein 2 from Homo sapiens
68% identity, 23% coverage
- function: May play a role in the scarless healing of cutaneous wounds during the first two trimesters of development.
- Identifying Differences in Molecular Characteristics Relevant for Remodeling of Periodontal Ligament Stem Cells from the Upper and Lower Jaw.
Malyaran, International journal of molecular sciences 2024 - “...P53778 SEBTGYVVTR 0.242 1.507 PTN6_558_570 P29350 KHKEDVYENLHTK 0.253 1.411 EGFR_1190_1202 P00533 STAENAEYLRVAP 0.584 1.407 PRRX2_202_214 Q99811 WTASSPYSTVPPY 0.266 1.404 RET_1022_1034 P07949 TPSDSLIYDDGLS 0.357 1.380 ZAP70_313_325 P43403 SVYESPYSDPEEL 0.329 1.368 CDK2_8_20 P24941 EKIGEGTYGVVYK 0.278 1.361 ANXA1_14_26 P04083 IENEEQEYVQTVK 0.374 1.358 VGFR2_1168_1180 P35968 AQQDGKDYIVLPI 0.322 1.307 STK ID...”
- Ex vivo multiplex profiling of protein tyrosine kinase activities in early stages of human lung adenocarcinoma.
Arni, Oncotarget 2017 - “...PLCG1_764_776 IGTAEPDYGALYE [771, 775] P19174 1-phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma-1 < 0.01 PRRX2_202_214 WTASSPYSTVPPY [208, 214] Q99811 Paired mesoderm homeobox protein 2 (PRX-2) < 0.01 RET_1022_1034 TPSDSLIYDDGLS [1029] P07949 Proto-oncogene tyrosine-protein kinase receptor ret precursor < 0.01 RON_1346_1358 SALLGDHYVQLPA [1353] Q04912 Macrophage-stimulating protein receptor precursor < 0.01...”
- Novel application of multi-stimuli network inference to synovial fibroblasts of rheumatoid arthritis patients.
Kupfer, BMC medical genomics 2014 - “...50515 Carbohydrate (chondroitin 4) sulfotransferase 11 Q9NPF2 - GC09P132427_at PRRX2 51450 Paired related homeobox 2 Q99811 TF GC12M028011_at PTHLH 5744 Parathyroid hormone-like hormone P12272 SF GC11M065421_at RELA 5970 v-rel reticuloendotheliosis viral oncogene homolog A (avian) Q04206 TF GC14M054416_at BMP4 652 Bone morphogenetic protein 4 P12644 SF...”
- CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
Jiang, Journal of experimental & clinical cancer research : CR 2022 - GeneRIF: CircLRFN5 inhibits the progression of glioblastoma via PRRX2/GCH1 mediated ferroptosis.
- [Effects of Prrx2 gene silencing on the proliferation of breast cancer and its molecular mechanisms].
Lü, Zhonghua yi xue za zhi 2020 (PubMed)- GeneRIF: Silencing Prrx2 expression can effectively inhibit the proliferation and growth of breast cancer
- Attenuation of PRRX2 and HEY2 enables efficient conversion of adult human skin fibroblasts to neurons.
Li, Biochemical and biophysical research communications 2019 - GeneRIF: Attenuation of PRRX2 and HEY2 enables efficient conversion of adult human skin fibroblasts to neurons.
- Inhibition of PRRX2 suppressed colon cancer liver metastasis via inactivation of Wnt/β-catenin signaling pathway.
Chai, Pathology, research and practice 2019 (PubMed)- GeneRIF: PRRX2 inhibition may reduce invasive and migrating abilities to hinder epithelial-mesenchymal transition (EMT), and suppress colon cancer liver metastasis through inactivation of Wnt/beta-catenin pathway.
- PRRX2 as a novel TGF-β-induced factor enhances invasion and migration in mammary epithelial cell and correlates with poor prognosis in breast cancer.
Juang, Molecular carcinogenesis 2016 (PubMed)- GeneRIF: These data suggest that upregulation of PRRX2 may be a mechanism contributing to TGF-beta-induced invasion and epithelial mesenchymal transition in breast cancer.
- Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study.
Nagy, The Journal of biological chemistry 2011 - GeneRIF: Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study.
- 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)
- Oxidation of Prx2 and phosphorylation of GRP58 by angiotensin II in human coronary smooth muscle cells identified by 2D-DIGE analysis.
Tokutomi, Biochemical and biophysical research communications 2007 (PubMed)- GeneRIF: Valsartan, a selective Ang II type 1 (AT1) receptor blocker, and N-acetylcysteine, an antioxidant, inhibited both of these modifications, indicating the contribution of AT1 receptor and reactive oxygen species to oxidation of Prx2.
- More
XP_005157364 pituitary homeobox 2 isoform X1 from Danio rerio
66% identity, 24% coverage
- Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
Ferre-Fernández, Human molecular genetics 2020 - GeneRIF: Disruption of foxc1 genes in zebrafish results in dosage-dependent phenotypes overlapping Axenfeld-Rieger syndrome.
- Early sarcomere and metabolic defects in a zebrafish pitx2c cardiac arrhythmia model.
Collins, Proceedings of the National Academy of Sciences of the United States of America 2019 - GeneRIF: Pitx2c controls cardiac rhythmicity in zebrafish larvae.
- PITX2 deficiency and associated human disease: insights from the zebrafish model.
Hendee, Human molecular genetics 2018 - GeneRIF: These data further support the link between PITX2 and the WNT pathway and suggest a new role in regulation of collagen gene expression during development.
- Pitx2c orchestrates embryonic axis extension via mesendodermal cell migration.
Collins, eLife 2018 - GeneRIF: Pitx2c orchestrates embryonic axis extension via mesendodermal cell migration.
- Mutations in zebrafish pitx2 model congenital malformations in Axenfeld-Rieger syndrome but do not disrupt left-right placement of visceral organs.
Ji, Developmental biology 2016 - GeneRIF: asymmetric expression of fatty acid elongase 6 gene is controlled by left right Nodal signaling and is independent of Pitx2 function in zebrafish
- Antagonistic interactions in the zebrafish midline prior to the emergence of asymmetric gene expression are important for left-right patterning.
Burdine, Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2016 - GeneRIF: Late zygotic oep mutants have strongly reduced or absent pitx2 expression in the lateral plate mesoderm (LPM), but this expression can be rescued to strong levels by restoring oep in midline structures only.
- Pitx2c ensures habenular asymmetry by restricting parapineal cell number.
Garric, Development (Cambridge, England) 2014 - GeneRIF: Antagonism between Nodal and Pitx2c activities sets an upper limit on parapineal cell numbers. Restricting parapineal cell number is crucial for the correct elaboration of epithalamic asymmetry.
- Pegasus, the 'atypical' Ikaros family member, influences left-right asymmetry and regulates pitx2 expression.
John, Developmental biology 2013 (PubMed)- GeneRIF: Pitx2, implicated in left-right asymmetry, possessed appropriate 'atypical' Pegasus binding sites in its promoter.
- More
UNC42_CAEEL / L8E946 Homeobox protein unc-42; Uncoordinated protein 42 from Caenorhabditis elegans (see 5 papers)
68% identity, 22% coverage
- function: Probable transcription factor (PubMed:11222641, PubMed:34165428, PubMed:9216999). Required for initial outgrowth and pathfinding of axon growth cones along the ventral nerve cord (VNC) (PubMed:11222641, PubMed:34165428, PubMed:9216999). Involved in specifying neuron identity, in concert with nuclear hormone receptor family member fax-1, or with transcription factors unc-3, cfi-1, or hlh-34, perhaps acting via positive feedforward loops (PubMed:10207148, PubMed:16183052, PubMed:34165428). Establishes electrically- and chemically-interconnected neuron circuits, acting by modulating the expression of neurotransmitter pathway genes, neurotransmitter receptors, neuropeptides, and neuropeptide receptors (PubMed:34165428). Required for cholinergic and glutamatergic synaptic communication (PubMed:34165428). Plays a role in locomotion and mechanosensory response, perhaps via regulation of chemosensory receptor expression, and is required for expression of glutamate receptors, including glr-1, glr-4 and glr-5 (PubMed:10207148, PubMed:11222641, PubMed:34165428).
NP_505519 Homeobox protein unc-42 from Caenorhabditis elegans
68% identity, 23% coverage
XP_018087945 paired like homeodomain 2 S homeolog isoform X2 from Xenopus laevis
66% identity, 20% coverage
NP_037241 homeobox protein OTX1 from Rattus norvegicus
59% identity, 19% coverage
G7YLP5 Visual system homeobox 1 from Clonorchis sinensis
62% identity, 24% coverage
- In silico prediction of secretory proteins of Opisthorchis viverrini, Clonorchis sinensis and Fasciola hepatica that target the host cell nucleus
Machicado, Heliyon 2021 - “...nucleic acid binding transcription, DNA-templated metal ion binding DNA-directed RNA polymerase activity csin111481 - + G7YLP5 Visual system homeobox 1 9.55 31.10 sequence-specific DNA binding regulation of transcription, DNA-dependent nucleus Yes No No No DNA binding Gene ontology (GO) obtained through Biomart, MF is Molecular Function,...”
- “...nucleic acid binding transcription, DNA-templated metal ion binding DNA-directed RNA polymerase activity csin111481 - + G7YLP5 Visual system homeobox 1 9.55 31.10 sequence-specific DNA binding regulation of transcription, DNA-dependent nucleus DNA binding csin102452 - + G7Y7Y9 Peptidyl-prolyl isomerase E (Cyclophilin E) 5.91 25.24 RNA binding nucleic...”
PRRX1_CHICK / Q05437 Paired mesoderm homeobox protein 1; GMHOX; Homeobox protein MHOX; Paired-related homeobox protein 1; PRX-1 from Gallus gallus (Chicken) (see 2 papers)
68% identity, 23% coverage
- function: May participate in maintenance of mesenchymal cell lineages derived from both mesoderm and the neural crest and in patterning of the limbs and the face
subunit: Interacts with MAF and MAFB.
ptx1 / CAA04801.1 Ptx1 homeodomain protein from Drosophila melanogaster (see paper)
55% identity, 14% coverage
PRRX1_MOUSE / P63013 Paired mesoderm homeobox protein 1; Homeobox protein K-2; Muscle homeobox protein; MHox; Paired-related homeobox protein 1; PRX-1 from Mus musculus (Mouse) (see 4 papers)
NP_035257 paired mesoderm homeobox protein 1 isoform a from Mus musculus
NP_722543 paired mesoderm homeobox protein 1 from Rattus norvegicus
68% identity, 23% coverage
- function: Master transcription factor of stromal fibroblasts for myofibroblastic lineage progression. Orchestrates the functional drift of fibroblasts into myofibroblastic phenotype via TGF-beta signaling by remodeling a super-enhancer landscape. Through this function, plays an essential role in wound healing process (PubMed:35589735). Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer (PubMed:1360403). May play a role in homeostasis and regeneration of bone, white adipose tissue and derm (PubMed:36456880).
function: [Isoform 1]: Transcriptional activator, when transfected in fibroblastic or myoblastic cell lines. This activity may be masked by the C-terminal OAR domain.
function: [Isoform 2]: Transcriptional repressor, when transfected in fibroblastic or myoblastic cell lines.
subunit: Interacts with SMAD3. - A proteomic analysis reveals that Snail regulates the expression of the nuclear orphan receptor Nuclear Receptor Subfamily 2 Group F Member 6 (Nr2f6) and interleukin 17 (IL-17) to inhibit adipocyte differentiation.
Peláez-García, Molecular & cellular proteomics : MCP 2015 - Identification of the homeobox protein Prx1 (MHox, Prrx-1) as a regulator of osterix expression and mediator of tumor necrosis factor α action in osteoblast differentiation
Lu, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2011 - “...Q5SUS9 PRX1 Paired mesoderm homeobox protein 1 Early limb bud, bone, and vascular differentiation factor P63013 TNF-displaced CRP-2 Cysteine-rich protein 2 (DLP-2) Mesenchyme smooth muscle differentiation factor; LIM protein expressed e9.5-e16.5 in smooth muscle P97315 HCC-1 DNA-binding factor, inhibits cell growth Q9D1J3 Moesin Membrane-organizing extension spike...”
- Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.
Tooze, Genetics in medicine : official journal of the American College of Medical Genetics 2023 - GeneRIF: Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.
- Age-Progressive and Gender-Dependent Bone Phenotype in Mice Lacking Both Ebf1 and Ebf2 in Prrx1-Expressing Mesenchymal Cells.
Nieminen-Pihala, Calcified tissue international 2022 - GeneRIF: Age-Progressive and Gender-Dependent Bone Phenotype in Mice Lacking Both Ebf1 and Ebf2 in Prrx1-Expressing Mesenchymal Cells.
- PRRX1 is a master transcription factor of stromal fibroblasts for myofibroblastic lineage progression.
Lee, Nature communications 2022 - GeneRIF: PRRX1 is a master transcription factor of stromal fibroblasts for myofibroblastic lineage progression.
- Genetic association and characterization of FSTL5 in isolated clubfoot.
Khanshour, Human molecular genetics 2021 - GeneRIF: Genetic association and characterization of FSTL5 in isolated clubfoot.
- Isolation of PRRX1-positive adult pituitary stem/progenitor cells from the marginal cell layer of the mouse anterior lobe.
Shintani, Stem cell research 2021 (PubMed)- GeneRIF: Isolation of PRRX1-positive adult pituitary stem/progenitor cells from the marginal cell layer of the mouse anterior lobe.
- PRRX1 deficiency induces mesenchymal-epithelial transition through PITX2/miR-200-dependent SLUG/CTNNB1 regulation in hepatocellular carcinoma.
Chen, Cancer science 2021 - GeneRIF: PRRX1 deficiency induces mesenchymal-epithelial transition through PITX2/miR-200-dependent SLUG/CTNNB1 regulation in hepatocellular carcinoma.
- Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.
Leavitt, Cell reports 2020 - GeneRIF: Prrx1 Fibroblasts Represent a Pro-fibrotic Lineage in the Mouse Ventral Dermis.
- Primary cilia are necessary for Prx1-expressing cells to contribute to postnatal skeletogenesis.
Moore, Journal of cell science 2018 - GeneRIF: Cambium layer osteochondroprogenitors cells expressing Prx1, are programmed to rapidly populate distant tissues and produce bone via a primary cilium-mediated mechanism in the postnatal skeleton.
- More
- Transcription Factor prrx1 Promotes Brown Adipose-Derived Stem Cells Differentiation to Sinus Node-Like Cells.
Yin, DNA and cell biology 2019 - GeneRIF: Overexpression of prrx1 can successfully induce sinus node-like cells.
- Paired related homeobox protein 1 regulates PDGF-induced chemotaxis of hepatic stellate cells in liver fibrosis.
Gong, Laboratory investigation; a journal of technical methods and pathology 2017 (PubMed)- GeneRIF: Studied and identified Prrx1 as a novel valuable target in liver fibrosis. Prxx1 was found to have a major role in PDGF-induced migration and chemotaxis.
- Expression of Peroxiredoxins and Pulmonary Surfactant Protein A Induced by Silica in Rat Lung Tissue.
Liu, Biomedical and environmental sciences : BES 2016 (PubMed)- GeneRIF: Prdx1 and Prdx6 proteins is involved in pulmonary fibrosis induced by silica.
- Expression of Prx1 and Tcf4 is decreased in the diaphragmatic muscle connective tissue of nitrofen-induced congenital diaphragmatic hernia.
Takahashi, Journal of pediatric surgery 2016 (PubMed)- GeneRIF: expression of Prx1 and Tcf4 is decreased in the developing diaphragm in the nitrofen-induced congenital diaphragmatic hernia in Sprague- Dawley rats animal model.
- PRRX1- and PRRX2-positive mesenchymal stem/progenitor cells are involved in vasculogenesis during rat embryonic pituitary development.
Higuchi, Cell and tissue research 2015 (PubMed)- GeneRIF: PRRX1- and PRRX2-positive mesenchymal stem/progenitor cells are present at the periphery of the embryonic pituitary and participate in pituitary vasculogenesis by differentiation into vascular endothelial cells and pericytes.
- PRRX1 and PRRX2 distinctively participate in pituitary organogenesis and a cell-supply system.
Higuchi, Cell and tissue research 2014 (PubMed)- GeneRIF: Thus, PRRX1 and PRRX2 might participate distinctly in pituitary organogenesis and the postnatal cell-supply system.
- Expression of Krüppel-like factor 6, KLF6, in rat pituitary stem/progenitor cells and its regulation of the PRRX2 gene.
Ueharu, The Journal of reproduction and development 2014 - GeneRIF: expression not stimulated by Klf6
- Temporospatial gene expression of Prx1 and Prx2 is involved in morphogenesis of cranial placode-derived tissues through epithelio-mesenchymal interaction during rat embryogenesis.
Higuchi, Cell and tissue research 2013 (PubMed)- GeneRIF: During advanced embryogenesis, either PRX2-positive cells become condensed in the border of SOX2-positive cells or PRX1 and/or PRX2 become co-localized with SOX2.
- More
PRRX1_HUMAN / P54821 Paired mesoderm homeobox protein 1; Homeobox protein PHOX1; Paired-related homeobox protein 1; PRX-1 from Homo sapiens (Human) (see 3 papers)
68% identity, 23% coverage
- function: Master transcription factor of stromal fibroblasts for myofibroblastic lineage progression. Orchestrates the functional drift of fibroblasts into myofibroblastic phenotype via TGF-beta signaling by remodeling a super-enhancer landscape. Through this function, plays an essential role in wound healing process (PubMed:35589735). Acts as a transcriptional regulator of muscle creatine kinase (MCK) and so has a role in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer (By similarity). May play a role in homeostasis and regeneration of bone, white adipose tissue and derm (By similarity).
function: [Isoform 1]: Transcriptional activator, when transfected in fibroblastic or myoblastic cell lines. This activity may be masked by the C-terminal OAR domain.
function: [Isoform 2]: Transcriptional repressor, when transfected in fibroblastic or myoblastic cell lines.
subunit: Interacts with SMAD3. - Hydrophilic Components as Key Active Ingredients in Adipose-Derived Matrix Bioscaffolds for Inducing Fat Regeneration.
Ma, Advanced healthcare materials 2024 - “...0.043098283 1.26 27 Q16656 NRF1 6.01 1.91728E06 0.202 28 Q8WVV4 POF1B 6.00 1.74875E05 0.873 29 P54821 PRRX1 5.98 1.50844E05 0.79 30 P19237 TNNI1 5.94 1.59647E06 0.791 John Wiley & Sons, Ltd. 3.3.2 Dynamic Water Contact Angle To confirm the hydrophilicity and hydrophobicity of HDAM and LDAM,...”
- Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.
Tooze, Genetics in medicine : official journal of the American College of Medical Genetics 2023 - “...the deletion extends beyond the PRRX1 gene. B. A schematic representation of the PRRX1a protein (P54821) showing the position of the homeodomain and the OAR domain. Variants identified in this study are highlighted in red, whereas variants reported in patients with agnathia-otocephaly are shown in blue....”
NP_001080981 pituitary homeobox 1 from Xenopus laevis
66% identity, 21% coverage
Q63410 Homeobox protein OTX1 from Rattus norvegicus
59% identity, 19% coverage
XP_014951176 pituitary homeobox 1 from Ovis aries
61% identity, 22% coverage
XP_006711451 paired mesoderm homeobox protein 1 isoform X1 from Homo sapiens
68% identity, 29% coverage
- LncRNA KIFAP3-5:1 inhibits epithelial-mesenchymal transition of renal tubular cell through PRRX1 in diabetic nephropathy.
Du, Cell biology and toxicology 2024 - GeneRIF: LncRNA KIFAP3-5:1 inhibits epithelial-mesenchymal transition of renal tubular cell through PRRX1 in diabetic nephropathy.
- A PRRX1 Signature Identifies TIM-3 and VISTA as Potential Immune Checkpoint Targets in a Subgroup of Microsatellite Stable Colorectal Cancer Liver Metastases.
Nygaard, Cancer research communications 2023 - GeneRIF: A PRRX1 Signature Identifies TIM-3 and VISTA as Potential Immune Checkpoint Targets in a Subgroup of Microsatellite Stable Colorectal Cancer Liver Metastases.
- Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.
Tooze, Genetics in medicine : official journal of the American College of Medical Genetics 2023 - GeneRIF: Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance.
- PRRX1 induced by BMP signaling decreases tumorigenesis by epigenetically regulating glioma-initiating cell properties via DNA methyltransferase 3A.
Tanabe, Molecular oncology 2022 - GeneRIF: PRRX1 induced by BMP signaling decreases tumorigenesis by epigenetically regulating glioma-initiating cell properties via DNA methyltransferase 3A.
- Transcription factor paired related homeobox 1 (PRRX1) activates matrix metalloproteinases (MMP)13, which promotes the dextran sulfate sodium-induced inflammation and barrier dysfunction of NCM460 cells.
Zhang, Bioengineered 2022 - GeneRIF: Transcription factor paired related homeobox 1 (PRRX1) activates matrix metalloproteinases (MMP)13, which promotes the dextran sulfate sodium-induced inflammation and barrier dysfunction of NCM460 cells.
- Paired related homeobox 1 attenuates autophagy via acetyl-CoA carboxylase 1-regulated fatty acid metabolism in salivary adenoid cystic carcinoma.
Gao, FEBS open bio 2022 - GeneRIF: Paired related homeobox 1 attenuates autophagy via acetyl-CoA carboxylase 1-regulated fatty acid metabolism in salivary adenoid cystic carcinoma.
- PRRX1 Is a Novel Prognostic Biomarker and Facilitates Tumor Progression Through Epithelial-Mesenchymal Transition in Uveal Melanoma.
Meng, Frontiers in immunology 2022 - GeneRIF: PRRX1 Is a Novel Prognostic Biomarker and Facilitates Tumor Progression Through Epithelial-Mesenchymal Transition in Uveal Melanoma.
- Exosomal circPRRX1 functions as a ceRNA for miR-596 to promote the proliferation, migration, invasion, and reduce radiation sensitivity of gastric cancer cells via the upregulation of NF-κB activating protein.
He, Anti-cancer drugs 2022 (PubMed)- GeneRIF: Exosomal circPRRX1 functions as a ceRNA for miR-596 to promote the proliferation, migration, invasion, and reduce radiation sensitivity of gastric cancer cells via the upregulation of NF-kappaB activating protein.
- More
XP_017207930 paired mesoderm homeobox protein 1b isoform X2 from Danio rerio
68% identity, 21% coverage
PITX1_MOUSE / P70314 Pituitary homeobox 1; Hindlimb-expressed homeobox protein backfoot; Homeobox protein P-OTX; Homeobox protein PITX1; Paired-like homeodomain transcription factor 1; Pituitary OTX-related factor from Mus musculus (Mouse) (see 3 papers)
XP_006517220 pituitary homeobox 1 isoform X1 from Mus musculus
61% identity, 22% coverage
- function: Sequence-specific transcription factor that binds gene promoters and activates their transcription. May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb. Can independently activate and synergize with PIT-1 on pituitary-specific target gene promoters, thus may subserve functions in generating both precursor and specific cell phenotypes in the anterior pituitary gland and in several other organs. Can activate pituitary transcription of the proopiomelanocortin gene.
subunit: Interacts with POU1F1. - Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer.
Rouco, Nature communications 2021 - GeneRIF: Cell-specific alterations in Pitx1 regulatory landscape activation caused by the loss of a single enhancer.
- Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.
Roseman, Journal of experimental zoology. Part B, Molecular and developmental evolution 2020 (PubMed)- GeneRIF: Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.
- De Novo PITX1 Expression Controls Bi-Stable Transcriptional Circuits to Govern Self-Renewal and Differentiation in Squamous Cell Carcinoma.
Sastre-Perona, Cell stem cell 2019 - GeneRIF: The PITX1 is specifically expressed in TPCs, where it co-localizes with SOX2 and TRP63 and determines cell fate in mouse and human squamous cell carcinoma (SCC).
- Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition.
Karam, Scientific reports 2019 - GeneRIF: Bone-Specific Overexpression of PITX1 Induces Senile Osteoporosis in Mice Through Deficient Self-Renewal of Mesenchymal Progenitors and Wnt Pathway Inhibition.
- PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets.
Wang, Developmental biology 2018 - GeneRIF: data suggest that PITX1 promotes chondrogenesis and myogenesis in the hindlimb by direct regulation of several key members of the cartilage and muscle transcriptional networks.
- Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development.
Sarro, Development (Cambridge, England) 2018 - GeneRIF: Pitx1 distal enhancer loss have only mild effects on Pitx1 expression in the hindlimb and no overt effects on hindlimb or mandibular morphology.
- Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis.
Kragesteen, Nature genetics 2018 - GeneRIF: Pitx1 is controlled by an enhancer (Pen) that shows activity in forelimbs and hindlimbs. Forelimbs and hindlimbs have fundamentally different chromatin configurations, whereby Pen and Pitx1 interact in hindlimbs and are physically separated in forelimbs. Structural variants can convert the inactive into the active conformation, thereby inducing Pitx1 misexpression in forelimbs.
- Pitx1 determines characteristic hindlimb morphologies in cartilage micromass culture.
Butterfield, PloS one 2017 - GeneRIF: Results indicate autonomously programmed differences in forelimb and hindlimb cartilage precursors of the limb skeleton are controlled, at least in part, by Pitx1 and suggest this has an important role in generating distinct limb-type morphologies.
- More
GSB_DROME / P09082 Protein gooseberry; BSH9; Protein gooseberry distal from Drosophila melanogaster (Fruit fly) (see paper)
NP_523863 gooseberry from Drosophila melanogaster
67% identity, 15% coverage
- function: Expressed in segmentally repeating pattern to define the polarity of embryonic segments.
- The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes
Wheat, Molecular and cellular biology 1999 - “...proximal (Gsb-p; P09083), Gooseberry distal (Gsb-d; P09082), Sparkling (AF010256), Eyeless (X79492), Pox-meso (P23757), and Pox-neuro (P23758); and C....”
- Differential and redundant functions of gooseberry and gooseberry neuro in the central nervous system and segmentation of the Drosophila embryo.
He, Developmental biology 2013 (PubMed)- GeneRIF: gsb and gsbn share overlapping functions in segmentation and the central nervous system.
- Formation and specification of a Drosophila dopaminergic precursor cell.
Watson, Development (Cambridge, England) 2012 - GeneRIF: Data show that the gooseberry/gooseberry-neuro (gsb/gsb-n) transcription factor genes act to specify MP3 cell fate.
- Synaptic homeostasis is consolidated by the cell fate gene gooseberry, a Drosophila pax3/7 homolog.
Marie, The Journal of neuroscience : the official journal of the Society for Neuroscience 2010 - GeneRIF: This study demonstrated that the transcription factor gooseberry is essential for the sustained expression of synaptic homeostasis at the Drosophila NMJ.
NP_001286652 orthopedia, isoform I from Drosophila melanogaster
67% identity, 15% coverage
OTP_DROME / P56672 Homeobox protein orthopedia from Drosophila melanogaster (Fruit fly) (see paper)
67% identity, 13% coverage
PITX1_HUMAN / P78337 Pituitary homeobox 1; Hindlimb-expressed homeobox protein backfoot; Homeobox protein PITX1; Paired-like homeodomain transcription factor 1 from Homo sapiens (Human) (see 4 papers)
NP_002644 pituitary homeobox 1 from Homo sapiens
64% identity, 20% coverage
- function: Sequence-specific transcription factor that binds gene promoters and activates their transcription. May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb.
subunit: Interacts with POU1F1 (PubMed:26612202). - PITX1 suppresses osteosarcoma metastasis through exosomal LINC00662-mediated M2 macrophage polarization.
Zhang, Clinical & experimental metastasis 2023 - GeneRIF: PITX1 suppresses osteosarcoma metastasis through exosomal LINC00662-mediated M2 macrophage polarization.
- What Is the Exact Contribution of PITX1 and TBX4 Genes in Clubfoot Development? An Italian Study.
Bianco, Genes 2022 - GeneRIF: What Is the Exact Contribution of PITX1 and TBX4 Genes in Clubfoot Development? An Italian Study.
- CircPITX1 Regulates Proliferation, Angiogenesis, Migration, Invasion, and Cell Cycle of Human Glioblastoma Cells by Targeting miR-584-5p/KPNB1 Axis.
Cao, Journal of molecular neuroscience : MN 2021 (PubMed)- GeneRIF: CircPITX1 Regulates Proliferation, Angiogenesis, Migration, Invasion, and Cell Cycle of Human Glioblastoma Cells by Targeting miR-584-5p/KPNB1 Axis.
- Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer.
Li, BMC cancer 2021 - GeneRIF: Differential gene expression identifies a transcriptional regulatory network involving ER-alpha and PITX1 in invasive epithelial ovarian cancer.
- PITX1 inhibits the growth and proliferation of melanoma cells through regulation of SOX family genes.
Ohira, Scientific reports 2021 - GeneRIF: PITX1 inhibits the growth and proliferation of melanoma cells through regulation of SOX family genes.
- Upregulated Transcription Factor PITX1 Predicts Poor Prognosis in Kidney Renal Clear Cell Carcinoma-Based Bioinformatic Analysis and Experimental Verification.
Zhang, Disease markers 2021 - GeneRIF: Upregulated Transcription Factor PITX1 Predicts Poor Prognosis in Kidney Renal Clear Cell Carcinoma-Based Bioinformatic Analysis and Experimental Verification.
- Rare and de novo duplications containing SHOX in clubfoot.
Sadler, Journal of medical genetics 2020 - GeneRIF: Rare and de novo duplications containing SHOX in clubfoot.
- Mandibular-pelvic-patellar syndrome is a novel PITX1-related disorder due to alteration of PITX1 transactivation ability.
Morel, Human mutation 2020 (PubMed)- GeneRIF: Mandibular-pelvic-patellar syndrome is a novel PITX1-related disorder due to alteration of PITX1 transactivation ability.
- More
K1QWY6 Paired box protein Pax-6 from Magallana gigas
61% identity, 20% coverage
- The Pax gene family: Highlights from cephalopods.
Navet, PloS one 2017 - “...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 Pax2/5/8 Crassostrea_gigas Mollusca_Bivalvia K1R3J2 Paired box protein Pax-2-A Pax Crassostrea_gigas Mollusca_Bivalvia K1S548 Paired box protein Pax-6 Pax(?) Crassostrea_gigas...”
- “...62 ]. Two sequences previously identified as Pax6 ( Lottia gigantea A0A0B6VJL1 and Crassostrea gigas K1QWY6) were in fact identified as eyegone homologues. This gene was also present in Pinctada genome: two sequences have already been signalled, most likely reflecting two allelic copies [ 55 ]....”
XP_015145717 paired mesoderm homeobox protein 1 isoform X2 from Gallus gallus
68% identity, 27% coverage
Smp_160670 putative paired box protein pax-6 from Schistosoma mansoni
63% identity, 5% coverage
- Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators
Wood, Pathogens (Basel, Switzerland) 2023 - “...factor 4 (Fgf4, Smp_035730), Cyclin dependent kinase 5 (Cdk5, Smp_073340), Paired box protein 6 (Pax6, Smp_160670), and Notch Receptor 1 (Notch1, Smp_311360) [ 5 , 9 , 14 , 45 , 49 , 50 ]. We were able to identify sequences that correlate to the Sox...”
CRX_MOUSE / O54751 Cone-rod homeobox protein from Mus musculus (Mouse) (see paper)
NP_031796 cone-rod homeobox protein isoform 1 from Mus musculus
67% identity, 19% coverage
- function: Transcription factor that binds and transactivates the sequence 5'-TAATC[CA]-3' which is found upstream of several photoreceptor-specific genes, including the opsin genes. Acts synergistically with other transcription factors, such as NRL, RORB and RAX, to regulate photoreceptor cell-specific gene transcription. Essential for the maintenance of mammalian photoreceptors.
subunit: Interacts (via the homeobox) with NRL (via the leucine-zipper domain). Interacts with PDC, RAX2, RORB and SCA7. - Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...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 P20612 Gnat1 guanine nucleotide-binding protein G(t) subunit alpha-1 86 modulator or...”
- Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors.
Shepherdson, Genome research 2024 - GeneRIF: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors.
- Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms.
Zheng, eLife 2023 - GeneRIF: Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms.
- Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development.
Yamamoto, Cell reports 2020 (PubMed)- GeneRIF: Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development.
- CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites.
Ruzycki, Epigenetics & chromatin 2018 - GeneRIF: CRX is required for chromatin remodeling at only a subset of its binding sites, which undergo retina or neuronal specific activation during photoreceptor differentiation.
- Cone-rod homeobox CRX controls presynaptic active zone formation in photoreceptors of mammalian retina.
Assawachananont, Human molecular genetics 2018 - GeneRIF: A Crx-dependent gene regulatory network was unraveled involving presynaptic genes that encode cytomatrix-associated proteins governing the organization of the photoreceptor ribbon synapse but not the formation of ribbon structure.
- A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo.
Hughes, Genome research 2018 - GeneRIF: Results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.
- [Exogenous CRX gene induces Müller cell-derived progenitors to differentiate into photoreceptors].
Ji, [Zhonghua yan ke za zhi] Chinese journal of ophthalmology 2018 (PubMed)- GeneRIF: CRX gene could induce the differentiation of Muller cell-derived progenitor into rod photoreceptors, indicating a new avenue to study muller cells as endogenous seed cells for retinal photoreceptor
- Diurnal expression of proteins in the retina of the blind cone-rod homeobox (Crx-/- ) mouse and the 129/Sv mouse: a proteomic study.
Møller, Acta ophthalmologica 2017 (PubMed)- GeneRIF: proteins involved in phototransduction were not detected in the Crx(-/-) mouse; in this phenotype, however, proteins from spots showing diurnal rhythms were specifically identified as enzymes involved in glucose metabolism, Krebs cycle, and mitochondrial enzymes.
- More
Smp_163140 pituitary homeobox protein-related from Schistosoma mansoni
57% identity, 8% coverage
CRX_HUMAN / O43186 Cone-rod homeobox protein from Homo sapiens (Human) (see 10 papers)
NP_000545 cone-rod homeobox protein from Homo sapiens
67% identity, 19% coverage
- function: Transcription factor that binds and transactivates the sequence 5'-TAATC[CA]-3' which is found upstream of several photoreceptor-specific genes, including the opsin genes. Acts synergistically with other transcription factors, such as NRL, RORB and RAX, to regulate photoreceptor cell-specific gene transcription. Essential for the maintenance of mammalian photoreceptors.
subunit: Interacts (via the homeobox) with NRL (via the leucine-zipper domain). Interacts with PDC, RAX2, RORB and SCA7. - Atypic Retinitis Pigmentosa Clinical Features Associated with a Peculiar CRX Gene Mutation in Italian Patients.
Piergentili, Medicina (Kaunas, Lithuania) 2024 - GeneRIF: Atypic Retinitis Pigmentosa Clinical Features Associated with a Peculiar CRX Gene Mutation in Italian Patients.
- Distantly Metastatic Retinoblastoma to Soft Tissue and Bone: A Challenging Diagnosis Highlighting the Utility of CRX.
Meredith, The American journal of surgical pathology 2021 (PubMed)- GeneRIF: Distantly Metastatic Retinoblastoma to Soft Tissue and Bone: A Challenging Diagnosis Highlighting the Utility of CRX.
- Downregulation of CRX, a Group 3-specific oncogenic transcription factor, inhibits TGF-β/activin signaling in medulloblastoma cells.
Masurkar, Biochemical and biophysical research communications 2021 (PubMed)- GeneRIF: Downregulation of CRX, a Group 3-specific oncogenic transcription factor, inhibits TGF-beta/activin signaling in medulloblastoma cells.
- Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model.
Chirco, Stem cell reports 2021 - GeneRIF: Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model.
- Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association.
Fujinami-Yokokawa, Scientific reports 2020 - GeneRIF: Clinical and Genetic Characteristics of 18 Patients from 13 Japanese Families with CRX-associated retinal disorder: Identification of Genotype-phenotype Association.
- A novel CRX variant (p.R98X) is identified in a Chinese family of Retinitis pigmentosa with atypical and mild manifestations.
Zhu, Genes & genomics 2019 (PubMed)- GeneRIF: A heterozygous nonsense variant c.292C > T (p.R98X) of CRX gene was identified in a Chinese family with atypical and mild manifestations of Retinitis pigmentosa.
- A case-control collapsing analysis identifies retinal dystrophy genes associated with ophthalmic disease in patients with no pathogenic ABCA4 variants.
Wolock, Genetics in medicine : official journal of the American College of Medical Genetics 2019 - GeneRIF: two known retinal dystrophy genes, PRPH2 and CRX, achieved study-wide significance (p < 1.33 x 10-6) under a dominant disease model
- Retinal dystrophies with bull's-eye maculopathy along with negative ERGs.
Nasser, Documenta ophthalmologica. Advances in ophthalmology 2019 (PubMed)- GeneRIF: The five patients with bull's-eye maculopathy along with a negative ERG had differing genotypes. Mutations were found in the CRX gene (2 patients), the ABCA4 gene (1 patient), and the GUCY2D gene (2 patients).
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- Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain.
Shepherdson, Genome research 2024 - “...[PDB; https://www.rcsb.org ] 1FJL), as well as the AlphaFold2-predicted structure for CRX (corresponding to UniProt O43186). Using UCSF ChimeraX (v1.7, https://www.cgl.ucsf.edu/chimerax/ ), we aligned the CRX-predicted structure to the paired homeodomain crystal structure with the matchmaker tool ( Meng et al. 2006 ). After alignment, we...”
- Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research.
Zheng, Frontiers in cellular neuroscience 2024 - “...comprehensive evidence on CRX protein functions. The Cone-rod homeobox ( CRX , OMIM: 602225, UniProt: O43186) gene encodes a homeodomain transcription factor that regulates gene expression programs essential for photoreceptor development, function, and maintenance. Coding variants in CRX have been associated with at least three types...”
- Structural and functional analysis of the human cone-rod homeobox transcription factor.
Clanor, Proteins 2022 - “...Computational sequence analysis DNA and protein sequences of human CRX were obtained from Uniprot entry O43186. For the sequence properties analysis in Figure 1B and D , the protein sequence was imported into R, and the amino acids were binned by properties. For visualization of the...”
- Genetic, environmental and other risk factors for progression of retinitis pigmentosa.
Huang, International journal of ophthalmology 2022 - In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements.
Hossain, Molecular vision 2018 - “...sites [ 25 ]. Homology modeling of human CRX binding site The UniProt accession number O43186 was used for modeling and assembly of human CRX [ 26 ]. The DNA binding domain of CRX, consisting of amino acids 3998, was generated using SWISS-MODEL [ 27 ]....”
- Priorities and trends in the study of proteins in eye research, 1924-2014
Semba, Proteomics. Clinical applications 2015 - “...angle, E; glaucoma, normal pressure; amyotrophic lateral sclerosis 12 3 isoforms 8 PTMs 60 variants O43186 CRX cone-rod homeobox protein 37 transcription factor, upstream of several photoreceptor-specific genes Leber congenital amaurosis 7; cone-rod dystrophy 2; retinitis pigmentosa 1 isoform 0 PTMs 47 variants P04637 TP53 cellular...”
- Genetic screening of LCA in Belgium: predominance of CEP290 and identification of potential modifier alleles in AHI1 of CEP290-related phenotypes.
Coppieters, Human mutation 2010 - “...( CRB1 ), Q16518 ( RPE65 ), Q02846 ( GUCY2D ), Q9NZN9 ( AIPL1 ), O43186 ( CRX ), Q96NR8 ( RDH12 ) and Q8N157 ( AHI1 ) ( http://www.uniprot.org/uniprot/ ). Variants were designated as unclassified variant (UV) if no consensus was seen in all prediction...”
PITX1_CHICK / P56673 Pituitary homeobox 1; Homeobox protein PITX1; Paired-like homeodomain transcription factor 1; cPTX1 from Gallus gallus (Chicken) (see 3 papers)
64% identity, 21% coverage
- function: Sequence-specific transcription factor that binds gene promoters and activates their transcription. May play a role in the development of anterior structures, and in particular, the brain and facies and in specifying the identity or structure of hindlimb. Acts as a transcriptional activator by binding to promoter sequences with a TAAT/GCC core motif.
- Quantitative iTRAQ LC-MS/MS proteomics reveals the proteome profiles of DF-1 cells after infection with subgroup J Avian leukosis virus.
Li, BioMed research international 2015 - “...Alpha-actinin-4 (Fragment) GN=ACTN4 515.20 0.834 71.6 6.09 Q5F4B1 Phosphoglycolate phosphatase GN=PGP 39.98 0.833 33.0 5.73 P56673 Pituitary homeobox 1 GN=PITX1 20.32 0.833 34.5 9.11 Q90611 72kDa type IV collagenase GN=MMP2 267.53 0.829 74.9 5.49 F1NME2 Integrin beta GN=ITGB5 51.04 0.828 88.4 6.71 F1NBZ7 Serine/threonine-protein phosphatase GN=PPP3CA...”
LOC100121225 paired mesoderm homeobox protein 2 from Nasonia vitripennis
64% identity, 24% coverage
- Bracon brevicornis Genome Showcases the Potential of Linked-Read Sequencing in Identifying a Putative Complementary Sex Determiner Gene
Ferguson, Genes 2020 - “...from this study) and searched with protein sequence from the following genes: tra (GeneID: 00121203), LOC100121225, LOC100678616, LOC100680007 originating from N. vitripennis ; fem (GeneID:724970), csd (GeneID:406074), LOC408733, LOC551408, LOC724886 originating from A. mellifera . The advanced settings for SimpleSynteny were as follows: BLAST E-value Threshold...”
- “...translocated closer to Nasonia tra and to a different scaffold in B. brevicornis. N. vitripennis LOC100121225 and LOC100678616 are encoded in opposing directions in both A. mellifera and N. vitripennis but are both downstream of tra in N. vitripennis and upstream of fem and csd in...”
NP_001284898 visual system homeobox 1, isoform B from Drosophila melanogaster
64% identity, 7% coverage
O96756 DtPax-6 protein from Girardia tigrina
54% identity, 12% coverage
- The Pax gene family: Highlights from cephalopods.
Navet, PloS one 2017 - “...Pax(f) Lottia_gigantea Mollusca_Gastropoda V3ZWA2 Uncharacterized protein PoxN(f) Lottia_gigantea Mollusca_Gastropoda Q25411 Pax6-like protein Pax6 Lineus_sanguineus Nemertea_Anopla O96756 DtPax-6 protein Pax6B Girardia_tigrina Platyhelminthes_Rhabditophora Accession: accession number or genome reference. Submitted name: name found in databases. Proposed name: our interpretation (grey background if different from a submitted name); (f)...”
NP_001161157 pituitary homeobox 1 from Gallus gallus
64% identity, 21% coverage
LOC107444630 homeobox protein unc-4 homolog from Parasteatoda tepidariorum
65% identity, 15% coverage
- Single-cell RNA sequencing of mid-to-late stage spider embryos: new insights into spider development
Medina-Jiménez, BMC genomics 2024 - “...cfGbs ) (LOC107446841), the transcription factor AP2.2 (LOC107443623) and the homeobox containing gene unc-4 like (LOC107444630) ( Drosophila DPHD-1 ). Information about the two top markers unc4096 and cfGbs is not available. AP2 , however, has been investigated in some detail. In Drosophila , this gene...”
- “...by two genes that have been investigated as top markers of other clusters, unc-4 like (LOC107444630) (Fig. 9 c-f, cf. Cluster-XV) and the uncharacterized gene unc6289 (LOC107436289) (Supplementary Fig. 23 , cf. Cluster-VIII). Both are expressed in similar patterns in the appendages suggesting a function during...”
HMOC_DROME / P22810 Homeotic protein ocelliless; Protein orthodenticle from Drosophila melanogaster (Fruit fly) (see 3 papers)
NP_001259345 ocelliless, isoform G from Drosophila melanogaster
62% identity, 12% coverage
- function: Transcriptional regulator involved in pattern formation and cell determination in the embryonic CNS and larval imaginal disks. Also later in development to coordinate the expression of regulatory and structural genes required for photoreceptor cell fate in the ocelli. Has a dual role in the terminal differentiation of subtypes of photoreceptors by regulating rhodopsin (rh) expression: essential for establishing the expression of rh genes in the pale subset of ommatidia as well as repressing Rh6 in outer photoreceptors.
disruption phenotype: In embryos, formation of an abnormal neuropil and the disappearance of the horizontal commissures associated with the midline of the CNS. In pupae, misshapen, duplicated, and shortened rhabdomeres within the eye. In adults, deletion of the ocelli. - Regulation of twin of eyeless during Drosophila development.
Skottheim, Gene expression patterns : GEP 2016 (PubMed)- GeneRIF: Our results indicate that the head-specific gap gene empty spiracles can act as a repressor of Toy, while ocelliless (oc) and spalt major (salm) appear to act as positive regulators of toy gene expression
- Orthodenticle Is Required for the Expression of Principal Recognition Molecules That Control Axon Targeting in the Drosophila Retina.
Mencarelli, PLoS genetics 2015 - GeneRIF: Otd is a main component of the gene regulatory network that regulates synaptic-column and layer targeting in the fly visual system.
- Orthodenticle and Kruppel homolog 1 regulate Drosophila photoreceptor maturation.
Fichelson, Proceedings of the National Academy of Sciences of the United States of America 2012 - GeneRIF: The conserved homeobox protein Orthodenticle acts together with the ecdysone receptor to directly repress the expression of Kruppel homolog 1.
- Orthodenticle is necessary for survival of a cluster of clonally related dopaminergic neurons in the Drosophila larval and adult brain.
Blanco, Neural development 2011 - GeneRIF: Orthodenticle is expressed in a group of clonally related dopamine neurons from first instar larvae to adulthood, making it possible to establish an identity relationship between larval and adult dopamine neuron clusters.
- Pph13 and orthodenticle define a dual regulatory pathway for photoreceptor cell morphogenesis and function.
Mishra, Development (Cambridge, England) 2010 - GeneRIF: Although Otd and Pph13 have been implicated in rhabdomere morphogenesis, we demonstrate that it is necessary to remove both factors to completely eliminate rhabdomere formation.
- Separable transcriptional regulatory domains within Otd control photoreceptor terminal differentiation events.
McDonald, Developmental biology 2010 - GeneRIF: Sequence analysis indicates that many of the transcriptional regulatory domains identified here are conserved in multiple Diptera Otd-related proteins.
- Analysis of the Otd-dependent transcriptome supports the evolutionary conservation of CRX/OTX/OTD functions in flies and vertebrates.
Ranade, Developmental biology 2008 - GeneRIF: Otd as a critical regulator of photoreceptor morphology and phototransduction
- Anteroposterior regionalization of the brain: genetic and comparative aspects.
Lichtneckert, Advances in experimental medicine and biology 2008 (PubMed)- GeneRIF: Data show that otd/Otx gene is involved in the specification of the anterior brain during embryonic CNS development in Drosophila.
- More
- Development of the larval anterior neurogenic domains of Terebratalia transversa (Brachiopoda) provides insights into the diversification of larval apical organs and the spiralian nervous system
Santagata, EvoDevo 2012 - “...(722629); Drosophila dll (NP (523857); Drosophila gsc (NP (476949); Drosophila homeobrain (NP (788420); Drosophila otd (P22810); Drosophila otp (P56672); Drosophila repo (NP (477026); Drosophila rx (NP (726006); Hydroides otx (ABK76302); Platynereis Arx (ADG26723); Platynereis Cdx (ACH87546); Platynereis Gsx (ACH87540); Platynereis Pax6 (CAJ40659); Platynereis Xlox (ACH87551); Platynereis...”
- Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development
Karlin, Proceedings of the National Academy of Sciences of the United States of America 1996 - “...Deformed (P07548) DGK (Q01583) Knirps (P10734) Orthodenticle (P22810) Topoisomerase I (P30189) Eyes absent (Q05201) Antennapedia (P02833) Cut (P10180) Hairless...”
XP_033105362 homeobox protein OTX-like isoform X1 from Anneissia japonica
57% identity, 23% coverage
NP_001027662 Otx from Ciona intestinalis
62% identity, 14% coverage
OTP_PARLI / O76971 Homeobox protein orthopedia; Orthopedia-related; PlOtp from Paracentrotus lividus (Common sea urchin) (see 2 papers)
71% identity, 14% coverage
- function: Involved in larval skeletal patterning.
- Differential regulation of the zebrafish orthopedia 1 gene during fate determination of diencephalic neurons
Del, BMC developmental biology 2006 - “...vulgata , Otp AF440099; Lv, Lytechinus variegatus , Otp AAR17090; Pl, Paracentrotus lividus , Otp O76971; Ht, Heliocidaris tuberculata , Otp AAS00592; He, Heliocidaris erythrogramma , Otp AAS00591; Ds, Drosophila subobscura , Antp X60995; Dv, Drosophila virilis , Antp AY333070; Am, Apis mellifera , Antp NM_001011571;...”
OTP_HELTB / Q6SR68 Homeobox protein orthopedia from Heliocidaris tuberculata (Sea urchin) (see paper)
71% identity, 14% coverage
- function: Involved in larval skeletal patterning
BARH1_DROME / Q24255 Homeobox protein B-H1; Homeobox protein BarH1 from Drosophila melanogaster (Fruit fly) (see 5 papers)
NP_523387 BarH1, isoform A from Drosophila melanogaster
44% identity, 14% coverage
- function: B-H1 and B-H2 are regulated by members of the wg signaling pathway; wg and dpp. B-H1 and B-H2 are coexpressed and functionally required in R1 and R6 receptor cells and primary pigment cells for normal eye development. Coexpression is also required for the fate determination of external sensory organs, formation of notal microchaetae, formation of presutural macrochaetae, antennal development and for distal leg morphogenesis; segmentation and specification of tarsal segments 3-5.
- Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria
Winchell, Development genes and evolution 2010 - “...ACN66454, CAJ38799, P53772, NP_001027820, NP_001123282, AAV85986, AAG41498, NP_571380, NP_001093727, NP_001074359, XP_001638618, NP_005211, Q18273, NP_001158403, CAJ38810, NP_523387, NP_031552. b Gene tree for sequences related to Drosophila dachshund , rooted with Ski and Sno homologs. GenBank accession numbers for the analyzed sequences, in order from top to bottom...”
UNC30_CAEEL / P52906 Homeobox protein unc-30; Uncoordinated protein 30 from Caenorhabditis elegans (see 4 papers)
NP_001021277 Homeobox protein unc-30 from Caenorhabditis elegans
56% identity, 23% coverage
OTP_SACKO / Q7YTC2 Homeobox protein orthopedia from Saccoglossus kowalevskii (Acorn worm) (see paper)
71% identity, 16% coverage
OTXH_CAEEL / Q9U2Z0 Homeobox protein ttx-1; Abnormal thermotaxis protein 1; OTX homeobox homolog ttx-1 from Caenorhabditis elegans (see 4 papers)
56% identity, 18% coverage
- function: Probable transcription factor (PubMed:21350017, PubMed:25614239). Binds to a motif including the sequence 5'-TAA[TG]-3' in regulatory promoter elements (PubMed:21350017, PubMed:25614239). Modulates expression of its own, and of various other, genes in the AFD thermosensory neurons or AMsh amphid sheath glia, incuding the nuclear hormone receptor nhr-38, the LIM homeobox ceh-14, cyclic nucleotide- gated channel tax-2, receptor-type guanylyl cyclase gcy-8 and VEGF- related protein ver-1 (PubMed:11580895, PubMed:21350017, PubMed:25614239). Required for the development and cell fate of AFD neurons (PubMed:11580895, PubMed:21350017, PubMed:22298710). In concert with ceh-14, perhaps as components in a complex, specifies identity of AFD neurons, acting by synergistically regulating gcy-8, gcy-18 and other genes (PubMed:25614239). Involved in thermosensory behavior, thereby regulating entry and exit into the dauer larval stage of development (PubMed:11580895). Required in amphid sheath AMsh glia remodeling during entry into dauer stage, acting by positively regulating the expression of ver-1 in AMsh of amphid sensory neurons (PubMed:21350017, PubMed:22298710). May be essential for early development (PubMed:22298710).
LOC724282 homeobox protein orthopedia from Apis mellifera
65% identity, 15% coverage
- Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies
Panyushev, Genes 2024 - “...]. Using a combination of markers (LOC413466 ( oaz ), LOC410657 ( acj6 ), and LOC724282 ( opt )), we identified two clusters of olfactory projection neurons (clusters 11 and 12) [ 49 , 52 ]. OLCs: The optic lobes of the honey bee are responsible...”
- Single-cell transcriptomic analysis of honeybee brains identifies vitellogenin as caste differentiation-related factor
Zhang, iScience 2022 - “...Suenami etal., 2018 ), and OPNs (clusters 6, 7, 26, and 39) were identified by LOC724282 ( otp ), LOC724148 ( C15 ), LOC410657 ( acj6 ), and LOC413466 ( oaz ) ( Davie etal., 2018 ); the highly abundant neurons of the optic lobe, collectively...”
NP_001287047 eyegone, isoform C from Drosophila melanogaster
63% identity, 9% coverage
- The Pax protein Eyegone (Eyg) interacts with the pi-RNA component Aubergine (Aub) and controls egg chamber development in Drosophila.
Blom-Dahl, Developmental biology 2018 (PubMed)- GeneRIF: Eyg interacts with Aubergine (Aub), a component of the pi-RNA pathway during egg chamber development. This interaction could be essential for Eyg to be retained in the cytoplasm and fulfill its functions there.
- Functional association between eyegone and HP1a mediates wingless transcriptional repression during development.
Salvany, Molecular and cellular biology 2012 - GeneRIF: eyg has a dose-dependent effect on heterochromatin gene silencing and identifies a genetic interaction with HP1a in this process.
- The role of eyg Pax gene in the development of the head vertex in Drosophila.
Wang, Developmental biology 2010 (PubMed)- GeneRIF: Eyg is required for the development of the lateral bristles in the head vertex.
- Differential requirements for the Pax6(5a) genes eyegone and twin of eyegone during eye development in Drosophila.
Yao, Developmental biology 2008 - GeneRIF: Eyg makes differential use of several domains when compared to Toe, and the number of repressor domains also differs between the two Pax6(5a) homologs.
- Temporal switching of regulation and function of eye gone (eyg) in Drosophila eye development.
Wang, Developmental biology 2008 (PubMed)- GeneRIF: The function of eyg in eye development is required only at the second instar larval stage, while its function for head and antenna development can be provided at any time during embryo and larval development.
- Eyg and Ey Pax proteins act by distinct transcriptional mechanisms in Drosophila development.
Yao, The EMBO journal 2005 - GeneRIF: eyg is the first dedicated repressor Pax protein; acts exclusively as a transcriptional repressor
- Growth and specification: fly Pax6 homologs eyegone and eyeless have distinct functions.
Rodrigues, BioEssays : news and reviews in molecular, cellular and developmental biology 2004 (PubMed)- GeneRIF: Notch signaling controls eye growth through Pax6 protein Eyegone (review)
- Localized Notch signal acts through eyg and upd to promote global growth in Drosophila eye.
Chao, Development (Cambridge, England) 2004 (PubMed)- GeneRIF: A major effector mediating the growth promotion function of Notch in the eye disc.
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NP_001024213 Homeobox protein ttx-1 from Caenorhabditis elegans
56% identity, 21% coverage
XP_018117181 orthodenticle homeobox 1 L homeolog isoform X1 from Xenopus laevis
64% identity, 17% coverage
ESX1_HUMAN / Q8N693 Homeobox protein ESX1; Extraembryonic, spermatogenesis, homeobox 1 from Homo sapiens (Human) (see 3 papers)
NP_703149 homeobox protein ESX1 from Homo sapiens
59% identity, 16% coverage
- function: May coordinately regulate cell cycle progression and transcription during spermatogenesis. Inhibits degradation of polyubiquitinated cyclin A and cyclin B1 and thereby arrests the cell cycle at early M phase. ESXR1-N acts as a transcriptional repressor. Binds to the sequence 5'-TAATGTTATTA-3' which is present within the first intron of the KRAS gene and inhibits its expression. ESXR1-C has the ability to inhibit cyclin turnover.
- ESX1 gene as a potential candidate responsible for male infertility in nonobstructive azoospermia.
Malcher, Scientific reports 2023 - GeneRIF: ESX1 gene as a potential candidate responsible for male infertility in nonobstructive azoospermia.
- Association of ESX1 gene variants with non-obstructive azoospermia in Chinese males.
Ma, Scientific reports 2021 - GeneRIF: Association of ESX1 gene variants with non-obstructive azoospermia in Chinese males.
- Could analysis of testis-specific genes, as biomarkers in seminal plasma, predict presence of focal spermatogenesis in non-obstructive azoospermia?
Hashemi, Andrologia 2020 (PubMed)- GeneRIF: Could analysis of testis-specific genes, as biomarkers in seminal plasma, predict presence of focal spermatogenesis in non-obstructive azoospermia?
- ESX1 mRNA expression in seminal fluid is an indicator of residual spermatogenesis in non-obstructive azoospermic men.
Pansa, Human reproduction (Oxford, England) 2014 (PubMed)- GeneRIF: ESX1 mRNA level decreases as the severity of spermatogenic defects increase in non-obstructive azoospermic men.
- ESX1 gene expression as a robust marker of residual spermatogenesis in azoospermic men.
Bonaparte, Human reproduction (Oxford, England) 2010 (PubMed)- GeneRIF: ESX1 emerges as a potentially reliable molecular marker of residual spermatogenesis in azoospermic men
- Homeobox gene ESX1L expression is decreased in human pre-term idiopathic fetal growth restriction.
Murthi, Molecular human reproduction 2006 (PubMed)- GeneRIF: In FGR-affected placentae, ESX1L levels were lower than in gestation-matched controls, indicating a potential role for the ESX1L gene within the growth control mechanism of the fetus, through its effect on placental function.
- Paired-like homeodomain protein ESXR1 possesses a cleavable C-terminal region that inhibits cyclin degradation.
Ozawa, Oncogene 2004 (PubMed)- GeneRIF: proteolytic processing of ESXR1 plays a role in concerted regulation of the cell cycle and transcription in human cells
- Molecular and morphologic analyses of expression of ESX1L in different stages of human placental development.
Figueiredo, Journal of cellular and molecular medicine - GeneRIF: ESX1L is expressed during all stages of placental development and is localized to sparse areas of trophoblast in terminal villi in association with cytotrophoblastic cells
- ESX1 gene as a potential candidate responsible for male infertility in nonobstructive azoospermia.
Malcher, Scientific reports 2023 - “...the NCBI Reference Sequence GRCh37.p13: NC_000023.10 103,494,719.103499614. Structural protein modelling The sequence of human ESX1 (Q8N693) was obtained from UniProt 18 , and residues 244378 were searched in software representing iterative improvements of AlphaFold2, ColabFold2 AlphaFold2 and ColabFold_AlphaFold2_advanced_beta without relaxation 17 , 19 . Alignments were...”
- Identification of a novel class of farnesylation targets by structure-based modeling of binding specificity.
London, PLoS computational biology 2011 - “...CSLI Q14CB8-5 - + ++ -1.90 MTO CLFE Q9UHP7-3 -- + -- -1.77 None CPFF Q8N693 --- - -- -1.69 STO CGVG A6NHS1 - - + -1.65 MTO CFDI Q8NEB5 -- ++ -- -1.59 None CHCI Q99988 -- + - -1.56 None CVCV O75391 - +...”
- “...motifs were found to undergo in vitro farnesylation under STO conditions. The Homeobox protein ESX1 (Q8N693; CPFF) is cleaved into an N' and C' domain; while the N' enters the nucleus, the C' domain is localized to the cytoplasm where it inhibits cyclin degradation [44] ....”
XP_012823826 homeobox protein OTX2 isoform X1 from Xenopus tropicalis
64% identity, 19% coverage
LOC109470978 homeobox protein goosecoid-like from Branchiostoma belcheri
62% identity, 25% coverage
XP_020958123 homeobox protein OTX2 isoform X1 from Sus scrofa
64% identity, 20% coverage
NP_001027541 homeobox protein OTX isoform beta from Strongylocentrotus purpuratus
64% identity, 20% coverage
XP_015142758 homeobox protein OTX2 isoform X1 from Gallus gallus
64% identity, 20% coverage
- OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification.
Ghinia, eLife 2020 - GeneRIF: OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification.
- Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors.
Emerson, Developmental cell 2013 - GeneRIF: Otx2 and Onecut1 are coexpressed in retinal progenitors and coregulate cis-regulatory module for the thyroid hormone receptor beta gene.
- MiR-206 regulates neural cells proliferation and apoptosis via Otx2.
Wang, Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 2012 (PubMed)- GeneRIF: OTX2 is down-regulated in chick embryos in sodium arsenite-induced neural tube defects.
- Mutual repression between Gbx2 and Otx2 in sensory placodes reveals a general mechanism for ectodermal patterning.
Steventon, Developmental biology 2012 - GeneRIF: Otx2 and Gbx2 provide a global mechanism for patterning of the embryonic ectoderm and ensure the coordinated development of the central and peripheral nervous system in the head.
- Otx2 is involved in the regional specification of the developing retinal pigment epithelium by preventing the expression of sox2 and fgf8, factors that induce neural retina differentiation.
Nishihara, PloS one 2012 - GeneRIF: Otx2 prevents the presumptive retinal pigment epithelium region from forming the neural retina (NR) by repressing the expression of both Fgf8 and Sox2 which induce the NR cell fate.
- Role of Gbx2 and Otx2 in the formation of cochlear ganglion and endolymphatic duct.
Miyazaki, Development, growth & differentiation 2006 (PubMed)- GeneRIF: Results suggest that the interaction between Otx2 and Gbx2 in developing inner ear defines Fgf10 expression domain to induce the cochlear ganglion.
- A distinct preisthmic histogenetic domain is defined by overlap of Otx2 and Pax2 gene expression in the avian caudal midbrain.
Hidalgo-Sánchez, The Journal of comparative neurology 2005 (PubMed)- GeneRIF: Chick embryo torus semicircularis (the inferior colliculus homolog) expressed Otx2 in its ventricular lining exclusively. The parvicellular isthmic nucleus never expressed Otx2.
- Otx2, Gbx2, and Fgf8 expression patterns in the chick developing inner ear and their possible roles in otic specification and early innervation.
Sánchez-Calderón, Gene expression patterns : GEP 2004 (PubMed)- GeneRIF: Otx2, Gbx2, and Fgf8 are expressed in the chick developing inner ear
XP_011243291 homeobox protein OTX2 isoform X2 from Mus musculus
64% identity, 20% coverage
OTX5B_XENLA / Q9PT61 Homeobox protein otx5-B; Orthodenticle homolog 5-B; XOtx5b from Xenopus laevis (African clawed frog) (see 5 papers)
NP_001081916 homeobox protein otx5-B from Xenopus laevis
64% identity, 20% coverage
OTX2A_XENLA / Q91813 Homeobox protein OTX2-A; xOTX2-A; Orthodenticle 2-A; Orthodenticle-A-like protein A from Xenopus laevis (African clawed frog) (see 3 papers)
XP_018087427 homeobox protein OTX2-A isoform X1 from Xenopus laevis
64% identity, 20% coverage
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