PaperBLAST
PaperBLAST Hits for 58 a.a. (RPRTTITAKQ...)
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>58 a.a. (RPRTTITAKQ...)
RPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK
Running BLASTp...
Found 264 similar proteins in the literature:
NP_001179714 LIM/homeobox protein Lhx4 from Bos taurus
100% identity, 15% coverage
LHX4_HUMAN / Q969G2 LIM/homeobox protein Lhx4; LIM homeobox protein 4 from Homo sapiens (Human) (see 4 papers)
100% identity, 15% coverage
- function: May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung. Binds preferentially to methylated DNA (PubMed:28473536).
5hodA / Q969G2 Structure of lhx4 transcription factor complexed with DNA (see paper)
100% identity, 95% coverage
NP_001116445 LIM/homeobox protein Lhx4 from Danio rerio
98% identity, 15% coverage
XP_063128548 LIM/homeobox protein Lhx4 isoform X1 from Rattus norvegicus
100% identity, 15% coverage
XP_015145978 LIM/homeobox protein Lhx4 from Gallus gallus
100% identity, 13% coverage
XP_011508407 LIM/homeobox protein Lhx4 isoform X1 from Homo sapiens
100% identity, 18% coverage
- Genetic diagnosis of congenital hypopituitarism in Turkish patients by a target gene panel: novel pathogenic variants in GHRHR, GLI2, LHX4 and POU1F1 genes.
Kırkgöz, Archives of endocrinology and metabolism 2023 - GeneRIF: Genetic diagnosis of congenital hypopituitarism in Turkish patients by a target gene panel: novel pathogenic variants in GHRHR, GLI2, LHX4 and POU1F1 genes.
- Contribution of LHX4 Mutations to Pituitary Deficits in a Cohort of 417 Unrelated Patients.
Cohen, The Journal of clinical endocrinology and metabolism 2017 (PubMed)- GeneRIF: LHX4 Mutation is associated with Pituitary Deficits.
- Novel Lethal Form of Congenital Hypopituitarism Associated With the First Recessive LHX4 Mutation.
Gregory, The Journal of clinical endocrinology and metabolism 2015 - GeneRIF: A novel homozygous mutation in LHX4 associated with a lethal phenotype, implying that recessive mutations in LHX4 may be incompatible with life.
- Identifying the Deleterious Effect of Rare LHX4 Allelic Variants, a Challenging Issue.
Rochette, PloS one 2015 - GeneRIF: The study identified 4 new LHX4 heterozygous allelic variants in patients with congenital hypopituitarism: W204X, delK242, N271S and Q346R.
- Oncogenicity of LHX4 in colorectal cancer through Wnt/β-catenin/TCF4 cascade.
Cha, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2014 (PubMed)- GeneRIF: we found that LHX4 upregulated beta-catenin levels in human colorectal cancer cell lines
- Pituitary stalk interruption syndrome in 58 Chinese patients: clinical features and genetic analysis.
Yang, Clinical endocrinology 2013 (PubMed)- GeneRIF: Data indicate that HESX1, LHX4 and SOX3 polymorphisms may be associated with pituitary stalk interruption syndrome (PSIS).
- Panhypopituitarism presenting as life-threatening heart failure caused by an inherited microdeletion in 1q25 including LHX4.
Filges, Pediatrics 2012 (PubMed)- GeneRIF: Variably penetrant pituitary insufficiency, including this severe and atypical presentation, can be correlated with LHX4 insufficiency and highlights the role of LHX4 for pituitary development.
- Gradual loss of ACTH due to a novel mutation in LHX4: comprehensive mutation screening in Japanese patients with congenital hypopituitarism.
Takagi, PloS one 2012 - GeneRIF: This study is the first to describe, a gradual loss of ACTH in a patient carrying an LHX4 mutation.
- More
XP_006529232 LIM/homeobox protein Lhx4 isoform X1 from Mus musculus
100% identity, 18% coverage
- Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
Renaux, Cellular and molecular life sciences : CMLS 2024 - GeneRIF: Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
- LIM-Homeodomain Transcription Factor LHX4 Is Required for the Differentiation of Retinal Rod Bipolar Cells and OFF-Cone Bipolar Subtypes.
Dong, Cell reports 2020 - GeneRIF: LIM-Homeodomain Transcription Factor LHX4 Is Required for the Differentiation of Retinal Rod Bipolar Cells and OFF-Cone Bipolar Subtypes.
- Mutation in a flexible linker modulates binding affinity for modular complexes.
Stokes, Proteins 2019 (PubMed)- GeneRIF: We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.
- Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors.
Buenaventura, Investigative ophthalmology & visual science 2019 - GeneRIF: The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones.
- Hypothalamic sonic hedgehog is required for cell specification and proliferation of LHX3/LHX4 pituitary embryonic precursors.
Carreno, Development (Cambridge, England) 2017 - GeneRIF: conditional deletion of Shh in the anterior hypothalamus results in a fully penetrant phenotype characterised by a complete arrest of (Rathke's pouch) RP development, with lack of Lhx3/Lhx4 expression in RP epithelium.
- Lhx4 deficiency: increased cyclin-dependent kinase inhibitor expression and pituitary hypoplasia.
Gergics, Molecular endocrinology (Baltimore, Md.) 2015 - GeneRIF: We discovered that expression of Cdkn1a is expanded dorsally in the pituitary primordium of both Lhx3 and Lhx4 mutants. Lhx4 mutants exhibit reduced cyclin D1 expression and have auxiliary pouch-like structures.
- Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification.
Gadd, The Journal of biological chemistry 2011 - GeneRIF: X-ray crystal- and small-angle x-ray scattering-derived solution structures of an Lhx4.Isl2 complex exhibit many similarities with that of Lhx3.Isl1; structural differences supported by mutagenic studies reveal differences in the mechanisms of binding.
- Crystallization and diffraction of an Lhx4-Isl2 complex.
Gadd, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: Successful purification and crystallization of an engineered complex comprising the LIM domains of motor neuron protein Lhx4 and the Lim binding domain of Isl2 (islet 2 protein) are reported.
- More
LHX3_XENLA / P36200 LIM/homeobox protein Lhx3; LIM homeobox protein 3; Homeobox protein LIM-3; xLIM-3 from Xenopus laevis (African clawed frog) (see paper)
98% identity, 15% coverage
- function: Transcription factor (By similarity). May be involved in the specification and maintenance of differentiation of distinct neuronal and neuroendocrine tissues. Early marker for the pituitary and pineal lineages, it may be involved in specifying these lineages.
subunit: Interacts with ldb1 and with the N-terminus of rnf12.
LHX3_CHICK / P53412 LIM/homeobox protein Lhx3; LIM homeobox protein 3; Homeobox protein LIM-3 from Gallus gallus (Chicken) (see paper)
98% identity, 15% coverage
- function: Transcription factor (By similarity). Defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways. Acts in conjunction with LIM-1, ISL-1 and ISL- 2.
NP_571283 LIM/homeobox protein Lhx3 from Danio rerio
97% identity, 15% coverage
Q9VJ02 Lim3, isoform A from Drosophila melanogaster
93% identity, 13% coverage
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...FBgn0026411 Lim1 Q9V472 Brain, CNS, Gut, Tracheal system, Hypopharynx, Vent nerve cord, LIM-HD FBgn0002023 Lim3 Q9VJ02 , M9PD53 CNS, Ventral nerve cord Head LIM-HD FBgn0265598 Beadex Q8IQX7 , M9PI02 , M9PHX4 Intestine, Brainlobes, Ovary, Testis N/A LIM-Only FBgn0267978 Ap P29673 Mesoderm, Brain, CNS, Tracheal system, Lymph...”
NP_001246088 Lim3, isoform F from Drosophila melanogaster
NP_724161 Lim3, isoform B from Drosophila melanogaster
93% identity, 11% coverage
- Knockdown of the neuronal gene Lim3 at the early stages of development affects mitochondrial function and lifespan in Drosophila.
Rybina, Mechanisms of ageing and development 2019 (PubMed)- GeneRIF: altered mitochondrial activity is crucial for the decrease of adult lifespan caused by Lim3 knockdown early in life. In adults that encountered Lim3 depletion early in life, the transcription of several genes remained altered, and mitochondrial membrane potential, ATP level and locomotion were increased, confirming the existence of carry-over effects.
- Polycomb/Trithorax group-dependent regulation of the neuronal gene Lim3 involved in Drosophila lifespan control.
Rybina, Biochimica et biophysica acta. Gene regulatory mechanisms 2018 (PubMed)- GeneRIF: we demonstrate that the evolutionary conserved Lim3 core promoter provides basic Lim3 expression, whereas structural changes in the Lim3 PRE of distal promoter provide stage-, and tissue-specific Lim3 expression. Therefore, we hypothesize that PcG/TrxG proteins, which are directly involved in Lim3 transcription regulation, participate in lifespan control.
- The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression.
Wolfram, The Journal of neuroscience : the official journal of the Society for Neuroscience 2014 - GeneRIF: These observations provide evidence for combinatorial activity of Isl and Lim3 in regulating ion channel gene expression
- A naturally occurring polymorphism at Drosophila melanogaster Lim3 Locus, a homolog of human LHX3/4, affects Lim3 transcription and fly lifespan.
Rybina, PloS one 2010 - GeneRIF: Polymorphism of Lim3 affects Lim3 transcription and fly lifespan.
- [Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population].
Simonenko, Genetika 2008 (PubMed)- GeneRIF: Molecular variation of the shuttle craft and Lim3 genes, controlling the development of the nervous system, in a natural Drosophila melanogaster population
- Specification of Drosophila motoneuron identity by the combinatorial action of POU and LIM-HD factors.
Certel, Development (Cambridge, England) 2004 (PubMed)- GeneRIF: the class III POU protein, Drifter (Ventral veinless), is co-expressed with Islet and Lim3 specifically in the ISNb motoneuron subclass
- 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 - “...NP_648567, ACA04473, NP_571291, NP_071758, BAH58087, XP_001945631, NP_572505, AEN75258, ABD59002, XP_002591838, NP_001158395, ACA04748, NP_001130018, EAW91078, XP_973330, NP_724161, XP_001638136, NP_476775, NP_001158279, NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, 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...”
M9PD53 Lim3, isoform G from Drosophila melanogaster
93% identity, 10% coverage
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...Q9V472 Brain, CNS, Gut, Tracheal system, Hypopharynx, Vent nerve cord, LIM-HD FBgn0002023 Lim3 Q9VJ02 , M9PD53 CNS, Ventral nerve cord Head LIM-HD FBgn0265598 Beadex Q8IQX7 , M9PI02 , M9PHX4 Intestine, Brainlobes, Ovary, Testis N/A LIM-Only FBgn0267978 Ap P29673 Mesoderm, Brain, CNS, Tracheal system, Lymph Glands, Segmented...”
XP_005213396 LIM/homeobox protein Lhx3 isoform X1 from Bos taurus
95% identity, 14% coverage
LHX3_PIG / O97581 LIM/homeobox protein Lhx3; LIM homeobox protein 3; Homeobox protein LIM-3; Homeobox protein P-LIM from Sus scrofa (Pig) (see paper)
95% identity, 15% coverage
- function: Transcription factor (PubMed:10195693). Recognizes and binds to the consensus sequence motif 5'-AATTAATTA-3' in the regulatory elements of target genes, such as glycoprotein hormones alpha chain CGA and visual system homeobox CHX10, positively modulating transcription; transcription can be co-activated by LDB2 (By similarity). Synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (PubMed:10195693). Required for the establishment of the specialized cells of the pituitary gland and the nervous system (By similarity). Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1 (By similarity).
subunit: Interacts with POU1F1 (By similarity). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1-LHX3 interaction, may explain differences in sequence specificity of the different complexes. Interacts with LDB2. May interact with CITED2/MRG1 (By similarity).
LHX3_HALRO / Q25132 LIM/homeobox protein Lhx3; Hr-Lhx3; LIM homeobox protein 3; LIM/homeobox protein LIM; HrLIM from Halocynthia roretzi (Sea squirt) (Cynthia roretzi) (see 2 papers)
93% identity, 8% coverage
NP_001290229 LIM/homeobox protein Lhx3 from Sus scrofa
95% identity, 14% coverage
NP_001184116 LIM/homeobox protein Lhx3 from Canis lupus familiaris
95% identity, 14% coverage
LHX3_MOUSE / P50481 LIM/homeobox protein Lhx3; LIM homeobox protein 3; Homeobox protein LIM-3; Homeobox protein P-LIM from Mus musculus (Mouse) (see 7 papers)
NP_034841 LIM/homeobox protein Lhx3 isoform b from Mus musculus
95% identity, 14% coverage
- function: Transcription factor (PubMed:10593900, PubMed:12150931, PubMed:18539116). Recognizes and binds to the consensus sequence motif 5'-AATTAATTA-3' in the regulatory elements of target genes, such as glycoprotein hormones alpha chain CGA and visual system homeobox CHX10, positively modulating transcription; transcription can be co-activated by LDB2 (PubMed:10593900, PubMed:18539116, PubMed:9192866). Synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (PubMed:7708713). Required for the establishment of the specialized cells of the pituitary gland and the nervous system (By similarity). Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1 (PubMed:12150931, PubMed:18539116).
subunit: Interacts with POU1F1 (By similarity). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1-LHX3 interaction, may explain differences in sequence specificity of the different complexes (PubMed:12150931, PubMed:18539116, PubMed:18583962). Interacts with LDB2 (PubMed:9192866). May interact with CITED2/MRG1 (PubMed:10593900). - A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice.
Dang, Genes 2024 - GeneRIF: A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice.
- Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
Renaux, Cellular and molecular life sciences : CMLS 2024 - GeneRIF: Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
- The LIM protein complex establishes a retinal circuitry of visual adaptation by regulating Pax6 α-enhancer activity.
Kim, eLife 2017 - GeneRIF: Together, the authors show the antagonistic regulation of the alpha-enhancer activity by Pax6 and the LIM protein complex is necessary for the establishment of an inner retinal circuitry, which controls visual adaptation.
- Hypothalamic sonic hedgehog is required for cell specification and proliferation of LHX3/LHX4 pituitary embryonic precursors.
Carreno, Development (Cambridge, England) 2017 - GeneRIF: conditional deletion of Shh in the anterior hypothalamus results in a fully penetrant phenotype characterised by a complete arrest of (Rathke's pouch) RP development, with lack of Lhx3/Lhx4 expression in RP epithelium.
- Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.
Rhee, Neuron 2016 - GeneRIF: Expression of motor neuron effector genes is maintained by transient enhancers bound by Isl1/Lhx3 in nascent motor neurons and Isl1/Onecut1 in maturing hypaxial motor neurons.
- Lhx4 deficiency: increased cyclin-dependent kinase inhibitor expression and pituitary hypoplasia.
Gergics, Molecular endocrinology (Baltimore, Md.) 2015 - GeneRIF: We discovered that expression of Cdkn1a is expanded dorsally in the pituitary primordium of both Lhx3 and Lhx4 mutants.
- Critical Roles of the LIM Domains of Lhx3 in Recruiting Coactivators to the Motor Neuron-Specifying Isl1-Lhx3 Complex.
Seo, Molecular and cellular biology 2015 - GeneRIF: Lhx3-LIM domains play critical roles in transactivation of the Isl1-Lhx3 complex by not only directing the assembly of the Isl1-Lhx3 complex but also recruiting coactivators to the complex.
- 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
- More
- Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification.
Smith, Journal of structural biology: X 2021 - “...Protein expression and purification Uniprot codes for the mouse protein sequences used are: LHX3 - P50481 (isoform 1), and ISL1- P61372 (isoform 1). Protein encoding constructs are detailed in the Supplemental Information and were expressed from a modified pET-DUET plasmid that encodes an N-terminal GST tag...”
- Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification.
Gadd, The Journal of biological chemistry 2011 - An amphioxus LIM-homeobox gene, AmphiLim1/5, expressed early in the invaginating organizer region and later in differentiating cells of the kidney and central nervous system.
Langeland, International journal of biological sciences 2006 - “...orthologs from zebrafish (NP 571291, 042286, NP 571293), Xenopus laevis (p29674, p36200, P37137), mouse (CA125420, P50481, BAE24281), human (NP 005559, AAF17292, AAI09231); invertebrate chordate sequences were our amphioxus AmphiLim1/5 (DQ399521), amphioxus islet (AAF34717), amphioxus Lim3 (BAB91364), Ciona intestinalis Lim1/5 (BAE6535), and Ciona savignyi Lim1/5 (BAB68342). Expression...”
LHX3_HUMAN / Q9UBR4 LIM/homeobox protein Lhx3; LIM homeobox protein 3 from Homo sapiens (Human) (see 5 papers)
NP_835258 LIM/homeobox protein Lhx3 isoform a from Homo sapiens
95% identity, 15% coverage
- function: Transcription factor. Recognizes and binds to the consensus sequence motif 5'-AATTAATTA-3' in the regulatory elements of target genes, such as glycoprotein hormones alpha chain CGA and visual system homeobox CHX10, positively modulating transcription; transcription can be co-activated by LDB2. Synergistically enhances transcription from the prolactin promoter in cooperation with POU1F1/Pit-1 (By similarity). Required for the establishment of the specialized cells of the pituitary gland and the nervous system (PubMed:21149718). Involved in the development of interneurons and motor neurons in cooperation with LDB1 and ISL1 (By similarity).
subunit: Interacts with POU1F1 (PubMed:26612202). At neuronal promoters, interacts with LDB1, in motor neurons LDB1 is displaced by ISL1 and a ternary complex is formed in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1-LHX3 interaction, may explain differences in sequence specificity of the different complexes. Interacts with LDB2. May interact with CITED2/MRG1 (By similarity). - 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 - “...H2EHT1, K7PPA8, P04637, Q53GA5 P53 hsa_V$P53_02 Cell cycle 8022 LHX3 Y N F1T0D5, F1T0D7, F1T0D9, Q9UBR4 Homeobox hsa_YTAATTAA_V$LHX3_01, hsa_V$LHX3_01 Pituitary development 27022 FOXD3 N Y Q9UJU5 Fork head hsa_V$FOXD3_01 Immune system 51176 LEF1 N Y Q659G9, Q9UJU2 HMG hsa_CTTTGA_V$LEF1_Q2, hsa_CTTTGT_V$LEF1_Q2, hsa_V$LEF1_Q2, hsa_V$LEF1_Q6 Cell differentiation, hair cell...”
- Two novel LHX3 mutations in patients with combined pituitary hormone deficiency including cervical rigidity and sensorineural hearing loss
Ramzan, BMC endocrine disorders 2017 - “...9q34.3, underlie combined pituitary hormone deficiency type 3 (CPHD3, MIM# 221750). The encoded protein (Uniprot: Q9UBR4) is a LIM-homeodomain (LIM-HD) transcription factor, which features two amino-terminal LIM domains (cysteine-rich zinc-binding domain) and a centrally-located DNA-binding homeodomain [ 6 ]. In addition, the LHX3 protein also possesses...”
- “...representation of intron-exon structure of LHX3 gene, domain graph of the encoded protein (Uniprot identifier: Q9UBR4), and the genetic variants. Exons are designated as boxes 16 and introns are shown by thin lines . A full-length wild type LHX3 protein is shown, with its N-terminus and...”
- Generation and optimization of highly pure motor neurons from human induced pluripotent stem cells via lentiviral delivery of transcription factors.
Sepehrimanesh, American journal of physiology. Cell physiology 2020 - GeneRIF: Generation and optimization of highly pure motor neurons from human induced pluripotent stem cells via lentiviral delivery of transcription factors.
- LHX3 is an advanced-stage prognostic biomarker and metastatic oncogene in hepatocellular carcinoma.
Huang, Cancer biomarkers : section A of Disease markers 2019 (PubMed)- GeneRIF: LHX3 expression is significantly increased in carcinoma tissues, and associated with clinical stage and metastasis of patients. LHX3 expression is much higher in the advanced-stage patients than the early-stage patients, and is sharply increased in metastasic patients.
- LHX3 is an early stage and radiosensitivity prognostic biomarker in lung adenocarcinoma.
Lin, Oncology reports 2017 - GeneRIF: Further functional studies show that forced expression of LHX3 in lung cancer cells obviously promotes cell proliferation and invasion, whereas inhibits cell apoptosis. In summary, LHX3 is an early-stage and radiosensitivity prognostic biomarker, and a novel potential oncogene in lung adenocarcinoma .
- Molecular analysis of brazilian patients with combined pituitary hormone deficiency and orthotopic posterior pituitary lobe reveals eight different PROP1 alterations with three novel mutations.
Madeira, Clinical endocrinology 2017 (PubMed)- GeneRIF: Study did not identify HESX1 and LHX3 mutations by Sanger in brazilian patients with combined pituitary hormone deficiency
- Lhx3 is required to maintain cancer cell development of high-grade oligodendroglioma.
Liu, Molecular and cellular biochemistry 2015 (PubMed)- GeneRIF: LHX3 is upregulated in high-grade oligodendroglioma.
- Molecular analysis of PROP1, POU1F1, LHX3, and HESX1 in Turkish patients with combined pituitary hormone deficiency: a multicenter study.
Baş, Endocrine 2015 (PubMed)- GeneRIF: investigated the specific mutations in PROP1, POU1F1, LHX3, and HESX1 genes in patients with combined pituitary hormone deficiency (CPHD) in Turkey
- A human FSHB promoter SNP associated with low FSH levels in men impairs LHX3 binding and basal FSHB transcription.
Benson, Endocrinology 2013 - GeneRIF: Data suggest that low serum FSH (follicle stimulating hormone) levels in men with SNP in promoter region of FSHB (FSH beta subunit; -211G/T) result from reduced LHX3 binding to FSHB promoter and down-regulation of FSHB transcription in gonadotrophs.
- Cell-specific actions of a human LHX3 gene enhancer during pituitary and spinal cord development.
Park, Molecular endocrinology (Baltimore, Md.) 2013 - GeneRIF: The downstream enhancer region of LHX3 in regulating gene expression at the cellular level during development, is reported.
- More
NP_001158395 lim domain homeobox 3/4 transcription factor from Saccoglossus kowalevskii
95% identity, 15% coverage
- Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Abril, BMC genomics 2010 - “...binding protein [Schistosoma mansoni] XP_002576324 6,00E-05 F6AJIXP02GEYYP lim domain homeobox 3/4 transcription factor [Saccoglossus kowalevskii) NP_001158395 4,00E-23 90_10783 lim homeobox protein [Schistosoma mansoni] XP_002579046 2,00E-13 90_11027 lim homeobox protein [Schistosoma mansoni] XP_002579046 1,00E-26 90_10828 LIM homeobox transcription factor 1 alpha [Mus musculus] EDL39177 2,00E-14 90_13775 LIM...”
HM14_CAEEL / P20271 LIM/homeobox protein ceh-14; Homeobox protein ceh-14 from Caenorhabditis elegans (see 6 papers)
NP_509273 LIM/homeobox protein ceh-14 from Caenorhabditis elegans
88% identity, 17% coverage
- function: Probable transcription factor, modulating expression of helix-loop-helix protein mbr-1 and homeobox protein ceh-63, perhaps acting in concert with ceh-63 (PubMed:22207033). Binds to a motif including the sequence 5'-CTAAT-3' in regulatory promoter elements (PubMed:25614239). Confers thermosensory function to neurons (PubMed:10774727). Required for correct AFD-mediated thermotaxis (PubMed:10774727). In concert with homeobox protein ttx-1, perhaps as components in a complex, specifies identity of AFD neurons, acting by synergistically regulating receptor-type guanylyl cyclase gcy-8, gcy-18 and other genes (PubMed:25614239). 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-17, together forming an autoregulatory loop in the ALA neuron (PubMed:20501595, PubMed:26096732). Required for initial pathfinding of the ALA axons, but largely dispensable for axon migration (PubMed:20501595). Involved in regulating postembryonic axon maintenance in the ventral nerve cord, acting in concert with LIM homeobox protein lim-6, via modulation of expression of immunoglobulin domain zig genes in the interneuron PVT (PubMed:12490565). Plays a role in controlling the peptidergic identity of the BDU neurons, regulating expression of flp-10, nlp-1, and nlp-15, thereby modulating the harsh touch response (PubMed:26096732).
subunit: Interacts (via LIM zinc-binding domains 1 and 2) with lim-7 (via LID domain) (PubMed:28676648). May interact with itself (PubMed:22207033). May interact with homeobox protein ceh-63 (PubMed:22207033).
disruption phenotype: RNAi-mediated knockdown causes severe defects in the ALA neuron in young adults (PubMed:20501595). RNAi-mediated knockdown abolishes expression of helix-loop-helix protein mbr-1 in the interneuron DVC (PubMed:22207033). - Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18 in C. elegans.
Kagoshima, Developmental biology 2015 (PubMed)- GeneRIF: Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18, and determines the fate of AFD neurons as terminal selector genes at the final step of cell specification.
- The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth.
Kagoshima, Developmental biology 2013 (PubMed)- GeneRIF: loss of a LIM domain in the ceh-14(ch2) allele causes a partial loss-of-function phenotype
- 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.
- Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans
Bhati, Scientific reports 2017 - “...for protein expression were generated as fusions of CEH-14 LIM1+2 (CEH-14 residues 42168; UniProt accession P20271) and LIM-7 LID (LIM-7 residues 347376; UniProt accession G5EC36) where the two domains are connected by an 11-residue glycine-serine linker as previously described for LHX3 LIM1+2 -ISL1 LID fusion constructs...”
Q9V472 DLim1 from Drosophila melanogaster
NP_572505 LIM homeobox 1, isoform A from Drosophila melanogaster
70% identity, 11% coverage
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...gland, Sensory system, Lymph Glands, Muscle system, Tracheal system, Amnioserosa, Mesoderm LIM protein FBgn0026411 Lim1 Q9V472 Brain, CNS, Gut, Tracheal system, Hypopharynx, Vent nerve cord, LIM-HD FBgn0002023 Lim3 Q9VJ02 , M9PD53 CNS, Ventral nerve cord Head LIM-HD FBgn0265598 Beadex Q8IQX7 , M9PI02 , M9PHX4 Intestine, Brainlobes,...”
- 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 - “...the tree, are: XP_790548, NP_001020338, NP_002307, NP_001083902, NP_001071756, NP_508204, NP_648567, ACA04473, NP_571291, NP_071758, BAH58087, XP_001945631, NP_572505, AEN75258, ABD59002, XP_002591838, NP_001158395, ACA04748, NP_001130018, EAW91078, XP_973330, NP_724161, XP_001638136, NP_476775, NP_001158279, NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, XP_001626470, XP_971202, NP_523907, NP_001004015, NP_001015899, CAA04012, AAV84105, XP_392622, NP_001139341, NP_001158443, XP_002592485,...”
LHX1_DANRE / Q90476 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_571291 LIM/homeobox protein Lhx1 from Danio rerio
74% identity, 14% coverage
LIN11_CAEEL / P20154 Protein lin-11; Abnormal cell lineage protein 11 from Caenorhabditis elegans (see 4 papers)
NP_492696 Protein lin-11 from Caenorhabditis elegans
75% identity, 14% coverage
- function: Probable transcription factor which is required for asymmetric division of vulval blast cells (PubMed:15466489, PubMed:1970421). Involved in olfactory plasticity probably by regulating the expression of transcription factor mbr-1 in RIF neurons (PubMed:19561603). Plays a role in the chemorepulsive response toward ascaroside pheromones mediated by the ADL sensory neurons, probably by regulating E-box motif 5'-CANNTG-3' containing target genes in the ADL neurons (PubMed:29672507). Plays a role in the differentiation of the ADL sensory neurons (PubMed:29672507).
- Intron-specific patterns of divergence of lin-11 regulatory function in the C. elegans nervous system.
Amon, Developmental biology 2017 (PubMed)- GeneRIF: neuronal expression of lin-11 involves multiple transcription factor regulators and regulatory modules some of which have diverged in Caenorhabditis nematodes.
- Dissection of lin-11 enhancer regions in Caenorhabditis elegans and other nematodes.
Marri, Developmental biology 2009 (PubMed)- GeneRIF: multiple factors cooperate to regulate pi-specific expression of lin-11 and together with other findings suggest that the mechanism of lin-11 regulation by LIN-12/Notch signaling is evolutionarily conserved in Caenorhabditis species.
NP_571293 LIM/homeobox protein Lhx5 from Danio rerio
74% identity, 14% coverage
LHX1_MOUSE / P63006 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1 from Mus musculus (Mouse) (see 5 papers)
LHX1_RAT / P63007 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1; Rlim from Rattus norvegicus (Rat) (see 2 papers)
NP_032524 LIM/homeobox protein Lhx1 from Mus musculus
74% identity, 14% coverage
- function: Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.
subunit: Interacts with LDB1 via the tandem LIM domains. - function: Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis (By similarity).
subunit: Interacts with LDB1 via the tandem LIM domains. - Role of FGFRL1 and other FGF signaling proteins in early kidney development.
Trueb, Cellular and molecular life sciences : CMLS 2013 - Differentiation of mouse embryonic stem cells into cells with spermatogonia-like morphology with chemical intervention-dependent increased gene expression of LIM homeobox 1 (Lhx1).
Moshfegh, Stem cell research 2022 (PubMed)- GeneRIF: Differentiation of mouse embryonic stem cells into cells with spermatogonia-like morphology with chemical intervention-dependent increased gene expression of LIM homeobox 1 (Lhx1).
- Neuronal Lhx1 expression is regulated by DNMT1-dependent modulation of histone marks.
Symmank, Epigenetics 2020 - GeneRIF: Neuronal Lhx1 expression is regulated by DNMT1-dependent modulation of histone marks.
- The Transcription Factor LHX1 Regulates the Survival and Directed Migration of POA-derived Cortical Interneurons.
Symmank, Cerebral cortex (New York, N.Y. : 1991) 2019 (PubMed)- GeneRIF: Study shows the Transcription Factor LHX1 Regulates the Survival and Directed Migration of POA-derived Cortical Interneurons.
- The islet-expressed Lhx1 transcription factor interacts with Islet-1 and contributes to glucose homeostasis.
Bethea, American journal of physiology. Endocrinology and metabolism 2019 - GeneRIF: data are the first to reveal that the Lhx1 transcription factor contributes to normal glucose homeostasis and Glp1 responses.
- An LHX1-Regulated Transcriptional Network Controls Sleep/Wake Coupling and Thermal Resistance of the Central Circadian Clockworks.
Bedont, Current biology : CB 2017 - GeneRIF: Loss of LHX1 is associated with loss of acute light control of sleep.
- Lhx1/5 control dendritogenesis and spine morphogenesis of Purkinje cells via regulation of Espin.
Lui, Nature communications 2017 - GeneRIF: Findings suggest that Lhx1/5, through regulating Espin protein expression, control dendritogenesis and spine morphogenesis in postnatal Purkinje cells (PCs).
- Context-specific function of the LIM homeobox 1 transcription factor in head formation of the mouse embryo.
Fossat, Development (Cambridge, England) 2015 (PubMed)- GeneRIF: LHX1 is required in the anterior mesendoderm, but not in the mesoderm, for formation of the head.
- Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development.
Costello, Genes & development 2015 - GeneRIF: Smad4/Eomes-dependent Lhx1 expression in the epiblast marks the entire definitive endoderm lineage, the anterior mesendoderm, and midline progenitors.
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LHX1_HUMAN / P48742 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1; hLim-1 from Homo sapiens (Human) (see paper)
NP_005559 LIM/homeobox protein Lhx1 from Homo sapiens
74% identity, 14% coverage
- function: Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.
subunit: Interacts with LDB1 via the tandem LIM domains. - Genetically identified spinal interneurons integrating tactile afferents for motor control.
Bui, Journal of neurophysiology 2015 - Comparative proteome analysis of untreated and Helicobacter pylori-treated HepG2
Zhang, World journal of gastroenterology 2005 - “...pI Mr (Da) Sequence coverage (%) 1 P05556 3 6 P17252 P48742 19/106 5.31 86 242 31.2 Chain 1: integrin -1 7/28 6/34 6.61 7.16 76 764 44 482 39.9 39.6 Protein...”
- The Lim1 oncogene as a new therapeutic target for metastatic human renal cell carcinoma.
Hamaidi, Oncogene 2019 (PubMed)- GeneRIF: The potential pro-metastatic role of Lim1 in advanced clear cell renal cell carcinoma in vitro, ex vivo, and in vivo in a nude mouse model. Lim1 was found constitutively expressed in all metastatic tissues. Lim1 silencing decreased pulmonary metastasis in the in vivo model. Lim1 is involved in the expression of various proteins regulating cell movements and EMT, and induced clonogenicity in CCC cells.
- Identification and functional analysis of a novel LHX1 mutation associated with congenital absence of the uterus and vagina.
Zhang, Oncotarget 2017 - GeneRIF: Report novel missense mutation in LHX1 in congenital absence of the uterus and vagina which could change the transcriptional activity of LHX1 and its effect on the regulation of the downstream target gene GSC.
- Genetic analysis of Mayer-Rokitansky-Kuster-Hauser syndrome in a large cohort of families.
Williams, Fertility and sterility 2017 - GeneRIF: Our MRKH families included 43 quads, 26 trios, and 30 duos. Of our MRKH probands, 87/147 (59%) had MRKH type 1 and 60/147 (41%) had type 2 with additional anomalies. CONCLUSION(S): Although the prevalence of WNT4, HNF1B, and LHX1 point mutations is low in people with MRKH, the prevalence of CNVs was approximately 19%.
- TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia.
Sandbacka, Orphanet journal of rare diseases 2013 - GeneRIF: Data have identified TBX6 as a new gene associated with Mullerian aplasia. The results also support the relevance of LHX1 and CNVs in the development of this congenital malformation.
- LHX1 mutation screening in 96 patients with müllerian duct abnormalities.
Xia, Fertility and sterility 2012 (PubMed)- GeneRIF: Mutations in the coding regions of LHX1 may not be a common genetic etiologic factor involved in Han Chinese patients with mullerian duct abnormalities.
- Lim1/LIM1 is expressed in developing and adult mouse and human endometrium.
Ye, Histochemistry and cell biology 2012 (PubMed)- GeneRIF: Lim1/LIM1 expression in neonatal, adult mouse and human endometrium suggesting Lim1/LIM1 may have a role in endometrial development and remodelling
- Frame shift mutation of LHX1 is associated with Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome.
Ledig, Human reproduction (Oxford, England) 2012 (PubMed)- GeneRIF: study concludes that heterozygous mutations of LHX1 might be one cause of the Mayer-Rokitansky-Kuster-Hauser syndrome in a subgroup of patients
- Functional genomics identifies drivers of medulloblastoma dissemination.
Mumert, Cancer research 2012 - GeneRIF: Data indicate that expression of ERAS, LHX1, and CCRK is increased in aggressive subgroups of medulloblastomas.
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LHX1_CHICK / P53411 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1 from Gallus gallus (Chicken) (see paper)
74% identity, 14% coverage
- function: Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways. Acts in conjunction with ISL-2.
LHX1_XENLA / P29674 LIM/homeobox protein Lhx1; LIM homeobox protein 1; Homeobox protein Lim-1; Xlim1; x-Lhx1; xLIM-1 from Xenopus laevis (African clawed frog) (see 23 papers)
NP_001084128 LIM/homeobox protein Lhx1 from Xenopus laevis
74% identity, 14% coverage
- function: Involved in the establishment of the body plan via the Spemann organizer during gastrulation. Transcriptional activator required to induce organizer gene expression downstream of siamois. Promotes head formation by binding to 5'-TAAT'-3' elements in the promoters of head organizer genes cer1 and gsc to stimulate expression. Binds as a complex with siamois and mix-A/mix.1 to the cer1 promoter, and with ldb1 and otx2 to the gsc promoter. Also involved in neural induction via the organizer, including a role in notochord formation. Acts synergistically with ldb1 and ssbp in subsequent axis formation. Involved in kidney development, acting synergistically with pax8 to establish the pronephric primordium in late gastrulae/early neurulae and with pax2 during pronephric morphogenesis in tailbud stages. Has a later role in mediating the activity of inhibitors of ventralization.
subunit: Interacts with ldb1 via the tandem LIM domains. Both LIM domains are required for optimal binding and binding relieves the inhibitory effect of the LIM domains and activates lhx1. Binding to ldb1 also prevents degradation of ldb1 by rnf12. The stoichiometry of lhx1 and ldb1 is important for their function and an excess of ldb1 can inhibit lhx1 function. Interacts with the N-terminal region of rnf12 by a homeobox-dependent mechanism. - The nephrogenic potential of the transcription factors osr1, osr2, hnf1b, lhx1 and pax8 assessed in Xenopus animal caps.
Drews, BMC developmental biology 2011 - GeneRIF: nephrogenic transcription factors (osr1, osr2, hnf1b, lhx1, pax8)play important role in nephrogenesis but have no pronephros induction potential upon overexpression; they activate transcription cascades reflecting activation by activin A, retinoic acid
- Lhx1 is required for specification of the renal progenitor cell field.
Cirio, PloS one 2011 - GeneRIF: These results demonstrate an essential role for Lhx1 in driving specification of the entire kidney field from the intermediate mesoderm.
- LIM-homeodomain genes as developmental and adult genetic markers of Xenopus forebrain functional subdivisions.
Moreno, The Journal of comparative neurology 2004 (PubMed)- GeneRIF: Substantial evidence is found for a prosomeric organization of the diencephalon based on alternating expression of Lhx1/5 and Lhx2/9 genes during larval development and in the adult.
- A comparative analysis of frog early development
del, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...C-terminal region (amino acids 275-403; Swissprot accession no. P29674) of the X. laevis homeodomain protein Lim1 fused to GST (GST-Lim1C). The Ab was...”
NP_032525 LIM/homeobox protein Lhx5 from Mus musculus
74% identity, 14% coverage
- Lhx1/5 control dendritogenesis and spine morphogenesis of Purkinje cells via regulation of Espin.
Lui, Nature communications 2017 - GeneRIF: Findings suggest that Lhx1/5, through regulating Espin protein expression, control dendritogenesis and spine morphogenesis in postnatal Purkinje cells (PCs).
- LIM-homeobox gene Lhx5 is required for normal development of Cajal-Retzius cells.
Miquelajáuregui, The Journal of neuroscience : the official journal of the Society for Neuroscience 2010 - GeneRIF: These results reveal a complex role for Lhx5 in regulating the development and normal distribution of Cajal-Retzius cells in the developing forebrain.
- Diverse expression patterns of LIM-homeodomain transcription factors (LIM-HDs) in mammalian inner ear development.
Huang, Developmental dynamics : an official publication of the American Association of Anatomists 2008 - GeneRIF: The second wave of expression at E12.5 includes Lhx3, 5, 9, Isl2, and Lmx1b in the differentiating sensory epithelia with cellular specificities.
- Lhx1 and Lhx5 maintain the inhibitory-neurotransmitter status of interneurons in the dorsal spinal cord.
Pillai, Development (Cambridge, England) 2007 (PubMed)- GeneRIF: Lhx1 and Lhx5 function together with Pax2, Pax5 and Pax8 to establish a GABAergic inhibitory-neurotransmitter program in dorsal horn interneurons.
- LIM-homeodomain proteins Lhx1 and Lhx5, and their cofactor Ldb1, control Purkinje cell differentiation in the developing cerebellum.
Zhao, Proceedings of the National Academy of Sciences of the United States of America 2007 - GeneRIF: Lhx1 and Lhx5, and their cofactor Ldb1, control Purkinje cell differentiation in the developing cerebellum.
NP_001259358 LIM homeobox 1, isoform B from Drosophila melanogaster
M9PJE4 LIM homeobox 1, isoform B from Drosophila melanogaster
70% identity, 16% coverage
- Beadex, the Drosophila LIM only protein, is required for the growth of the larval neuromuscular junction.
Chitre, Journal of neurophysiology 2024 (PubMed)- GeneRIF: Beadex, the Drosophila LIM only protein, is required for the growth of the larval neuromuscular junction.
- Notch-dependent epithelial fold determines boundary formation between developmental fields in the Drosophila antenna.
Ku, PLoS genetics 2017 - GeneRIF: During antennal development, expression of the selector genes Lim1 and Dll was sharply segregated. Notch signaling induces actomyosin-dependent apical constriction and epithelial fold. Disruption of Notch signaling or the actomyosin network reduces apical constriction and epithelial fold.
- The transcriptional co-factor Chip acts with LIM-homeodomain proteins to set the boundary of the eye field in Drosophila.
Roignant, Development (Cambridge, England) 2010 - GeneRIF: Data show that Arrowhead and Lim1 act redundantly, using Chip as a co-factor, to prevent retinal differentiation in regions of the eye disc destined to become ventral head tissue.
- 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
- Analysis of insect nuclear small heat shock proteins and interacting proteins
Moutaoufik, Cell stress & chaperones 2021 - “...Q8INI8 DmHsp27 P02518 AP-MS Guruharsha et al. (2011) Lim1 M9PJE4 DmHsp27 P02518 Two-hybrid Giot et al. (2003) Lis1 Q7KNS3 DmHsp27 P02518 Two-hybrid Giot et al....”
NP_071758 LIM/homeobox protein Lhx5 from Homo sapiens
Q9H2C1 LIM/homeobox protein Lhx5 from Homo sapiens
74% identity, 14% coverage
LHX5_XENLA / P37137 LIM/homeobox protein Lhx5; LIM homeobox protein 5; Homeobox protein LIM-5; xLIM-5; xLIM-2A from Xenopus laevis (African clawed frog) (see paper)
NP_001084038 LIM/homeobox protein Lhx5 from Xenopus laevis
74% identity, 14% coverage
- function: Probably involved in the patterning of the nervous system, in particular in the early specification of the diencephalon
subunit: Interacts with ldb1 and with the N-terminus of rnf12. - An amphioxus LIM-homeobox gene, AmphiLim1/5, expressed early in the invaginating organizer region and later in differentiating cells of the kidney and central nervous system
Langeland, International journal of biological sciences 2006 - “...2, and 5 orthologs from zebrafish (NP 571291, 042286, NP 571293), Xenopus laevis (p29674, p36200, P37137), mouse (CA125420, P50481, BAE24281), human (NP 005559, AAF17292, AAI09231); invertebrate chordate sequences were our amphioxus AmphiLim1/5 (DQ399521), amphioxus islet (AAF34717), amphioxus Lim3 (BAB91364), Ciona intestinalis Lim1/5 (BAE6535), and Ciona savignyi...”
- LIM-homeodomain genes as developmental and adult genetic markers of Xenopus forebrain functional subdivisions.
Moreno, The Journal of comparative neurology 2004 (PubMed)- GeneRIF: Substantial evidence is found for a dual origin of olfactory bulb neurons, based on Lhx5 expression in the forebrain during larval development and in the adult.
MEC3_CAEEL / P09088 Mechanosensory protein 3 from Caenorhabditis elegans (see 5 papers)
NP_001023111 Mechanosensory protein 3 from Caenorhabditis elegans
61% identity, 18% coverage
- function: Transcription factor (PubMed:10899123, PubMed:26096732). Specifies differentiation of the set of six touch receptor neurons (TRNs) (PubMed:2898300). May positively modulate expression of both its own gene and also of homeobox ARX homolog alr-1 in TRNs, forming a positive feedback loop with alr-1, thereby restricting the variability of expression of mec-3 (PubMed:21368126). Required to determine the identity of ALM sensory neurons, acting by interacting with unc-86, thereby preventing unc-86 cooperating with pag-3 to induce BDU-neuron specific genes (PubMed:26096732). Binds cooperatively as a heterodimer with unc-86 to sites in the mec-3 gene promoter (PubMed:10899123, PubMed:1361171). Promotes outgrowth of lateral dendritic branches on the PVD nociceptive neurons, probably acting both directly, and upstream of zinc finger protein egl-46 (PubMed:29031632).
subunit: Interacts with unc-86; the heterooligomer binds to the promoters of mec-3, mec-4 and mec-7. - MBL-1 and EEL-1 affect the splicing and protein levels of MEC-3 to control dendrite complexity.
Xie, PLoS genetics 2023 - GeneRIF: MBL-1 and EEL-1 affect the splicing and protein levels of MEC-3 to control dendrite complexity.
- The Caenorhabditis elegans spalt-like gene sem-4 restricts touch cell fate by repressing the selector Hox gene egl-5 and the effector gene mec-3.
Toker, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: Data show that sem-4 indirectly modulates mec-3 expression through its repression of egl-5 and that this negative regulation is required for proper determination of neuronal fates.
- High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans.
Toms, BMC developmental biology 2001 - GeneRIF: A sequence in the mec-3 upstream region has been identified that, when present in high copy extrachromosomal arrays, causes the ALM touch receptor neurons to migrate aberrantly and causes PLM touch receptor neuron axonal defects.
NP_729801 LIM homeobox transcription factor 1 alpha, isoform B from Drosophila melanogaster
Q9VTW5 LIM homeobox transcription factor 1 alpha, isoform B from Drosophila melanogaster
55% identity, 9% coverage
LIM6_CAEEL / Q21192 LIM/homeobox protein lim-6 from Caenorhabditis elegans (see 6 papers)
NP_001256980 LIM/homeobox protein lim-6 from Caenorhabditis elegans
61% identity, 18% coverage
- function: Transcription factor (By similarity). Required for the terminal differentiation of sensory- and motor-neurons, especially GABAergic neurons, and for morphological aspects of uterine development (PubMed:10068647). Plays a role in the cell-type-specific regulation of glutamic acid decarboxylase unc-25 (PubMed:10068647). Involved in promoting sleep-like behavioral quiescence, acting by modulating expression of transcription factor aptf-1 in the single sleep-active ring interneuron RIS (PubMed:26949257). Plays a role in regulation of RIS differentiation (PubMed:14568548). Required for the functional asymmetry of the ASER and ASEL chemosensory neuron pair, conferring the ability to discriminate sodium from chloride, perhaps by modulating expression of receptor-type guanylate cyclases, such as gcy-5 (PubMed:11287956, PubMed:21555395). Involved in regulating postembryonic axon maintenance in the ventral nerve cord, acting in concert with LIM homeobox protein ceh-14, via modulation of expression of immunoglobulin domain zig genes in the interneuron PVT (PubMed:12490565). May play a role in the functions of the excretory gland cell (PubMed:10068647).
- A left/right asymmetric neuronal differentiation program is controlled by the Caenorhabditis elegans lsy-27 zinc-finger transcription factor.
Zhang, Genetics 2011 - GeneRIF: Transciption factor lsy-27 is broadly and exclusively expressed in the embryo and acts during the initiation, but not during the maintenance phase of asymmetric neuronal differentiation program to assist in the initiation of lim-6 expression.
- LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system.
Tsalik, Developmental biology 2003 - GeneRIF: lim-6 Lhx gene is required for specific aspects of RIS interneuron differentiation.
LMX1A_HUMAN / Q8TE12 LIM homeobox transcription factor 1-alpha; LIM/homeobox protein 1.1; LMX-1.1; LIM/homeobox protein LMX1A from Homo sapiens (Human) (see 2 papers)
NP_001167540 LIM homeobox transcription factor 1-alpha from Homo sapiens
NP_796372 LIM homeobox transcription factor 1-alpha from Homo sapiens
58% identity, 15% coverage
- function: Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity).
- Novel KCNQ4 variants in different functional domains confer genotype- and mechanism-based therapeutics in patients with nonsyndromic hearing loss
Lee, Experimental & molecular medicine 2021 - “...variant uncertain significance, NA not available. Refseq transcript accession number NM_001174069.1; Refseq protein accession number NP_001167540. HGVS: Human Genome Variation Society ( https://www.hgvs.org/ ). Sequence Variant Nomenclature ( http://varnomen.hgvs.org/ ). CADD: Combined Annotation Dependent Depletion ( https://cadd.gs.washington.edu/ ). REVEL: Rare Exome Variant Ensemble Learner ( https://sites.google.com/site/revelgenomics/...”
- Forced LMX1A expression induces dorsal neural fates and disrupts patterning of human embryonic stem cells into ventral midbrain dopaminergic neurons.
Rifes, Stem cell reports 2024 - GeneRIF: Forced LMX1A expression induces dorsal neural fates and disrupts patterning of human embryonic stem cells into ventral midbrain dopaminergic neurons.
- Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
Oziębło, Human genetics 2022 (PubMed)- GeneRIF: Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
- ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
Yu, Genes & genomics 2022 (PubMed)- GeneRIF: ceRNA network of lncRNA MIR210HG/miR-377-3p/LMX1A in malignant proliferation of glioma cells.
- Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
Wu, International journal of molecular sciences 2020 - GeneRIF: Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells.
- Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
Lee, Human mutation 2020 (PubMed)- GeneRIF: Novel genotype-phenotype correlation of functionally characterized LMX1A variants linked to sensorineural hearing loss.
- Gene variations in PBX1, LMX1A and SLITRK1 are associated with obsessive-compulsive disorder and its clinical features.
Melo-Felippe, Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia 2019 (PubMed)- GeneRIF: Our results indicate an important influence of the neurodevelopment genes, PBX1, LMX1A, and SLITRK1 in obsessive-compulsive disorder susceptibility
- Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
Zong, Journal of cellular and molecular medicine 2019 - GeneRIF: Knockdown of LncRNA SCAMP1 suppressed malignant biological behaviours of glioma cells via modulating miR-499a-5p/LMX1A/NLRC5 pathway.
- LMX1A inhibits C-Myc expression through ANGPTL4 to exert tumor suppressive role in gastric cancer.
Qian, PloS one 2019 - GeneRIF: Knockdown of ANGPTL4 rescued the tumor suppressive phenotype of LMX1A overexpression, which indicated that LMX1A upregulates ANGPTL4 to exert its role. Mechanistically, we found that LMX1A inhibited the expression of the oncogene C-Myc, which is alleviated by ANGPTL4 knockdown.
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NP_001020339 LIM homeobox transcription factor 1, beta a isoform 2 from Danio rerio
58% identity, 15% coverage
XP_017454198 LIM homeobox transcription factor 1-alpha isoform X1 from Rattus norvegicus
58% identity, 15% coverage
Q9JKU8 LIM homeobox transcription factor 1-alpha from Mus musculus
XP_017177173 LIM homeobox transcription factor 1-alpha isoform X1 from Mus musculus
58% identity, 15% coverage
- Zebrafish Lmx1b.1 and Lmx1b.2 are required for maintenance of the isthmic organizer.
O'Hara, Development (Cambridge, England) 2005 - Lmx1a is a master regulator of the cortical hem.
Iskusnykh, eLife 2023 - GeneRIF: Lmx1a is a master regulator of the cortical hem.
- Identification of a novel mutant allele of LIM homeobox transcription factor 1 alpha (dreher) in mice.
Suto, Congenital anomalies 2022 (PubMed)- GeneRIF: Identification of a novel mutant allele of LIM homeobox transcription factor 1 alpha (dreher) in mice.
- Lmx1a-Dependent Activation of miR-204/211 Controls the Timing of Nurr1-Mediated Dopaminergic Differentiation.
Pulcrano, International journal of molecular sciences 2022 - GeneRIF: Lmx1a-Dependent Activation of miR-204/211 Controls the Timing of Nurr1-Mediated Dopaminergic Differentiation.
- Interaction with ectopic cochlear crista sensory epithelium disrupts basal cochlear sensory epithelium development in Lmx1a mutant mice.
Nichols, Cell and tissue research 2020 - GeneRIF: Interaction with ectopic cochlear crista sensory epithelium disrupts basal cochlear sensory epithelium development in Lmx1a mutant mice.
- Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer.
Fregoso, Development (Cambridge, England) 2019 (PubMed)- GeneRIF: homeobox TF Lmx1a can activate the Cux2 enhancer through activation of a conserved intronic enhancer
- Reciprocal Negative Regulation Between Lmx1a and Lmo4 Is Required for Inner Ear Formation.
Huang, The Journal of neuroscience : the official journal of the Society for Neuroscience 2018 - GeneRIF: we provide genetic evidence that a transcription factor, Lmx1a, interacts with its negative regulator, Lmo4, to pattern various vestibular and auditory components of the mammalian inner ear.
- A variant in LMX1A causes autosomal recessive severe-to-profound hearing impairment.
Schrauwen, Human genetics 2018 - GeneRIF: Homozygous Lmx1a mutant mice (Dreher) are deaf with dysmorphic ears with an abnormal morphogenesis and fused and misshapen sensory organs; however, computed tomography performed on a hearing-impaired family member did not reveal any cochleovestibular malformations.
- Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation.
Chabrat, Nature communications 2017 - GeneRIF: Lmx1a and Lmx1b regulate Plxnc1 expression.Lmx1a is required for the topographical organization of dopaminergic innervation in the striatum.
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XP_006497809 LIM homeobox transcription factor 1-beta isoform X1 from Mus musculus
58% identity, 14% coverage
- Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity.
Castilla-Ibeas, Cell reports 2023 (PubMed)- GeneRIF: Failure of digit tip regeneration in the absence of Lmx1b suggests Lmx1b functions disparate from dorsoventral polarity.
- Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.
Haro, Nature communications 2021 - GeneRIF: Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.
- A novel small deletion of LMX1B in a large Chinese family with nail-patella syndrome.
Yan, BMC medical genetics 2019 - GeneRIF: identified a novel NPS-causing LMX1B mutation and expanded the spectrum of mutations in the LMX1B gene. The c.712_714delTTC mutation may affect the quaternary structure of LMX1B, which is essential for the specification of dorsal limb fate at both zeugopodal and autopodal levels, leading to typical NPS
- Lmx1b is required at multiple stages to build expansive serotonergic axon architectures.
Donovan, eLife 2019 - GeneRIF: The authors report that LIM homeodomain factor 1b (Lmx1b)-deficient serotonin (5-HT) neurons fail to generate axonal projections to the forebrain and spinal cord. Stage-specific targeting demonstrates that Lmx1b is required at successive stages to control 5-HT axon primary outgrowth, selective routing, and terminal arborization.
- Anti-osteogenic function of a LIM-homeodomain transcription factor LMX1B is essential to early patterning of the calvaria.
Cesario, Developmental biology 2018 - GeneRIF: Authors conclude that Lmx1b plays a key role as an anti-osteogenic factor in patterning the head mesenchyme into areas with different osteogenic competence. In turn, this patterning event is crucial to generating the proper organization of the bones and soft tissue joints of the calvaria.
- Lmx1b-targeted cis-regulatory modules involved in limb dorsalization.
Haro, Development (Cambridge, England) 2017 (PubMed)- GeneRIF: This is the first report to describe genome-wide Lmx1b binding during limb development.
- Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation.
Chabrat, Nature communications 2017 - GeneRIF: Lmx1b is required for the topographical organization of dopaminergic innervation in the striatum.Lmx1b regulates Plxnc1 expression.
- Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons.
Doucet-Beaupré, Proceedings of the National Academy of Sciences of the United States of America 2016 - GeneRIF: Data show that sustained expression of Lmx1a and Lmx1b is required for the survival of adult midbrain dopaminergic neurons.
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LMX1B_HUMAN / O60663 LIM homeobox transcription factor 1-beta; LIM/homeobox protein 1.2; LMX-1.2; LIM/homeobox protein LMX1B from Homo sapiens (Human) (see 12 papers)
58% identity, 14% coverage
- function: Transcription factor involved in the regulation of podocyte- expressed genes (PubMed:24042019, PubMed:28059119). Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.
subunit: Interacts with DHX9 (PubMed:23308148). - Recent Advances in Molecular and Cellular Functions of S100A10.
Okura, Biomolecules 2023 - “...protein 1 Q9UHB6 Cytoplasm AC-MS 1 [ 50 ] LMX1B LIM homeobox transcription factor 1 O60663 Nucleus AC-MS 1 [ 53 ] LUC7L3 Luc7-like protein 3 O95232 Nucleus AC-MS 1 [ 43 ] MAEA E3 ubiquitin-protein transferase MAEA Q7L5Y9 Cytoplasm; Nucleus PL-MS 3 [ 43 ]...”
- VarSite: Disease variants and protein structure.
Laskowski, Protein science : a publication of the Protein Society 2020 - “...protein we will be using in this article: LIM homeobox transcription factor 1beta (UniProt accession O60663). This protein plays a central role in the dorsoventral patterning of vertebrate limbs, and is associated with nailpatella syndrome 32 (disease id NPS; OMIM reference: 161200)an inherited developmental disorder that...”
- “...1 Disease association for variants in the LIM homeobox transcription factor 1beta protein (UniProt accession O60663). List of diseasesin this case just nailpatella syndromeand a schematic diagram of the affected organs (highlighted in red): eyes, kidneys, bones, skin, and nails. Clicking on any of these opens...”
- Proteome evaluation of human cystic echinococcosis sera using two dimensional gel electrophoresis.
Sadjjadi, Gastroenterology and hepatology from bed to bench 2018 - “...Suppress 255 ATPase inhibitor, mitochondrial Q9UII2 7.22 9517 Suppress 308 LIM homeobox transcription factor 1-beta O60663 6.22 44917 Suppress 479 Isoform 3 of Emopamil-binding protein-like Q9BY08-3 6.38 10873 Suppress 240 Uncharacterized protein C3orf14 Q9HBI5 5.67 15007 Down 257 Protein S100-B P04271 4.57 10582 Down Figure 4...”
- Genetically identified spinal interneurons integrating tactile afferents for motor control.
Bui, Journal of neurophysiology 2015
NP_001167617 LIM homeobox transcription factor 1-beta isoform 3 from Homo sapiens
58% identity, 14% coverage
8ik5C / Q8TE12 Transcription factor lmx1a homeobox domain in complex with wnt1 promoter
58% identity, 85% coverage
O88609 LIM homeobox transcription factor 1-beta from Mus musculus
58% identity, 14% coverage
- A dominant-negative mutation of mouse Lmx1b causes glaucoma and is semi-lethal via LDB1-mediated dimerization [corrected].
Cross, PLoS genetics 2014 - “...AF078166, is highlighted. This transversion causes a V265D mutation in the homeodomain numbering from entry O88609 in http://www.uniprot.org . (B) The Icst mutation impairs binding of LMX1B. Bandshift analysis using a fixed amount of 32 P-labelled FLAT LMX1B binding element [21] with increasing amounts (as indicated...”
- “...sequence in the database has been revised to include these extra 23 amino acids (entry O88609 in http://www.uniprot.org ). In addition, there is a direct duplication of 18 bp encoding the first 6 amino acids of the 372 amino acid protein in the mouse genome sequence...”
P53413 LIM/homeobox protein LMX-1.2 from Gallus gallus
NP_990689 LIM/homeobox protein LMX-1.2 from Gallus gallus
58% identity, 14% coverage
LMX1B_XENLA / Q8UVR3 LIM homeobox transcription factor 1-beta.1; LIM homeobox protein 1b; Xlmx1b from Xenopus laevis (African clawed frog) (see 3 papers)
58% identity, 14% coverage
- function: Required for early specification of the kidney glomus, lying upstream of wt1 in the pathway controlling glomus differentiation. The balance in levels and expression patterns of binding partners such as lhx1/lim-1 influences differentiation into glomus or tubule derivatives. Involved in specification of serotonergic neurons.
XP_018087415 LIM homeobox transcription factor 1-beta.1 isoform X1 from Xenopus laevis
58% identity, 15% coverage
CG4328, NP_648567 uncharacterized protein from Drosophila melanogaster
Q9VTW3 FI06571p from Drosophila melanogaster
53% identity, 9% coverage
- Knockout of a single Pax6 gene (toy but not ey) leads to compound eye deficiency and small head in honeybees
Hu, Communications biology 2024 - “...proteins were predicted to be interacted with Toy, including Ey, Eya, Optix, Tio, So, Six4, CG4328, Dmrt99B, Fd59A, Hipk, CG13331, Zif, Tim9a, Tim9b, CG31229, SdhD, Wsck, and Fd3F (Fig. 6C ). We checked the differential expression profiles of these 18 protein-coding genes in our honeybee transcriptome...”
- “...were down-regulated at least in one period after toy editing. The expression of CG31229 , CG4328 , fd3F , SdhD , Six4 , Tim9a , Tim9b , Wsck , and Zif had no difference between edited mutants and wildtypes. There is no gene in honeybee corresponding...”
- Transcription factor expression landscape in Drosophila embryonic cell lines
Drewell, BMC genomics 2024 - “...6.69 CG8301 41160 83.34 0.81 3559 35 6.65 Blimp-1 38638 1.16 0.02 71 1 6.49 CG4328 39405 0.78 0 21 0 5.93 cad 35341 1.36 0.03 46 1 5.74 CG43689 31353 0.34 0 32 0 4.75 CG10654 39428 1.18 0.06 26 1 4.52 fd19B 33010 2.8...”
- Comparative exploration of mammalian deafness gene homologues in the Drosophila auditory organ shows genetic correlation between insect and vertebrate hearing
Sutton, PloS one 2024 - “...8 DFNA2A KCNQ4 KCNQ 7 DFNA4 MYH14 zip 8 DFNA6/14/38 WFS1 wfs1 10 DFNA7 LMX1A cg4328 9 DFNA10 EYA4 eya 8 DFNA15 POU4F3 acj6 8 DFNA17 MYH9 zip 9 DFNA20/26 ACTG1 Act5C 8 DFNA20/26 ACTG1 Act42A 8 DFNA23 SIX1 so 9 DFNA25 SLC17A8 VGlut 9 DFNA27...”
- The continuum of Drosophila embryonic development at single-cell resolution
Calderon, Science (New York, N.Y.) 2022 - “...as enriched in mature neurons as well as two genes, complexin ( cpx ) and CG4328, identified in our analysis as enriched in the monoaminergic cluster, which includes midline neurons ( Fig. 3H ). This neuronal subtype enrichment is unexpected for cpx, which encodes a presynaptic...”
- “...situ hybridization of stage 16 embryos, showing the expression of lncRNA CR31451, cpx , and CG4328 in the nervous system. A tissue marker ( elav ) is provided in the top panel. A lateral and ventral embryo view is shown for each gene. Fig. 4. Dynamic...”
- Transcriptional profiling from whole embryos to single neuroblast lineages in Drosophila
Seroka, Developmental biology 2022 - “...and scro ), while some HDTFs only expressed at significant levels in mature neurons ( CG4328 , Dfd , and Nk7.1 ) ( Figure 7I , Supplemental Figure 4 ). Most of these CSMs have expression restricted to mature neurons consistent with a role in neuron...”
- Dissection of the Regulatory Elements of the Complex Expression Pattern of Puckered, a Dual-Specificity JNK Phosphatase
Karkali, International journal of molecular sciences 2021 - “...observed RS4-directed faint VNC expression in embryos, binding sites for the LIM homeobox transcription factors CG4328 and LIM3 and for the NKL homeobox factor Exex are found adjacent. CG4328 is expressed in the embryonic brain (ventral midline) and the larval ventral nerve cord and is predicted...”
- Post-transcriptional modulators and mediators of the circadian clock
Anna, Chronobiology international 2021 - “...to identify the potential RNA targets of these microRNAs and genetic inhibition of miR-274 targets CG4328 (a predicted LIM-homeodomain transcription factor) and MESK2 (involved in Ras/ERK signaling and has homology with N-myc downstream-regulated gene 2 ) resulted in significantly reduced rhythmicity. This genetic screen identified the...”
- “...( Vodala et al. 2012 ) miR-124 ( Zhang et al 2016 ) miR-274 MESK2, CG4328 ( You et al. 2018 ) Phenotype study using RNAi line miR-263b You et al.(2018) miR-210 Fas2 ( Niu et al. 2019 ) Phenotype study in mutated Fas2 3UTR flies...”
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...Dorsal epidermis, Embryonic brain, sophagus, Foregut, Stomatogastric LIM-HD FBgn0032196 CG5708 Q9VL21 N/A NA LIM-Only FBgn0036274 CG4328 Q9VTW3 Ventral nerve, cord,CNS NA LIM-HD FBgn0052105 Lmx1a Q9VTW5 Ventral nerve cord,CNS CNS, Trunk mesoderm, Longitudinal visceral mesoderm LIM-HD FBgn0030530 Jub Q9VY77 N/A N/A LIM-Only FBgn0265597 Rad X2JBI1X2JDH0 N/A N/A...”
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- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...epidermis, Embryonic brain, sophagus, Foregut, Stomatogastric LIM-HD FBgn0032196 CG5708 Q9VL21 N/A NA LIM-Only FBgn0036274 CG4328 Q9VTW3 Ventral nerve, cord,CNS NA LIM-HD FBgn0052105 Lmx1a Q9VTW5 Ventral nerve cord,CNS CNS, Trunk mesoderm, Longitudinal visceral mesoderm LIM-HD FBgn0030530 Jub Q9VY77 N/A N/A LIM-Only FBgn0265597 Rad X2JBI1X2JDH0 N/A N/A LIM...”
LOC100644486 insulin gene enhancer protein ISL-1 from Bombus terrestris
48% identity, 12% coverage
HESXB_XENLA / Q91898 Homeobox expressed in ES cells 1-B; Homeobox protein ANF-1; XANF-1; Xanf1 from Xenopus laevis (African clawed frog) (see 9 papers)
NP_001156042 homeobox expressed in ES cells 1-B from Xenopus laevis
50% identity, 30% coverage
ISL2A_DANRE / P53406 Insulin gene enhancer protein isl-2a; Islet-2A; Insulin gene enhancer protein isl-2; Islet-2 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_571045 insulin gene enhancer protein isl-2a from Danio rerio
48% identity, 16% coverage
- function: Binds to one of the cis-acting domain of the insulin gene enhancer. May be involved in subtype specialization of primary motoneurons
- The isl2a transcription factor regulates pituitary development in zebrafish.
Yan, Frontiers in endocrinology 2023 - GeneRIF: The isl2a transcription factor regulates pituitary development in zebrafish.
- Interaction of transcription factors Islet2 and Nr2f1b to control vascular patterning during zebrafish development.
Wang, Biochemical and biophysical research communications 2022 (PubMed)- GeneRIF: Interaction of transcription factors Islet2 and Nr2f1b to control vascular patterning during zebrafish development.
- Investigation of Islet2a function in zebrafish embryos: Mutants and morphants differ in morphologic phenotypes and gene expression.
Moreno, PloS one 2018 - GeneRIF: differentiation of the CaP motor neuron's stereotypic large inward and outward currents does not have a specific requirement for Islet2a.
- The LIM-homeodomain transcription factor Islet2a promotes angioblast migration.
Lamont, Developmental biology 2016 (PubMed)- GeneRIF: Isl2a is expressed in the lateral posterior mesoderm prior to angioblast migration. Isl2a-deficient angioblasts show disorganized migration to the midline to form axial vessels. Its expression is negatively regulated by Notch activity. It positively regulates flt4, a VEGF-C receptor repressed by Notch during angiogenesis. Isl2a may be an intermediate between Notch signaling and genetic programs controlling angioblasts.
- Prdm14 acts upstream of islet2 transcription to regulate axon growth of primary motoneurons in zebrafish.
Liu, Development (Cambridge, England) 2012 (PubMed)- GeneRIF: Prdm14 regulates caudal rimary axon outgrowth through activation of islet2 expression.
- Islet1 and Islet2 have equivalent abilities to promote motoneuron formation and to specify motoneuron subtype identity.
Hutchinson, Development (Cambridge, England) 2006 (PubMed)- GeneRIF: primary motoneuron subtypes are likely to be specified by factors that act in parallel to or upstream of islet1 and islet2
- PlexinA4 is necessary as a downstream target of Islet2 to mediate Slit signaling for promotion of sensory axon branching.
Miyashita, Development (Cambridge, England) 2004 (PubMed)- GeneRIF: Results show that PlexinA4, a transmembrane protein known to be a co-receptor for class III semaphorins, acts downstream of Islet2 to promote branching of the peripheral axons of the primary sensory neurons.
ISL2B_DANRE / P53407 Insulin gene enhancer protein isl-2b; Islet-2B; Insulin gene enhancer protein isl-3; Islet-3 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_571039 insulin gene enhancer protein isl-2b from Danio rerio
48% identity, 16% coverage
HESXA_XENLA / Q91617 Homeobox expressed in ES cells 1-A; Homeobox protein ANF-2; xANF-2 from Xenopus laevis (African clawed frog) (see paper)
50% identity, 31% coverage
- function: Appears to be involved in the regional specification of the anterior head of Xenopus embryos.
NP_001158279 tailup from Tribolium castaneum
48% identity, 13% coverage
- 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 - “...NP_071758, BAH58087, XP_001945631, NP_572505, AEN75258, ABD59002, XP_002591838, NP_001158395, ACA04748, NP_001130018, EAW91078, XP_973330, NP_724161, XP_001638136, NP_476775, NP_001158279, NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, 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 -...”
XP_005165321 insulin gene enhancer protein isl-1 isoform X1 from Danio rerio
48% identity, 16% coverage
- A BMP4-p38 MAPK signaling axis controls ISL1 protein stability and activity during cardiogenesis.
Jing, Stem cell reports 2021 - GeneRIF: A BMP4-p38 MAPK signaling axis controls ISL1 protein stability and activity during cardiogenesis.
- Nkx genes establish second heart field cardiomyocyte progenitors at the arterial pole and pattern the venous pole through Isl1 repression.
Colombo, Development (Cambridge, England) 2018 - GeneRIF: Nkx2-5 and nkx2.7 genes restrict proliferation of heart field progenitors in the outflow tract, delimit the number of progenitors at the venous pole and pattern the sinoatrial node acting through Isl1 repression.
- ISL1 is a major susceptibility gene for classic bladder exstrophy and a regulator of urinary tract development.
Zhang, Scientific reports 2017 - GeneRIF: ISL1 is a major susceptibility gene for bladder exstrophy and a regulator of urinary tract development.
- Analysis of transcriptional codes for zebrafish dopaminergic neurons reveals essential functions of Arx and Isl1 in prethalamic dopaminergic neuron development.
Filippi, Developmental biology 2012 (PubMed)- GeneRIF: Arx contributes to patterning in the prethalamic region, while Isl1 is required for differentiation of prethalamic dopaminergic neurons.
- The LIM protein Ajuba restricts the second heart field progenitor pool by regulating Isl1 activity.
Witzel, Developmental cell 2012 - GeneRIF: Ajuba plays a central role in regulating the second heart field during heart development by linking retinoic acid signaling to the function of Isl1, a key transcription factor in cardiac progenitor cells.
- Islet1 selectively promotes peripheral axon outgrowth in Rohon-Beard primary sensory neurons.
Tanaka, Developmental dynamics : an official publication of the American Association of Anatomists 2011 (PubMed)- GeneRIF: Isl1 is required for the selective outgrowth of the peripheral axons of Rohon-beard neurons.
- prdm1a Regulates sox10 and islet1 in the development of neural crest and Rohon-Beard sensory neurons.
Olesnicky, Genesis (New York, N.Y. : 2000) 2010 - GeneRIF: prdm1a Regulates sox10 and islet1 in the development of neural crest and Rohon-Beard sensory neurons.
- Nkx6 proteins specify one zebrafish primary motoneuron subtype by regulating late islet1 expression.
Hutchinson, Development (Cambridge, England) 2007 - GeneRIF: Nkx6 proteins regulate MiP motorneuron development at least in part by maintaining the islet1 expression that is required both to promote the MiP subtype and to suppress interneuron development.
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ISL1_DANRE / P53405 Insulin gene enhancer protein isl-1; Islet-1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
48% identity, 16% coverage
- function: DNA-binding transcriptional activator. Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA-3' in promoter of target genes. Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation. May be involved in subtype specialization of primary motoneurons. May bind to insulin gene enhancer sequences. Essential for heart development (By similarity).
ISL1_CHICK / P50211 Insulin gene enhancer protein ISL-1; Islet-1 from Gallus gallus (Chicken) (see paper)
NP_990745 insulin gene enhancer protein ISL-1 from Gallus gallus
48% identity, 16% coverage
- function: Acts as a transcriptional regulator (PubMed:7528105). Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA- 3' in promoter of target genes. Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation. Binds to insulin gene enhancer sequences (By similarity). Defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways (PubMed:7528105). Acts in conjunction with LHX1, LHX3 and ISL2 (PubMed:7528105). Binds to insulin gene enhancer sequences (By similarity). Essential for heart development (By similarity).
- Cadherin-6B is required for the generation of Islet-1-expressing dorsal interneurons.
Park, Biochemical and biophysical research communications 2015 - GeneRIF: Knockdown or loss of function of Cadherin-6B suppressed the generation of Islet-1-expressing cells in the dorsal neural tube, but not the Lim-1/2 positive dorsal cell population.
- The sinus venosus myocardium contributes to the atrioventricular canal: potential role during atrioventricular node development?
Kelder, Journal of cellular and molecular medicine 2015 - GeneRIF: Data indicate that myocardial markers ISL1, TNNI2 and NKX2-5 and HCN4 were studied in sequential stages of chick embryo development.
- Developmental delay in islet-1-positive motor neurons in chick spina bifida.
Wang, The Journal of veterinary medical science 2011 (PubMed)- GeneRIF: A defect in the production and elimination of excess motor neurons in the early developmental stages in spina bifida aperta may be involved in the pathological mechanism of the motor complications of this disease.
- Isl-1 down-regulates DRG cell proliferation during chicken embryo development.
Chen, Neuro endocrinology letters 2010 (PubMed)- GeneRIF: Isl-1 negatively modulates DRG cell proliferation.
- Axon-bearing and axon-less horizontal cell subtypes are generated consecutively during chick retinal development from progenitors that are sensitive to follistatin.
Edqvist, BMC developmental biology 2008 - GeneRIF: HC progenitors are sensitive to follistatin and become committed to produce Isl1+ HC subtypes concomitantly with or early after their own generation
- Developmental changes of Islet-1 and its co-localization with pituitary hormones in the pituitary gland of chick embryo by immunohistochemistry.
Liu, Cell and tissue research 2005 (PubMed)- GeneRIF: These results suggest that Islet-1 is involved in determining the cell lineages, proliferation, differentiation and maintenance of hormone-secreting functions of pituitary gonadotrophs and thyrotrophs of chick embryo.
- Islet-1 expression in the developing chicken inner ear.
Li, The Journal of comparative neurology 2004 (PubMed)- GeneRIF: The data of this study is consistent with a role for islet-1 in differentiating inner ear neurons and sensory epithelia cells, perhaps in the specification of cellular subtypes in conjunction with other LIM/homeodomain proteins.
ISL1_HUMAN / P61371 Insulin gene enhancer protein ISL-1; Islet-1 from Homo sapiens (Human) (see 2 papers)
ISL1_MOUSE / P61372 Insulin gene enhancer protein ISL-1; Islet-1 from Mus musculus (Mouse) (see 7 papers)
ISL1_MESAU / P61373 Insulin gene enhancer protein ISL-1; Islet-1 from Mesocricetus auratus (Golden hamster) (see paper)
ISL1_RAT / P61374 Insulin gene enhancer protein ISL-1; Islet-1 from Rattus norvegicus (Rat) (see 2 papers)
NP_059035 insulin gene enhancer protein ISL-1 from Rattus norvegicus
NP_002193 insulin gene enhancer protein ISL-1 from Homo sapiens
XP_004017051 insulin gene enhancer protein ISL-1 from Ovis aries
48% identity, 16% coverage
- function: DNA-binding transcriptional activator. Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA-3' in promoter of target genes. Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation. Cooperates with the transcription factor POU4F2 to achieve maximal levels of expression of RGC target genes and RGC fate specification in the developing retina. Involved in the specification of motor neurons in cooperation with LHX3 and LDB1 (By similarity). Binds to insulin gene enhancer sequences (By similarity). Essential for heart development. Marker of one progenitor cell population that give rise to the outflow tract, right ventricle, a subset of left ventricular cells, and a large number of atrial cells as well, its function is required for these progenitors to contribute to the heart. Controls the expression of FGF and BMP growth factors in this cell population and is required for proliferation and survival of cells within pharyngeal foregut endoderm and adjacent splanchnic mesoderm as well as for migration of cardiac progenitors into the heart (By similarity).
subunit: At neuronal promoters, displaces LDB1 from LHX3 LIM domain to form a ternary complex in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1:LHX3 interaction, may explain differences in sequence specificity of the different complexes. Interacts with LHX3. Interacts (via C-terminus) with POU4F2 (via C-terminus) isoform 1. Interacts with POU3F2. Interacts with POU4F3. Interacts (via N-terminal domain) with MLIP; the interaction represses ISL1 transactivator activity. Interacts with GCN5/KAT2A. Interactions of ISL1 with MLIP1 or KAT2A may be mutually exclusive (By similarity). - function: DNA-binding transcriptional activator (PubMed:14664703, PubMed:18539116, PubMed:22343712, PubMed:24643061, PubMed:25775587). Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA- 3' in promoter of target genes (PubMed:18539116, PubMed:24643061, PubMed:25775587). Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation (PubMed:25775587). Cooperates with the transcription factor POU4F2 to achieve maximal levels of expression of RGC target genes and RGC fate specification in the developing retina (PubMed:24643061, PubMed:25775587). Involved in the specification of motor neurons in cooperation with LHX3 and LDB1 (PubMed:18583962). Binds to insulin gene enhancer sequences (By similarity). Essential for heart development. Marker of one progenitor cell population that give rise to the outflow tract, right ventricle, a subset of left ventricular cells, and a large number of atrial cells as well, its function is required for these progenitors to contribute to the heart. Controls the expression of FGF and BMP growth factors in this cell population and is required for proliferation and survival of cells within pharyngeal foregut endoderm and adjacent splanchnic mesoderm as well as for migration of cardiac progenitors into the heart (PubMed:14667410).
subunit: At neuronal promoters, displaces LDB1 from LHX3 LIM domain to form a ternary complex in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1:LHX3 interaction, may explain differences in sequence specificity of the different complexes (PubMed:18539116, PubMed:18583962). Interacts with LHX3 (PubMed:18539116). Interacts (via C-terminus) with POU4F2 (via C-terminus) isoform 1 (PubMed:24643061). Interacts with POU3F2 (PubMed:24643061). Interacts with POU4F3 (PubMed:24643061). Interacts (via N-terminal domain) with MLIP; the interaction represses ISL1 transactivator activity (PubMed:22343712, PubMed:36112854). Interacts with GCN5/KAT2A. Interactions of ISL1 with MLIP1 or KAT2A may be mutually exclusive (PubMed:36112854).
disruption phenotype: Embryonic mutants exhibit growth retardation at approximately 9.5 dpc and die at approximately 10.5 dpc. Between 9.0 dpc and 9.5 dpc hearts are severely abnormal, appear misshapen and unlooped. Hearts are completely missing the outflow tract, right ventricle, and much of the atria (PubMed:14667410). Conditional mutants for retina expression show a decrease in several gene expression levels involved in the differentiation of retinal ganglion cells (RGC) (PubMed:24643061). - function: DNA-binding transcriptional activator. Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA-3' in promoter of target genes. Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation. Cooperates with the transcription factor POU4F2 to achieve maximal levels of expression of RGC target genes and RGC fate specification in the developing retina. Involved in the specification of motor neurons in cooperation with LHX3 and LDB1 (By similarity). Binds to insulin gene enhancer sequences (By similarity). Essential for heart development. Marker of one progenitor cell population that give rise to the outflow tract, right ventricle, a subset of left ventricular cells, and a large number of atrial cells as well, its function is required for these progenitors to contribute to the heart. Controls the expression of FGF and BMP growth factors in this cell population and is required for proliferation and survival of cells within pharyngeal foregut endoderm and adjacent splanchnic mesoderm as well as for migration of cardiac progenitors into the heart (By similarity).
subunit: At neuronal promoters, displaces LDB1 from LHX3 LIM domain to form a ternary complex in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1:LHX3 interaction, may explain differences in sequence specificity of the different complexes. Interacts with LHX3. Interacts (via C-terminus) with POU4F2 (via C-terminus) isoform 1. Interacts with POU3F2. Interacts with POU4F3. Interacts (via N-terminal domain) with MLIP; the interaction represses ISL1 transactivator activity. Interacts with GCN5/KAT2A. Interactions of ISL1 with MLIP1 or KAT2A may be mutually exclusive (By similarity). - function: DNA-binding transcriptional activator. Recognizes and binds to the consensus octamer binding site 5'-ATAATTAA-3' in promoter of target genes. Plays a fundamental role in the gene regulatory network essential for retinal ganglion cell (RGC) differentiation. Cooperates with the transcription factor POU4F2 to achieve maximal levels of expression of RGC target genes and RGC fate specification in the developing retina. Involved in the specification of motor neurons in cooperation with LHX3 and LDB1 (By similarity). Binds to insulin gene enhancer sequences (PubMed:1691825). Essential for heart development. Marker of one progenitor cell population that give rise to the outflow tract, right ventricle, a subset of left ventricular cells, and a large number of atrial cells as well, its function is required for these progenitors to contribute to the heart. Controls the expression of FGF and BMP growth factors in this cell population and is required for proliferation and survival of cells within pharyngeal foregut endoderm and adjacent splanchnic mesoderm as well as for migration of cardiac progenitors into the heart (By similarity).
subunit: At neuronal promoters, displaces LDB1 from LHX3 LIM domain to form a ternary complex in which ISL1 contacts both LHX3 and LDB1; allosteric structural changes in the DNA binding domain of LHX3, induced by the ISL1:LHX3 interaction, may explain differences in sequence specificity of the different complexes. Interacts with LHX3. Interacts (via C-terminus) with POU4F2 (via C-terminus) isoform 1. Interacts with POU3F2. Interacts with POU4F3. Interacts (via N-terminal domain) with MLIP; the interaction represses ISL1 transactivator activity. Interacts with GCN5/KAT2A. Interactions of ISL1 with MLIP1 or KAT2A may be mutually exclusive (By similarity). - Missense mutation of ISL1 (E283D) is associated with the development of type 2 diabetes.
Zhang, Diabetologia 2024 (PubMed)- GeneRIF: Missense mutation of ISL1 (E283D) is associated with the development of type 2 diabetes.
- An in vitro model for the assessment of stem cell fate following implantation within the infarct microenvironment identifies ISL-1 expression as the strongest predictor of c-Kit(+) cardiac progenitor cells' therapeutic potential.
Sullivan, Journal of molecular and cellular cardiology 2015 - GeneRIF: An in vitro model for the assessment of stem cell fate following implantation within the infarct microenvironment identifies ISL-1 expression as the strongest predictor of c-Kit(+) cardiac progenitor cells' therapeutic potential.
- LIM homeobox transcription factor 1B is associated with pro-fibrotic components and apoptosis in hypoxia/reoxygenation renal tubular epithelial cells.
Zhou, Apoptosis : an international journal on programmed cell death 2014 (PubMed)- GeneRIF: Overexpression of LMX1B was associated with reduced cell apoptosis, whilst downregulation of LMX1B was associated with increased cell apoptosis in H-R RTEC.
- Islet-1 is a dual regulator of fibrogenic epithelial-to-mesenchymal transition in epicardial mesothelial cells.
Brønnum, Experimental cell research 2013 (PubMed)- GeneRIF: Isl1 is a key regulatory molecule in adult cardiac epithelial-to-mesenchymal transition.
- Fusion protein Isl1-Lhx3 specifies motor neuron fate by inducing motor neuron genes and concomitantly suppressing the interneuron programs.
Lee, Proceedings of the National Academy of Sciences of the United States of America 2012 - GeneRIF: Isl1-Lhx3, a LIM-complex mimicking fusion, induces a signature of motor neuron transcriptome & suppresses interneuron differentiation programs. An equimolar ratio of Isl1 & Lhx3 & the LIM domain of Lhx3 are crucial for this.
- Reprogramming of neonatal SVZ progenitors by islet-1 and neurogenin-2.
Rogelius, Molecular and cellular neurosciences 2008 (PubMed)- GeneRIF: Subventricular zone neurons can be redirected from their normal migration route and directed towards other brain regions when they are infected with retroviruses encoding the developmentally important transcription factors islet-1 and neurogenin-2.
- [Discovery of rat Islet-1 gene variant and its expression in NSC].
Liu, Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology 2007 (PubMed)- GeneRIF: expression of Islet-1 was found in NSC by immunocytochemical staining
- The LIM-homeodomain proteins Isl-1 and Lhx3 act with steroidogenic factor 1 to enhance gonadotrope-specific activity of the gonadotropin-releasing hormone receptor gene promoter.
Granger, Molecular endocrinology (Baltimore, Md.) 2006 (PubMed)- GeneRIF: data suggest the occurrence of a specific LIM-HD pituitary code and designate the GnRH-R gene as the first identified transcriptional target of Isl-1 in the anterior pituitary
- More
- Isl1 promotes gene transcription through physical interaction with Set1/Mll complexes.
Liu, European journal of cell biology 2023 (PubMed)- GeneRIF: Isl1 promotes gene transcription through physical interaction with Set1/Mll complexes.
- Genetic Variants of ISL1 Gene Promoter Identified from Congenital Tetralogy of Fallot Patients Alter Cellular Function Forming Disease Basis.
Yin, Biomolecules 2023 - GeneRIF: Genetic Variants of ISL1 Gene Promoter Identified from Congenital Tetralogy of Fallot Patients Alter Cellular Function Forming Disease Basis.
- Human breast milk cells are positive for the pioneer transcription factor ISL1.
Piras, European review for medical and pharmacological sciences 2023 (PubMed)- GeneRIF: Human breast milk cells are positive for the pioneer transcription factor ISL1.
- The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
Maven, Stem cell reports 2023 - GeneRIF: The multi-lineage transcription factor ISL1 controls cardiomyocyte cell fate through interaction with NKX2.5.
- Investigation of promoter methylation patterns association with genes expression profile of ISL1, MGMT and DMNT3b in tissue of breast cancer patients.
Yari, Molecular biology reports 2022 (PubMed)- GeneRIF: Investigation of promoter methylation patterns association with genes expression profile of ISL1, MGMT and DMNT3b in tissue of breast cancer patients.
- ISL1 Promotes Human Glioblastoma-Derived Stem Cells' Self-Renewal by Activation of Sonic Hedgehog/GLI1 Function.
Liu, Stem cells and development 2022 (PubMed)- GeneRIF: ISL1 Promotes Human Glioblastoma-Derived Stem Cells' Self-Renewal by Activation of Sonic Hedgehog/GLI1 Function.
- Identification and functional analysis of genetic variants of ISL1 gene promoter in human atrial septal defects.
Yin, The journal of gene medicine 2022 (PubMed)- GeneRIF: Identification and functional analysis of genetic variants of ISL1 gene promoter in human atrial septal defects.
- Association of ISL1 polymorphisms and eosinophilic levels among otitis media patients.
Kondyarpu, Journal of clinical laboratory analysis 2021 - GeneRIF: Association of ISL1 polymorphisms and eosinophilic levels among otitis media patients.
- More
- Zika Virus Infection of Sertoli Cells Alters Protein Expression Involved in Activated Immune and Antiviral Response Pathways, Carbohydrate Metabolism and Cardiovascular Disease
Rashid, Viruses 2022 - “...cyclase type 10 4.39 8.8 10 5 4.19 2.8 10 4 1.00 9.1 10 1 P61371 ISL1 Insulin gene enhancer protein ISL-1 4.11 1.6 10 4 P10145 CXCL8 Interleukin-8 3.83 1.8 10 4 3.07 4.5 10 4 P20591 MX1 Interferon-induced GTP-binding protein Mx1 3.53 8.1 10...”
- An Anticancer Rhenium Tricarbonyl Targets Fe-S Cluster Biogenesis in Ovarian Cancer Cells.
Neuditschko, Angewandte Chemie (International ed. in English) 2022 - “...The 171 proteins with at least 2fold enrichment are shown. ISL1=Insulin gene enhancer protein ISL1 (P61371), MUM1=PWWP domain containing protein MUM1 (Q2TAK8), SCD=AcylCoA desaturase (O00767), and PFKL=ATPdependent 6phosphofructokinase (P17858). B)The inhibition profiles of the indicated potential interactors are shown and their concentrations at which half of...”
- “...A). Among the most significantly enriched proteins, we identified insulin gene enhancer protein ISL1 (ISL1, P61371), PWWP domain containing protein MUM1 (MUM1, Q2TAK8), AcylCoA desaturase (SCD, O00767) and ATPdependent 6phosphofructokinase (PFKL, P17858). The latter was found with high intensity, but corresponds to a lowspecific interactor as...”
- A mutant α1antitrypsin in complex with heat shock proteins as the primary antigen in type 1 diabetes in silico investigation.
Finotti, Scientific reports 2021 - “...Glucose 6-phosphatase 2 (IGRP, Q9NQR9), Urocortin 3 (UCN3, Q969E3), Insulin gene enhancer protein isl-1 (ISL-1, P61371). To detect sequence similarities, pairwise alignment of the proteins was performed using two progressive alignment methods, the Clustal Omega programme (UniProtKB) and the T-Coffee (Tree-based Consistency Objective Function for alignment...”
- Towards a Central Role of ISL1 in the Bladder Exstrophy⁻Epispadias Complex (BEEC): Computational Characterization of Genetic Variants and Structural Modelling.
Sharma, Genes 2018 - “...variant protein. The structures were generated using the wild type amino acid sequences (UniProt ID: P61371) and the mutant amino acid sequence (with p.Ala46Gly), by the Iterative Threading ASSEmbly Refinement method (I-TASSER) available online. For generating both models, I-TASSER used the template of the 4JCJ crystal...”
- Genetically identified spinal interneurons integrating tactile afferents for motor control.
Bui, Journal of neurophysiology 2015 - Contrasting DNA-binding behaviour by ISL1 and LHX3 underpins differential gene targeting in neuronal cell specification.
Smith, Journal of structural biology: X 2021 - “...codes for the mouse protein sequences used are: LHX3 - P50481 (isoform 1), and ISL1- P61372 (isoform 1). Protein encoding constructs are detailed in the Supplemental Information and were expressed from a modified pET-DUET plasmid that encodes an N-terminal GST tag with an HRV 3C protease...”
- Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...roles in cell differentiation, proliferation, and survival defects in Mitf cause microphthalmia (mi) 9 isoforms P61372 Isl1 insulin gene enhancer protein ISL-1 129 regulates promoters of insulin, glucagon, and somatostatin genes -- 2 isoforms Q63934 Pou4f2 POU domain, class 4, transcription factor 2 127 transcription factor...”
- Islet-1 expression and its colocalization with luteinising hormone, thyroid-stimulating hormone and oestrogen receptor alpha in the developing pituitary gland of the sheep foetus.
Liu, Journal of neuroendocrinology 2005 (PubMed)- GeneRIF: Islet-1-immunoreactive (ir) cells were distributed throughout the pituitary gland from day 60 of gestation until birth
XP_006510819 insulin gene enhancer protein ISL-2 isoform X1 from Mus musculus
48% identity, 15% coverage
- Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2.
Lee, eLife 2023 - GeneRIF: Transcriptional control of motor pool formation and motor circuit connectivity by the LIM-HD protein Isl2.
- Mutation in a flexible linker modulates binding affinity for modular complexes.
Stokes, Proteins 2019 (PubMed)- GeneRIF: We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.
- Slit and Semaphorin signaling governed by Islet transcription factors positions motor neuron somata within the neural tube.
Lee, Experimental neurology 2015 - GeneRIF: lack both Isl1 and Isl2, large numbers of motor neurons exited the neural tube, even prior to the appearance of boundary cap cells at the ventral exit points
- Structural basis for partial redundancy in a class of transcription factors, the LIM homeodomain proteins, in neural cell type specification.
Gadd, The Journal of biological chemistry 2011 - GeneRIF: X-ray crystal- and small-angle x-ray scattering-derived solution structures of an Lhx4.Isl2 complex exhibit many similarities with that of Lhx3.Isl1; structural differences supported by mutagenic studies reveal differences in the mechanisms of binding.
- Crystallization and diffraction of an Lhx4-Isl2 complex.
Gadd, Acta crystallographica. Section F, Structural biology and crystallization communications 2009 - GeneRIF: Successful purification and crystallization of an engineered complex comprising the LIM domains of motor neuron protein Lhx4 and the Lim binding domain of Isl2 (islet 2 protein) are reported.
- Islet-to-LMO stoichiometries control the function of transcription complexes that specify motor neuron and V2a interneuron identity.
Song, Development (Cambridge, England) 2009 - GeneRIF: Data describe how the dosage of LIM homeodomain proteins Isl1 and Isl2 and LIM-only protein Lmo4 influences the assembly and function of complexes involved in the generation of spinal motor neurons (MNs) and V2a interneurons (INs).
- Diverse expression patterns of LIM-homeodomain transcription factors (LIM-HDs) in mammalian inner ear development.
Huang, Developmental dynamics : an official publication of the American Association of Anatomists 2008 - GeneRIF: The second wave of expression at E12.5 includes Lhx3, 5, 9, Isl2, and Lmx1b in the differentiating sensory epithelia with cellular specificities.
- Magnitude of binocular vision controlled by islet-2 repression of a genetic program that specifies laterality of retinal axon pathfinding.
Pak, Cell 2004 (PubMed)- GeneRIF: Isl2 specifies RGC laterality by repressing an ipsilateral pathfinding program unique to VTC RGCs and involving Zic2 and EphB1. This genetic hierarchy controls binocular vision
NP_001104188 ISL LIM homeobox 1 S homeolog from Xenopus laevis
48% identity, 16% coverage
ISL2_MOUSE / Q9CXV0 Insulin gene enhancer protein ISL-2; Islet-2 from Mus musculus (Mouse) (see paper)
48% identity, 16% coverage
- function: Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways.
subunit: Interacts with LHX4. - Priorities and trends in the study of proteins in eye research, 1924-2014.
Semba, Proteomics. Clinical applications 2015 - “...isoforms P28236 Gja8 gap junction alpha-8 protein 52 component of gap junction -- 1 isoform Q9CXV0 Isl2 insulin gene enhancer protein ISL-2 52 transcriptional factor -- 1 isoform P51491 Opn1sw short-wave-sensitive opsin 1 50 visual pigment -- 1 isoform P20443 Sag S-arrestin 50 binds to photoactivated-phosphorylated...”
T265_11894 hypothetical protein from Opisthorchis viverrini
44% identity, 22% coverage
- In silico prediction of secretory proteins of Opisthorchis viverrini, Clonorchis sinensis and Fasciola hepatica that target the host cell nucleus
Machicado, Heliyon 2021 - “...No T265_14284 - + A0A074ZCR2 Uncharacterized protein 7.64 36.92 nucleic acid binding Yes No No T265_11894 + - A0A074YXA4 Homeobox domain-containing protein 9.00 27.36 sequence-specific DNA binding regulation of transcription, DNA-templated nucleus Yes No No DNA binding T265_01616 + - A0A075AIX5 Uncharacterized protein 6.00 30.82 integral...”
- “...- + A0A074ZT78 Uncharacterized protein 6.55 30.17 T265_13583 - + A0A074ZRH1 Uncharacterized protein 5.73 21.73 T265_11894 + + A0A074YXA4 Homeobox domain-containing protein 8.85 27.36 T265_00902 - + A0A075AJD9 TFIIB-type domain-containing protein 5.68 15.38 core RNA polymerase III binding transcription factor activity transcription from RNA polymerase III...”
NP_001016712 homeobox expressed in ES cells 1 from Xenopus tropicalis
46% identity, 30% coverage
B5LDT8 Lim1 (Fragment) from Trichoplax adhaerens
48% identity, 93% coverage
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...or RK )! The TriPaxB penetratin RVVQVWFQNQRAKLKK from the Trichoplax adhaerens protein Lim1 (UniProt entry B5LDT8) served as a query (named TriPaxB) for extended penetratins in other simple organisms (see Table 2 ). T. adhaerens has a high regeneration and rejuvenation potential, partially due to the...”
NP_476775 tailup, isoform A from Drosophila melanogaster
Q9VJ37 Tailup, isoform A from Drosophila melanogaster
46% identity, 10% coverage
- Tailup expression in Drosophila larval and adult cardiac valve cells.
Meyer, Genesis (New York, N.Y. : 2000) 2023 (PubMed)- GeneRIF: Tailup expression in Drosophila larval and adult cardiac valve cells.
- Chip/Ldb1 interacts with Tailup/islet1 to regulate cardiac gene expression in Drosophila.
Werner, Genesis (New York, N.Y. : 2000) 2017 (PubMed)- GeneRIF: tup interacts with Chip to regulate the generation of different cardiac cell types. Tup directly regulates eve expression.
- Org-1-dependent lineage reprogramming generates the ventral longitudinal musculature of the Drosophila heart.
Schaub, Current biology : CB 2015 (PubMed)- GeneRIF: Reinitiation of a transcriptional program previously employed for embryonic alary muscle development, in which the factors Org-1 and Tailup are key components, leads to the development of adult Drosophila ventral longitudinal heart muscles.
- The transcription factors islet and Lim3 combinatorially regulate ion channel gene expression.
Wolfram, The Journal of neuroscience : the official journal of the Society for Neuroscience 2014 - GeneRIF: These observations provide evidence for combinatorial activity of Isl and Lim3 in regulating ion channel gene expression
- An Org-1-Tup transcriptional cascade reveals different types of alary muscles connecting internal organs in Drosophila.
Boukhatmi, Development (Cambridge, England) 2014 (PubMed)- GeneRIF: An Org-1-Tup transcriptional cascade reveals different types of alary muscles connecting internal organs in Drosophila.
- 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 - “...NP_571291, NP_071758, BAH58087, XP_001945631, NP_572505, AEN75258, ABD59002, XP_002591838, NP_001158395, ACA04748, NP_001130018, EAW91078, XP_973330, NP_724161, XP_001638136, NP_476775, NP_001158279, NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, 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...”
- Tailup plays multiple roles during cardiac outflow assembly in Drosophila.
Zmojdzian, Cell and tissue research 2013 (PubMed)- GeneRIF: Tailup is expressed in the main Drosophila cardiac outflow components, i.e., heart anchoring cells (HANC) and cardiac outflow muscles (COM) and that loss of its function and/or tissue-specific knockdowns dramatically affect cardiac outflow morphogenesis.
- The LIM-homeodomain protein islet dictates motor neuron electrical properties by regulating K(+) channel expression.
Wolfram, Neuron 2012 - GeneRIF: This study demonistratedt that therole of Islet on the excitability patterns characteristic of motoneuron subtypes.
- More
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...FBgn0051624 CG31624 Q2XYF8 N/A N/A LIM-Only FBgn0039055 Rassf Q9VCQ7 N/A N/A LIM protein FBgn0003896 Tup Q9VJ37 Amnioserosa, API, Foregut, Head, Tracheal system, Muscles, Dorsal vessel Amnioserosa, Leading edge cell, CNS, Dorsal epidermis, Embryonic brain, sophagus, Foregut, Stomatogastric LIM-HD FBgn0032196 CG5708 Q9VL21 N/A NA LIM-Only FBgn0036274 CG4328...”
P79775 Homeobox protein ANF-1 from Gallus gallus
46% identity, 29% coverage
XP_068078243 zinc finger homeobox protein 3 isoform X1 from Danio rerio
50% identity, 1% coverage
NP_001158238 zinc finger homeobox protein 3 isoform B from Homo sapiens
50% identity, 2% coverage
- Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease.
Wallenius, American journal of human genetics 2024 - GeneRIF: Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease.
- Adaptive Long-Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4.
Chen, Movement disorders : official journal of the Movement Disorder Society 2024 (PubMed)- GeneRIF: Adaptive Long-Read Sequencing Reveals GGC Repeat Expansion in ZFHX3 Associated with Spinocerebellar Ataxia Type 4.
- Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus.
Casalino-Matsuda, JCI insight 2024 - GeneRIF: Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus.
- Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability.
Pérez, American journal of human genetics 2024 - GeneRIF: Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability.
- ZFHX3 variants cause childhood partial epilepsy and infantile spasms with favourable outcomes.
He, Journal of medical genetics 2024 - GeneRIF: ZFHX3 variants cause childhood partial epilepsy and infantile spasms with favourable outcomes.
- Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.
Paucar, Journal of internal medicine 2024 (PubMed)- GeneRIF: Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.
- Influence of ZFHX3 Polymorphisms on the Risk of Ischemic Stroke in Chinese Han Population.
Hu, Cardiovascular toxicology 2023 (PubMed)- GeneRIF: Influence of ZFHX3 Polymorphisms on the Risk of Ischemic Stroke in Chinese Han Population.
- Loss of the Atrial Fibrillation-Related Gene, Zfhx3, Results in Atrial Dilation and Arrhythmias.
Jameson, Circulation research 2023 - GeneRIF: Loss of the Atrial Fibrillation-Related Gene, Zfhx3, Results in Atrial Dilation and Arrhythmias.
- More
XP_006530648 zinc finger homeobox protein 3 isoform X1 from Mus musculus
50% identity, 1% coverage
- Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus.
Casalino-Matsuda, JCI insight 2024 - GeneRIF: Myeloid Zfhx3 deficiency protects against hypercapnia-induced suppression of host defense against influenza A virus.
- Evaluation of Potential Roles of Zinc Finger Homeobox 3 (Zfhx3) Expressed in Chondrocytes and Osteoblasts on Skeletal Growth in Mice.
Gomez, Calcified tissue international 2024 - GeneRIF: Evaluation of Potential Roles of Zinc Finger Homeobox 3 (Zfhx3) Expressed in Chondrocytes and Osteoblasts on Skeletal Growth in Mice.
- Loss of the Atrial Fibrillation-Related Gene, Zfhx3, Results in Atrial Dilation and Arrhythmias.
Jameson, Circulation research 2023 - GeneRIF: Loss of the Atrial Fibrillation-Related Gene, Zfhx3, Results in Atrial Dilation and Arrhythmias.
- A missense mutation in zinc finger homeobox-3 (ZFHX3) impedes growth and alters metabolism and hypothalamic gene expression in mice.
Nolan, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2023 - GeneRIF: A missense mutation in zinc finger homeobox-3 (ZFHX3) impedes growth and alters metabolism and hypothalamic gene expression in mice.
- Zfhx3 modulates retinal sensitivity and circadian responses to light.
Hughes, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021 - GeneRIF: Zfhx3 modulates retinal sensitivity and circadian responses to light.
- Zfhx3 is essential for progesterone/progesterone receptor signaling to drive ductal side-branching and alveologenesis in mouse mammary glands.
Ma, Journal of genetics and genomics = Yi chuan xue bao 2019 (PubMed)- GeneRIF: Zfhx3 as an integral transcription factor of Pg/PR signaling in driving side-branching and alveologenesis during mammary gland development
- MicroRNA-133 suppresses ZFHX3-dependent atrial remodelling and arrhythmia.
Cheng, Acta physiologica (Oxford, England) 2019 (PubMed)- GeneRIF: MicroRNA-133 suppresses ZFHX3-dependent atrial remodelling and arrhythmia.
- Zfhx3 is required for the differentiation of late born D1-type medium spiny neurons.
Zhang, Experimental neurology 2019 (PubMed)- GeneRIF: Zfhx3 plays a critical role in the differentiation and survival of late born dopamine receptor D1 medium spiny neurons
- More
ZFHX3_MOUSE / Q61329 Zinc finger homeobox protein 3; AT motif-binding factor 1; AT-binding transcription factor 1; Alpha-fetoprotein enhancer-binding protein; Zinc finger homeodomain protein 3; ZFH-3 from Mus musculus (Mouse) (see 5 papers)
50% identity, 1% coverage
- function: Transcriptional regulator which can act as an activator or a repressor. Inhibits the enhancer element of the AFP gene by binding to its AT-rich core sequence. In concert with SMAD-dependent TGF-beta signaling can repress the transcription of AFP via its interaction with SMAD2/3 (By similarity). Regulates the circadian locomotor rhythms via transcriptional activation of neuropeptidergic genes which are essential for intercellular synchrony and rhythm amplitude in the suprachiasmatic nucleus (SCN) of the brain (PubMed:26232227). Regulator of myoblasts differentiation through the binding to the AT-rich sequence of MYF6 promoter and promoter repression. Down-regulates the MUC5AC promoter in gastric cancer. In association with RUNX3, up- regulates CDKN1A promoter activity following TGF-beta stimulation (By similarity).
subunit: Interacts with ALKBH4 and PIAS3 (By similarity). Interacts with FNBP3. Interacts with ESR1, RUNX3, TRIM25, SMAD2 and SMAD3 (By similarity). - Dynamin-1 co-associates with native mouse brain BKCa channels: proteomics analysis of synaptic protein complexes.
Gorini, FEBS letters 2010 - “...chain (uniprotkb:P99024), V-type proton ATPase subunit d 1 (uniprotkb:P51863), Zinc finger homeobox protein 3 (uniprotkb: Q61329 ), Tubulin beta-2A chain (uniprotkb:Q7TMM9), Synaptophysin (uniprotkb:Q62277), Gapdh (uniprotkb: P16858 ), Basement membrane-specific heparan sulfate proteoglycan core protein (uniprotkb: Q05793 ), Tubulin alpha-4A chain (uniprotkb: P68368 ), Tubulin alpha-1A chain...”
ZFHX3_HUMAN / Q15911 Zinc finger homeobox protein 3; AT motif-binding factor 1; AT-binding transcription factor 1; Alpha-fetoprotein enhancer-binding protein; Zinc finger homeodomain protein 3; ZFH-3 from Homo sapiens (Human) (see 14 papers)
50% identity, 1% coverage
- function: Transcriptional regulator which can act as an activator or a repressor. Inhibits the enhancer element of the AFP gene by binding to its AT-rich core sequence. In concert with SMAD-dependent TGF-beta signaling can repress the transcription of AFP via its interaction with SMAD2/3 (PubMed:25105025). Regulates the circadian locomotor rhythms via transcriptional activation of neuropeptidergic genes which are essential for intercellular synchrony and rhythm amplitude in the suprachiasmatic nucleus (SCN) of the brain (By similarity). Regulator of myoblasts differentiation through the binding to the AT-rich sequence of MYF6 promoter and promoter repression (PubMed:11312261). Down-regulates the MUC5AC promoter in gastric cancer (PubMed:17330845). In association with RUNX3, up-regulates CDKN1A promoter activity following TGF-beta stimulation (PubMed:20599712). Inhibits estrogen receptor (ESR1) function by selectively competing with coactivator NCOA3 for binding to ESR1 in ESR1-positive breast cancer cells (PubMed:20720010).
subunit: Interacts with FNBP3 (By similarity). Interacts with ALKBH4 and PIAS3. Interacts with ESR1. Interacts with RUNX3. Interacts with TRIM25. Interacts with SMAD2 and SMAD3. - Chemoproteomic analysis reveals RECQL4 as a mediator of nitroalkene-dependent double-strand break repair inhibition in cancer.
Braden, Research square 2025 - “...transport Q13355 Probable methyltransferase TARBP1 TARB1 DVIHCTMITHQILLR tRNA methylation Q15884 Protein FAM189A2 F1892 ILVARFLEQSSCTMTPDIHELVENIK Unclear Q15911 Zinc finger homeobox protein 3 ZFHX3 MEGCDSPVVSGK Transcription regulation Q5JXX5 Glycine receptor subunit alpha-4 GLRA4 ITLILSCLMDLK Unclear Q6NSI3 Protein FAM53A FA53A SLSEPEELVRCR Protein transport into nucleus O94761 ATP-dependent helicase-like Q4...”
- Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation.
Villanueva-Cañas, iScience 2024 - “...P52657 ), GTF2E2 (UniProt: P29084 ), FOXE1 (UniProt: O00358 ), MZF1 (UniProt: P28698 ), ZFHX3_(UniProt: Q15911 ) binding motifs ( Figure6 D; TableS4 ). Meanwhile, the upregulated genes showed significant enrichment in the promoter regions for motifs that can bind ZNF92 (UniProt: Q03936 ), METTL14 (UniProt:...”
- Genome-wide prediction of disease variant effects with a deep protein language model.
Brandes, Nature genetics 2023 - “...weights. Bottom: normalized weights. ( e ) Example of how a specific protein (UniProt ID Q15911 ) is tiled, as in (c). As shown in the two examples, the effect scores tend to be consistent across different windows (with edge effects sometimes being more pronounced). Extended...”
- Proteomic Investigation in Plasma from Women with Fibromyalgia in Response to a 15-wk Resistance Exercise Intervention
Wåhlén, Medicine and science in sports and exercise 2022 - “...P11226 MBL2 MBL2 1.68 0.40 40/25 34,118 (34,718) 24,066 (32,527) 1.42 Zinc finger homeobox protein Q15911 ZFHX3 ZFHX3 1.66 0.39 40/25 520,290 (181,228) 602,514 (96,569) 0.86 Histone H2A type 1-B/E P04908 H2A1B HIST1H2AB 1.66 0.38 37/25 21,929 (17,326) 26,473 (15,365) 0.83 Collectin-11 Q9BWP8 COL11 COLEC11 1.64...”
- “...CO1A1 COL1A1 1.85 0.49 21/24 5732 (5235) 10,209 (11,923) 0.56 Zinc finger homeobox protein 3 Q15911 ZFHX3 ZFHX3 1.74 0.46 21/24 450,572 (110,794) 563,444 (141,784) 0.80 Tubulin beta chain P07437 TBB5 TUBB 1.70 0.43 13/17 5712 (7492) 11,064 (35,939) 0.52 Hemoglobin subunit gamma 1 P69891 HBG1...”
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...homeobox protein 3 has four homeobox domains in its long sequence of 3703 residues (see Q15911) with four associated penetratins, which are, however, of low similarity to pAntp penetratin. Example 2: Nematodes, cnidarians, and tunicates Previously mentioned arginine-rich analog ARIQVWFSNRRAKWRR is present in the Vab-3 transcription...”
- The structural basis for cohesin-CTCF-anchored loops.
Li, Nature 2020 - “...1.19 24 ZFHX4 Human Wild-type Q86UP3 2144 KDSP YNF SNPP n.b. 25 ZFHX3 Human Wild-type Q15911 2205 KDSP YNF SNPP n.b. 26 MDC1 Human Wild-type Q14676 320 RAQP FGF IDSD n.b. 27 CHD6 Human Wild-type Q8TD26 2177 HRRP YEF EVER ND 28 TFIIH Human Wild-type Q13888...”
- Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells
Murillo, EuPA open proteomics 2017 - “...protein (SMN1) 0.30 3.58E-02 Ser28(0.53); Ser31(0.53) P24941 Cyclin-dependent kinase 2 (CDK2) 0.31 5.64E-04 Thr14(0.31); Tyr15(0.31) Q15911 Zinc finger homeobox protein 3 (ZFHX3) 0.38 1.03E-02 P48681 Nestin (NES) 0.42 3.89E-06 Ser471(0.56) Q16512 Serine/threonine-protein kinase N1 (PKN1) 0.42 1.00E-02 Ser916(0.42) Q9Y6A5 Transforming acidic coiled-coil-containing protein 3 (TACC3) 0.45...”
- Acetylation-regulated interaction between p53 and SET reveals a widespread regulatory mode.
Wang, Nature 2016 - “...Q12873-3 Q96KQ7 Q8IX15 Q8WYB5 P19338 Q5H9L4 Q13029 P27797 Q9UER7 Q4LE39 Q9UPS6-2 P39687 P09429 Q9BT43 P17480 Q15911 Q9UK99 Q9Y4B6 Proline-, glutamic acid- and leucine-rich protein 1 Acidic leucine-rich nuclear phosphoprotein 32 family member B Myelin transcription factor 1-like protein Myelin transcription factor 1 Zinc finger and BTB...”
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ZFHX2_HUMAN / Q9C0A1 Zinc finger homeobox protein 2; Zinc finger homeodomain protein 2; ZFH-2 from Homo sapiens (Human) (see paper)
50% identity, 2% coverage
- function: Transcriptional regulator that is critical for the regulation of pain perception and processing of noxious stimuli.
- The Modulation of Septic Shock: A Proteomic Approach.
Alves, International journal of molecular sciences 2024 - “...beta-3 174.14 2.37 10 6 4.476 TNC P24821 Tenascin 36.37 8.73 10 6 4.307 ZFHX2 Q9C0A1 Zinc finger homeobox protein 2 14.11 0.0001 4.104 ESRP2 Q9H6T0 Epithelial splicing regulatory protein 2 16.19 1.7 10 5 4.011 MYH10 P35580 Myosin-10 76.79 3.25 10 5 3.879 COG4 Q9H9E3...”
- A survey of well conserved families of C2H2 zinc-finger genes in Daphnia
Seetharam, BMC genomics 2010 - “...(NP_001956) ZFH1/2 ZEB1 (P37275) ZFH1 (P28166) ZAG1 (Q94196) ZFH1 (Dappu-225224) 31:791001-795287 ZEB2 (O60315) ZFH3/4 ZFHX2 (Q9C0A1) ZFH2 (P28167) ZC123.3 (O45019) ZFH2 (Dappu-233159) 2:1855545-1862285 ZFHX3 (Q15911) ZFHX4 (Q86UP3) SPALT SALL1 (Q9NSC2) SPALTm (P39770) SEM4(NP_491997) SALL (Dappu-111734) 88:97830-103728 SALL2 (Q9Y467) SPALTr (NP_523548) SALL3 (Q9BXA9) SALL4 (Q9UJQ4) DISCO BNC1...”
- Rules for nuclear localization sequence recognition by karyopherin beta 2.
Lee, Cell 2006
ZFHX4_MOUSE / Q9JJN2 Zinc finger homeobox protein 4; Zinc finger homeodomain protein 4; ZFH-4 from Mus musculus (Mouse) (see 2 papers)
50% identity, 2% coverage
- function: May play a role in neural and muscle differentiation. May be involved in transcriptional regulation.
ZFHX4_HUMAN / Q86UP3 Zinc finger homeobox protein 4; Zinc finger homeodomain protein 4; ZFH-4 from Homo sapiens (Human) (see paper)
50% identity, 2% coverage
- function: May play a role in neural and muscle differentiation (By similarity). May be involved in transcriptional regulation.
- Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models.
Ishorst, European journal of human genetics : EJHG 2025 - “...Sanger sequencing. ZFHX4 protein structure modeling The protein structure of human ZFHX4 (UniProt accession code Q86UP3; 3567 aa) was modeled with AlphaFold3, adding 20 zinc atoms as optional ligands [ 27 ]. Protein graphics were generated using the PyMOL Molecular Graphics System (Version 2.5.5 Schrdinger, LLC)....”
- NMR structure verifies the eponymous zinc finger domain of transcription factor ZNF750.
Rua, Journal of structural biology: X 2023 - “...Q9NQX0 557579 C559, C562, H575, C582 c ZFAT-2 Q9P243 116141 C118, C121, H134, C136 ZFHX4-15 Q86UP3 22672291 C2269, C2272, H2285, C2290 ZFHX4-19 Q86UP3 33543378 C3356, C3359, H3372, C3377 ZFP57-7 Q9NU63 356378 C358, C361, H374, C391 c , d ZN131-4 P52739 356381 C358, C361, H374, C378 ZN292-8...”
- Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.
, Briefings in bioinformatics 2022 - “...1,40E-23 midline QQQQQQQQQQQQQQQQQQQQQQQ Ataxin-2 (Q99700) QQQQQQQQQQQQQQQQQQQQQQQ (165 - 187) 3 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 3,61E-10 midline PPPPPPPPPPPP Inactive histone-lysine N-methyltransferase 2E (Q3UG20) PPPPPPPPPPPP (1719 - 1730) 4 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 1,84E-09 midline PPPPPPPPPPPP...”
- “...Translation initiation factor IF-2 (Q2G5E7) AAPTAAPAAAATPAPTPVAPPPPPPPPPPPP (53 - 83) 5 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 7,75E-10 midline PPPPPPPPPPPP Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (Q64467) PPPPPPPPPPPPPPPPPPPP (83 - 99) Instead of Table 2 BLAST can give ambiguous results; longer homopolymer of serine has higher...”
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.
Jarnot, Briefings in bioinformatics 2022 - “...1,40E-23 midline QQQQQQQQQQQQQQQQQQQQQQQ Ataxin-2 (Q99700) QQQQQQQQQQQQQQQQQQQQQQQ (165 - 187) 3 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 3,61E-10 midline PPPPPPPPPPPP Inactive histone-lysine N-methyltransferase 2E (Q3UG20) PPPPPPPPPPPP (1719 - 1730) 4 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 1,84E-09 midline PPPPPPPPPPPP...”
- “...Translation initiation factor IF-2 (Q2G5E7) AAPTAAPAAAATPAPTPVAPPPPPPPPPPPP (53 - 83) 5 Zinc finger homeobox protein 4 (Q86UP3) PPPPPPPPPPPP (3112 - 3123) 7,75E-10 midline PPPPPPPPPPPP Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (Q64467) PPPPPPPPPPPPPPPPPPPP (83 - 99) The first alignment presents homopolymers of serine that consist of 25 amino acids with e-value...”
- The structural basis for cohesin-CTCF-anchored loops.
Li, Nature 2020 - “...23 ZGPAT Human Wild-type Q8N5A5 411 PRNV FDF LNEK 4.03 1.19 24 ZFHX4 Human Wild-type Q86UP3 2144 KDSP YNF SNPP n.b. 25 ZFHX3 Human Wild-type Q15911 2205 KDSP YNF SNPP n.b. 26 MDC1 Human Wild-type Q14676 320 RAQP FGF IDSD n.b. 27 CHD6 Human Wild-type Q8TD26...”
- Standardization of a protocol for shotgun proteomic analysis of saliva
Ventura, Journal of applied oral science : revista FOB 2018 - “...WAP four-disulfide core domain protein 2 1637.99 33.87 E9PDB0 WD repeat-containing protein 49 424.40 5.02 Q86UP3 Zinc finger homeobox protein 4 205.12 3.06 Q5FWF6 Zinc finger protein 789 138.52 9.41 Q17R98 Zinc finger protein 827 296.41 2.87 P25311 Zinc-alpha-2-glycoprotein 5026.17 55.03 Q96DA0 Zymogen granule protein 16...”
- Biological pathways modulated by antipsychotics in the blood plasma of schizophrenia patients and their association to a clinical response.
Martins-de-Souza, NPJ schizophrenia 2015 - “...finger CCCH domain-containing protein 13 Reg. nucleic acid metab Transcription regulatory protein Transcription regulator activity Q86UP3 ZFHX4_HUMAN ZFHX4 35 398,157 7.38 Up 7.307 2 Zinc finger homeobox protein 4 Reg. nucleic acid metab Transcription factor Transcription factor activity Q9UL58 ZN215_HUMAN ZNF215 40 60,922 0.02 Down 9.007...”
- Quantitative gingival crevicular fluid proteome in health and periodontal disease using stable isotope chemistries and mass spectrometry
Carneiro, Journal of clinical periodontology 2014 - “...0.48 SNS 3 2 Q15911 Zinc finger homeobox protein 3 0.49 0.19 SNS 3 2 Q86UP3 Zinc finger homeobox protein 4 1.14 0.92 SNS 3 3 Q86YH2 Zinc finger protein 280B 0.66 0.45 SNS 3 2 O94822 Zinc finger protein 294 1.23 0.53 SNS 3 3...”
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XP_036019316 zinc finger homeobox protein 4 isoform X1 from Mus musculus
50% identity, 2% coverage
XP_010816072 homeobox expressed in ES cells 1 isoform X4 from Bos taurus
45% identity, 31% coverage
ZFHX2_MOUSE / Q2MHN3 Zinc finger homeobox protein 2; Zinc finger homeodomain protein 5 from Mus musculus (Mouse) (see 3 papers)
50% identity, 2% coverage
- function: Transcriptional regulator that is critical for the regulation of pain perception and processing of noxious stimuli.
disruption phenotype: Knockout mice exhibit a range of subtle behavioral abnormalities. Locomotor activity is generally increased, but only in familiar environments. There is a slight increase in depression-like behavior, most notably increased immobility in the tail suspension test. Assays of anxiety-like behavior give conflicting results; the open field test indicates a slight reduction in anxiety- like behavior whereas other tests show no significant behavioral changes (PubMed:23300874). Knockout mice are hyposensitive to noxious mechanical stimuli applied to the tail and hypersensitive to noxious heat (PubMed:29253101).
HESX1_HUMAN / Q9UBX0 Homeobox expressed in ES cells 1; Homeobox protein ANF; hAnf from Homo sapiens (Human) (see 6 papers)
XP_005265583 homeobox expressed in ES cells 1 isoform X1 from Homo sapiens
45% identity, 30% coverage
- function: Required for the normal development of the forebrain, eyes and other anterior structures such as the olfactory placodes and pituitary gland. Possible transcriptional repressor. Binds to the palindromic PIII sequence, 5'-AGCTTGAGTCTAATTGAATTAACTGTAC-3'. HESX1 and PROP1 bind as heterodimers on this palindromic site, and, in vitro, HESX1 can antagonize PROP1 activation.
subunit: Can form heterodimers with PROP1 in binding to DNA (By similarity). Interacts with TLE1. - Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein.
Zeng, Nature communications 2024 - “...Data 1 ). In Fig. 4b , five single DBD human TFs (UniProtKB ID: P35713, Q9UBX0, P58021, Q9NX45, and Q10587) separately containing five typical DBDs, i.e., HMG box, Homeobox, Fork-head, bHLH, and bZIP, as well as one multi-DBD TF (UniProt ID: P51449) containing two domains, i.e.,...”
- “...Q10587. Moreover, the contribution of a residue in a non-DBD region is also evident on Q9UBX0. After all, DBD and non-DBD of a protein sequence do not exist in isolation but have an interactive relationship. Residues in the non-DBD region also may affect the binding pattern...”
- Homozygous HESX1 and COL1A1 Gene Variants in a Boy with Growth Hormone Deficiency and Early Onset Osteoporosis.
Alesi, International journal of molecular sciences 2021 - GeneRIF: Homozygous HESX1 and COL1A1 Gene Variants in a Boy with Growth Hormone Deficiency and Early Onset Osteoporosis.
- Molecular analysis of brazilian patients with combined pituitary hormone deficiency and orthotopic posterior pituitary lobe reveals eight different PROP1 alterations with three novel mutations.
Madeira, Clinical endocrinology 2017 (PubMed)- GeneRIF: Study did not identify HESX1 and LHX3 mutations by Sanger in brazilian patients with combined pituitary hormone deficiency
- HESX1 mutations in patients with congenital hypopituitarism: variable phenotypes with the same genotype.
Fang, Clinical endocrinology 2016 - GeneRIF: HESX1 mutations cause variable clinical features in congenital hypopituitarism patients, which suggests an influence of modifier genes or environmental factors on the phenotype
- Molecular analysis of PROP1, POU1F1, LHX3, and HESX1 in Turkish patients with combined pituitary hormone deficiency: a multicenter study.
Baş, Endocrine 2015 (PubMed)- GeneRIF: investigated the specific mutations in PROP1, POU1F1, LHX3, and HESX1 genes in patients with combined pituitary hormone deficiency (CPHD) in Turkey
- Novel Mutations in HESX1 and PROP1 Genes in Combined Pituitary Hormone Deficiency.
Avbelj, Hormone research in paediatrics 2015 (PubMed)- GeneRIF: A novel heterozygous mutation in the HESX1 gene and a novel homozygous mutation in the PROP1 gene were detected in 2 pedigrees with combined pituitary hormone deficiency
- Pituitary stalk interruption syndrome in 58 Chinese patients: clinical features and genetic analysis.
Yang, Clinical endocrinology 2013 (PubMed)- GeneRIF: Data indicate that HESX1, LHX4 and SOX3 polymorphisms may be associated with pituitary stalk interruption syndrome (PSIS).
- Identification of HESX1 mutations in Kallmann syndrome.
Newbern, Fertility and sterility 2013 - GeneRIF: expand the phenotypic spectrum of HESX1 mutations in Kallman syndrome.
- Pituitary stalk interruption syndrome in 83 patients: novel HESX1 mutation and severe hormonal prognosis in malformative forms.
Reynaud, European journal of endocrinology 2011 (PubMed)- GeneRIF: A novel HESX1 causative mutation was found in a consanguineous family, and two LHX4 mutations were present in familial Pituitary stalk interruption syndrome.
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P28167 Zinc finger protein 2 from Drosophila melanogaster
48% identity, 2% coverage
- CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search.
Schmidt, BMC bioinformatics 2024 - “...queries are: P02232, P05013, P14942, P07327, P01008, P03435, P42357, P21177, Q38941, P27895, P07756, P04775, P19096, P28167, P0C6B8, P20930, P08519, Q7TMA5, P33450, and Q9UKN1, listed in the ascending order of sequence length. All SW-based tools are executed using the scoring scheme with BLOSUM62, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts}...”
- “...accession numbers P02232, P05013, P14942, P07327, P01008, P03435, P42357, P21177, Q38941, P27895, P07756, P04775, P19096, P28167, P0C6B8, P20930, P08519, Q7TMA5, P33450, Q9UKN1: https://github.com/asbschmidt/CUDASW4/allqueries.fasta . Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they have...”
- Identification of protein related to dietary vitamin B3 deficiency in Mediterranean fruit fly larvae
Cho, Analytical science advances 2021 - “...Accession number Biological function A. Imaginal disc development Zinc finger protein 2 6 58 (31) P28167 Imaginal discderived wing morphogenesis Kinesinlike protein costa 4 54 (32) O16844 Imaginal discderived wing morphogenesis Protein apterous ( LHX2 ) 4 32 (30) P29673 Imaginal discderived wing morphogenesis Carboxypeptidase D...”
- CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions.
Liu, BMC bioinformatics 2013 - “...queries are: P02232, P05013, P14942, P07327, P01008, P03435, P42357, P21177, Q38941, P27895, P07756, P04775, P19096, P28167, P0C6B8, P20930, P08519, Q7TMA5, P33450, and Q9UKN1, listed in the ascending order of sequence length. The Swiss-Prot database consists of 191,240,745 amino acids in 538,585 sequences and has the largest...”
- DOPA: GPU-based protein alignment using database and memory access optimizations.
Hasan, BMC research notes 2011 - “...1000 8.60 21.38 P07756 1500 12.91 21.36 P04775 2005 17.27 21.35 P19096 2504 21.54 21.37 P28167 3005 25.88 21.35 P0C6B8 3564 30.67 21.37 P20930 4061 34.97 21.35 Q9UKN1 5478 47.15 21.36 The table displays performance results, where execution time in seconds and performance in GCUPS are...”
- Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.
Rognes, BMC bioinformatics 2011 - “...P10318), P07327, P01008, P10635, P58229, P25705, P03435, P42357, P21177, Q38941, O60341, P27895, P07756, P04775, P19096, P28167, P0C6B8, P20930, P08519, Q7TMA5, P33450 and Q9UKN1, ranging in length from 24 to 5478 residues were retrieved from the UniProt database [ 18 ]. Most of them have previously been...”
- A survey of well conserved families of C2H2 zinc-finger genes in Daphnia
Seetharam, BMC genomics 2010 - “...ZEB1 (P37275) ZFH1 (P28166) ZAG1 (Q94196) ZFH1 (Dappu-225224) 31:791001-795287 ZEB2 (O60315) ZFH3/4 ZFHX2 (Q9C0A1) ZFH2 (P28167) ZC123.3 (O45019) ZFH2 (Dappu-233159) 2:1855545-1862285 ZFHX3 (Q15911) ZFHX4 (Q86UP3) SPALT SALL1 (Q9NSC2) SPALTm (P39770) SEM4(NP_491997) SALL (Dappu-111734) 88:97830-103728 SALL2 (Q9Y467) SPALTr (NP_523548) SALL3 (Q9BXA9) SALL4 (Q9UJQ4) DISCO BNC1 (Q01954) DISCO...”
- CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions.
Liu, BMC research notes 2010 - “...16.2 17.36 16.9 13.04 16.8 P19096 2504 22.89 16.0 21.49 17.0 21.19 17.3 17.50 16.7 P28167 3005 28.54 15.4 26.08 16.8 25.53 17.2 21.89 16.7 P0C6B8 3564 32.44 16.1 30.56 17.0 29.60 17.6 26.41 16.6 P20930 4061 40.47 14.7 36.07 16.5 34.31 17.3 31.35 16.6 P08519...”
- “...26.0 10.79 27.3 10.26 28.7 P19096 2504 14.32 25.7 13.34 27.6 12.99 28.4 12.79 28.8 P28167 3005 18.31 24.1 16.46 26.9 15.56 28.4 15.33 28.8 P0C6B8 3564 21.09 24.9 19.34 27.1 17.99 29.1 18.20 28.8 P20930 4061 26.75 22.3 23.35 25.6 20.76 28.8 20.77 28.8 P08519...”
- Ccm1, a regulatory gene controlling the induction of a carbon-concentrating mechanism in Chlamydomonas reinhardtii by sensing CO2 availability
Fukuzawa, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...(Xen) TFIIIa2 (K02938), Drosophila melanogaster (Dro) ZFH2 (P28167), Dro Kruppel (X03414), Petunia hybrida (Pet) EPF1-1 (X60700), and Triticum aestivum (Tri)...”
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NP_001245425 Zn finger homeodomain 2, isoform B from Drosophila melanogaster
48% identity, 2% coverage
- ZFH-2 is required for Drosophila ovarian follicle development and is expressed at the band/interband boundaries of polytene chromosomes.
Guntur, Developmental biology 2023 (PubMed)- GeneRIF: ZFH-2 is required for Drosophila ovarian follicle development and is expressed at the band/interband boundaries of polytene chromosomes.
- Zfh-2 facilitates Notch-induced apoptosis in the CNS and appendages of Drosophila melanogaster.
Guntur, Developmental biology 2021 (PubMed)- GeneRIF: Zfh-2 facilitates Notch-induced apoptosis in the CNS and appendages of Drosophila melanogaster.
- zfh2 controls progenitor cell activation and differentiation in the adult Drosophila intestinal absorptive lineage.
Rojas, PLoS genetics 2019 - GeneRIF: Study identifies the cascade of cellular changes and regulatory steps that control differentiation in the adult fly midgut and identifies zfh2 as a major player in these processes.
- Identification of Drosophila Zfh2 as a Mediator of Hypercapnic Immune Regulation by a Genome-Wide RNA Interference Screen.
Helenius, Journal of immunology (Baltimore, Md. : 1950) 2016 - GeneRIF: these results identify Zfh2 as the first in vivo mediator of hypercapnic immune suppression.
- The zinc finger homeodomain-2 gene of Drosophila controls Notch targets and regulates apoptosis in the tarsal segments.
Guarner, Developmental biology 2014 (PubMed)- GeneRIF: results demonstrate the key role of zfh-2 in the control of cell death and Notch signaling during leg development
- The Drosophila gene zfh2 is required to establish proximal-distal domains in the wing disc.
Terriente, Developmental biology 2008 (PubMed)- GeneRIF: In discs lacking zfh2 the limits of the expression domains of the genes tsh, nub, rn, dve and nab coincide, and expression of wg in the wing hinge, is lost.
- Multiple roles of the gene zinc finger homeodomain-2 in the development of the Drosophila wing.
Perea, Mechanisms of development (PubMed)- GeneRIF: Zfh2 plays an important role controlling the expression of several wing genes and in the specification of cellular properties that define the differences in cell proliferation between proximal and distal domains of the wing disc.
D4AEG9 Homeobox expressed in ES cells 1 from Rattus norvegicus
45% identity, 30% coverage
HESX1_MOUSE / Q61658 Homeobox expressed in ES cells 1; Anterior-restricted homeobox protein; Homeobox protein ANF; Rathke pouch homeo box from Mus musculus (Mouse) (see 2 papers)
45% identity, 30% coverage
- function: Required for the normal development of the forebrain, eyes and other anterior structures such as the olfactory placodes and pituitary gland. Possible transcriptional repressor. Binds to the palindromic PIII sequence, 5'-AGCTTGAGTCTAATTGAATTAACTGTAC-3'. HESX1 and PROP1 bind as heterodimers on this palindromic site, and, in vitro, HESX1 can antagonize PROP1 activation.
subunit: Can form heterodimers with PROP1 in binding to DNA Interacts with TLE1.
L8HQC4 Zinc finger homeobox protein 2 from Bos mutus
50% identity, 2% coverage
LOC118272755 zinc finger homeobox protein 3 from Spodoptera frugiperda
48% identity, 2% coverage
XP_047287780 zinc finger homeobox protein 2 isoform X5 from Homo sapiens
50% identity, 2% coverage
GSBN_DROME / P09083 Protein gooseberry-neuro; BSH4; Protein gooseberry proximal from Drosophila melanogaster (Fruit fly) (see paper)
NP_523862 gooseberry-neuro from Drosophila melanogaster
45% identity, 12% 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),...”
FGSG_09019 hypothetical protein from Fusarium graminearum PH-1
49% identity, 8% coverage
- Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum
Guo, BMC genomics 2020 - “...(Fig. 5 a). On the other hand, the top two regulators of M16, FSGG_07928 and FGSG_09019, negatively regulate M16 gene expression during plant infection. However, disruption mutants of these TFs are nonpathogenic to wheat. GO enrichment of the M16 genes suggested that the module is highly...”
- A Large-Scale Functional Analysis of Putative Target Genes of Mating-Type Loci Provides Insight into the Regulation of Sexual Development of the Cereal Pathogen Fusarium graminearum
Kim, PLoS genetics 2015 - “...fewer P, no AS DDD FGSG_07869 Short-chain dehydrogenases Metabolism fewer P, no AS, DDD Meiosis FGSG_09019 TF carrying homeodomain Regulation fewer P, VG, T, no V DNN Ascus development FGSG_00348 Argonaute-like protein RNA interference fewer AS/AP DDD Spore formation and perithecium maturation FGSG_00532 Vesicle coat complex...”
- Development of a novel multiplex DNA microarray for Fusarium graminearum and analysis of azole fungicide responses
Becher, BMC genomics 2011 - “...involved in calcineurin- and Ca 2+ /calmodulin-dependent signaling [ 37 ]. The proteins encoded by FGSG_09019, FGSG_01293, FGSG_01936, and FGSG_13828 are putative regulators of metabolic processes, which may be indirectly compromised by fungicide treatment. These genes exhibit similarities to yeast's transcription factors involved in phosphate metabolism,...”
NP_001025475 homeobox protein aristaless-like 4 from Bos taurus
48% identity, 14% coverage
NP_001073284 mix-type homeobox gene 2 from Danio rerio
51% identity, 18% coverage
NP_001009767 homeobox protein prophet of Pit-1 from Ovis aries
46% identity, 25% 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
53% identity, 17% 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.
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
48% identity, 14% 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.
XP_006501135 LIM/homeobox protein Lhx8 isoform X1 from Mus musculus
41% identity, 17% coverage
- FIGLA, LHX8 and SOHLH1 transcription factor networks regulate mouse oocyte growth and differentiation.
Wang, Nucleic acids research 2020 - GeneRIF: findings substantiate a major role for FIGLA, LHX8 and SOHLH1 as multifunctional regulators of networks necessary for oocyte maintenance and differentiation during early folliculogenesis.
- Lhx8 ablation leads to massive autophagy of mouse oocytes associated with DNA damage.
D'Ignazio, Biology of reproduction 2018 - GeneRIF: Ablation of Lhx8 causes premature loss of germ cells by autophagy associated with impairment of DNA damage repair during meiosis.
- Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2.
Cesario, Human molecular genetics 2015 - GeneRIF: Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2
- Lhx8 regulates primordial follicle activation and postnatal folliculogenesis.
Ren, BMC biology 2015 - GeneRIF: LHX8 can bind to the Lin28a promoter, and the depletion of Lin28a in Lhx8-deficient oocytes partially suppresses primordial oocyte activation.
- Lhx6 and Lhx8: cell fate regulators and beyond.
Zhou, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2015 - GeneRIF: Studies indicate that LIM homeobox proteins Lhx6 and -8 mRNAs are primarily expressed in the ventral telencephalon, specifically in the medial ganglionic eminence (MGE) of the basal forebrain and in subsets of neurons in the striatum.
- Identification of a face enhancer reveals direct regulation of LIM homeobox 8 (Lhx8) by wingless-int (WNT)/β-catenin signaling.
Landin, The Journal of biological chemistry 2014 - GeneRIF: WNT/beta-catenin signaling is essential for the expression of Lhx8 in the maxillary arch cells.
- Transcription factor LIM homeobox 7 (Lhx7) maintains subtype identity of cholinergic interneurons in the mammalian striatum.
Lopes, Proceedings of the National Academy of Sciences of the United States of America 2012 - GeneRIF: The homeodomain protein LIM homeobox (Lhx)7 is essential for maintaining the morphological and molecular characteristics of cholinergic interneurons of the striatum.
- Expression and epigenetic dynamics of transcription regulator Lhx8 during mouse oogenesis.
Zhang, Gene 2012 (PubMed)- GeneRIF: Lhx8 expression is related with the activation of primordial follicles, which is highly correlated with the demethylation of Lhx8-3' untranslated region and the high acetylation of histone H3.
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NP_571015 homeobox protein MIXL1 from Danio rerio
45% identity, 17% coverage
O35652 LIM/homeobox protein Lhx8 from Mus musculus
41% identity, 15% coverage
8osbE / Q9H161 Twist1-tcf4-alx4 complex on specific DNA (see paper)
51% identity, 85% coverage
NP_001088995 paired box 7 L homeolog from Xenopus laevis
46% identity, 11% 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:...”
Q68G74 LIM/homeobox protein Lhx8 from Homo sapiens
NP_001001933 LIM/homeobox protein Lhx8 isoform 1 from Homo sapiens
41% identity, 16% coverage
- Proteomic Analysis of Aqueous Humor Proteins in Association with Cataract Risks: Diabetes and Smoking.
Chang, Journal of clinical medicine 2021 - “...proteoglycan 2 P02765 Alpha-2-HS-glycoprotein P01042 Kininogen-1 P01023 Alpha-2-macroglobulin P02750 Leucine-rich alpha-2-glycoprotein P02489 Alpha-crystallin A chain Q68G74 LIM/homeobox protein Lhx8 A0A140G945 Alpha-crystallin A2 chain P51884 Lumican P02511 Alpha-crystallin B chain P61626 Lysozyme C P06733 Alpha-enolase P01033 Metalloproteinase inhibitor 1 P03950 Angiogenin P05408 Neuroendocrine protein 7B2 P01019 Angiotensinogen...”
- “...P01042 Kininogen-1 P01780 Immunoglobulin heavy variable 37 P02750 Leucine-rich alpha-2-glycoprotein A0A0B4J1Y9 Immunoglobulin heavy variable 372 Q68G74 LIM/homeobox protein Lhx8 A0A0B4J1X5 Immunoglobulin heavy variable 374 P51884 Lumican A0A0J9YXX1 Immunoglobulin heavy variable 5-10-1 P61626 Lysozyme C A0A0B4J1U7 Immunoglobulin heavy variable 6-1 P01033 Metalloproteinase inhibitor 1 P01834 Immunoglobulin kappa...”
- Proteomic Profiling Comparing the Effects of Different Heat Treatments on Camel (Camelus dromedarius) Milk Whey Proteins.
Benabdelkamel, International journal of molecular sciences 2017 - “...1.140 Non-significant 1.760 Down 287 P02679 Fibrinogen chain Enzyme 0.003 2.042 Down 4.523 Down 543 Q68G74 LIM/homeobox protein Lhx8 Binding protein 0.009 1.284 Down 3.709 Down 540 Q68G74 LIM/homeobox protein Lhx8 Binding protein 0.009 1.284 Down 4.609 Down 546 Q6AYB4 Heat shock 70 kDa protein 14...”
- LIM homeobox 8 reduced apoptosis and promoted periodontal tissue regeneration function of dental pulp stem cells.
Ma, Tissue & cell 2024 (PubMed)- GeneRIF: LIM homeobox 8 reduced apoptosis and promoted periodontal tissue regeneration function of dental pulp stem cells.
- Validation of ASCL1 and LHX8 Methylation Analysis as Primary Cervical Cancer Screening Strategy in South African Women with Human Immunodeficiency Virus.
Vink, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2023 - GeneRIF: Validation of ASCL1 and LHX8 Methylation Analysis as Primary Cervical Cancer Screening Strategy in South African Women with Human Immunodeficiency Virus.
- Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8.
Wang, eLife 2023 - GeneRIF: Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8.
- Posttreatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3.
Vink, AIDS (London, England) 2022 (PubMed)- GeneRIF: Posttreatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3.
- Heterozygous loss-of-function variants in LHX8 cause female infertility characterized by oocyte maturation arrest.
Zhao, Genetics in medicine : official journal of the American College of Medical Genetics 2022 (PubMed)- GeneRIF: Heterozygous loss-of-function variants in LHX8 cause female infertility characterized by oocyte maturation arrest.
- Upregulation of Lhx8 increase VAChT expression and ACh release in neuronal cell line SHSY5Y.
Li, Neuroscience letters 2014 (PubMed)- GeneRIF: Increasing Lhx8 expression in neuronal cell lines also increased acetylcholine release.
- Evaluation of the LIM homeobox genes LHX6 and LHX8 as candidates for Tourette syndrome.
Paschou, Genes, brain, and behavior 2012 (PubMed)- GeneRIF: Our tagging-single nucleotide polymorphism (tSNP)-based association analysis was negative for Tourette syndrome association with LHX8.
- Comparative study of LHX8 expression between odontoma and dental tissue-derived stem cells.
Kim, Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology 2011 (PubMed)- GeneRIF: LHX8 might play an important role in odontoma formation. This is 1st report on comparison of LHX8 expression between human odontoma-derived mesenchymal cells and normal adult dental mesenchymal stem cells and its overexpression in human samples.
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DUXA_HUMAN / A6NLW8 Double homeobox protein A from Homo sapiens (Human) (see paper)
47% identity, 26% coverage
- function: Transcription factor that acts as a repressor.
- DUX4 is a multifunctional factor priming human embryonic genome activation
Vuoristo, iScience 2022 - “...Cat# 10620010 DUX4 protein sequence Homo sapiens UniProt Q9UBX2 DUXA protein sequence Homo sapiens UniProt A6NLW8 DUXB protein sequence Homo sapiens UniProt A0A1W2PPF3 DUX1 protein sequence Homo sapiens UniProt O43812 DUX3 protein sequence Homo sapiens UniProt Q96PT4 DUX5 protein sequence Homo sapiens UniProt Q96PT3 DUX4 protein...”
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...homeobox domains and two different penetratin-like peptides (see some examples at UniProt links O43812, Q96PT3, A6NLW8, and P0CJ85). Human Zink finger homeobox protein 3 has four homeobox domains in its long sequence of 3703 residues (see Q15911) with four associated penetratins, which are, however, of low...”
- Proteomic analysis to identify candidate biomarkers associated with type 1 diabetes
do, Diabetes, metabolic syndrome and obesity : targets and therapy 2018 - “...globulin 45,141 6/23 27.90 371.10 P04003 C4b binding protein alpha chain 67,033 13/45 30.82 1,198.61 A6NLW8 Double homeobox protein A 23,817 1/21 13.24 142.05 O43543 DNA repair protein XRCC2 31,957 2/19 10.36 182.94 Q9NPG1 Frizzled 3 76,263 2/54 6.16 148.64 P06396 Gelsolin 85,968 17/51 32.86 661.02...”
- Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4.
Eidahl, Human molecular genetics 2016 - “...following UniProt/Swiss-Prot identifications were used DUX4_HUMAN (Accession Q9UBX2), A1JVI8_MOUSE (Accession A1JVI8), Q7TNE6_MOUSE (Accession Q7TNE6), DUXA_HUMAN (A6NLW8), DUX1_HUMAN (O43812) and DUX5_HUMAN (Q96PT3) for the amino acid sequence alignments of DUX4, Dux, Duxbl, DUXA, DUX1 and DUX5, respectively. Cell culture Human embryonic kidney cells (HEK293) were cultured in...”
MIXL1_CHICK / O73592 Homeobox protein MIXL1; Homeodomain protein MIX; cMIX; MIX1 homeobox-like protein 1; Mix.1 homeobox-like protein from Gallus gallus (Chicken) (see 2 papers)
46% identity, 26% coverage
- function: Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation. Required for efficient differentiation of cells from the primitive streak stage to blood (By similarity).
XP_018080096 paired box 7 L homeolog isoform X1 from Xenopus laevis
46% identity, 11% coverage
Q8MJI9 Homeobox protein prophet of Pit-1 from Bos taurus
46% identity, 25% coverage
AWH_DROME / Q8IRC7 LIM/homeobox protein Awh; Protein arrowhead from Drosophila melanogaster (Fruit fly) (see paper)
NP_728906 arrowhead, isoform B from Drosophila melanogaster
45% identity, 20% coverage
XP_015327641 homeobox protein prophet of Pit-1 isoform X1 from Bos taurus
46% identity, 25% coverage
NP_523907 arrowhead, isoform A from Drosophila melanogaster
45% identity, 26% coverage
- 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 - “...EAW91078, XP_973330, NP_724161, XP_001638136, NP_476775, NP_001158279, NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, 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...”
PAX3H_CAEEL / G5ED66 Paired box protein 3 homolog from Caenorhabditis elegans (see paper)
NP_496189 Paired box protein 3 homolog from Caenorhabditis elegans
43% identity, 18% coverage
- function: Transcriptional activator (By similarity). Regulates the lateral/ventral epidermal cell fate decision (PubMed:26953187).
disruption phenotype: RNAi-mediated knockdown causes embryonic lethality, vulval and gonad migration defects, and animals that survive have mild to severe body morphology defects (PubMed:26953187). A marker of the lateral hypodermal (seam cell) fate, scm, is expressed ectopically in some P cell nuclei during the early larval L1 stage (PubMed:26953187). - The Paired-box protein PAX-3 regulates the choice between lateral and ventral epidermal cell fates in C. elegans.
Thompson, Developmental biology 2016 - GeneRIF: Data indicate taht Paired-box protein pax-3 is the first gene required for specification of the ventral hypodermal fate.
ZAG1_CAEEL / G5EBU4 Zinc finger E-box-binding homeobox protein zag-1; Zinc finger involved in axon guidance 1; ZAG-1 from Caenorhabditis elegans (see 4 papers)
NP_500424 Zinc finger E-box-binding homeobox protein zag-1 from Caenorhabditis elegans
41% identity, 9% coverage
- function: Transcription factor (PubMed:12835394, PubMed:12835395, PubMed:25474681, PubMed:30291162). Down-regulates expression of genes involved in either the synthesis or reuptake of serotonin, dopamine and GABA (PubMed:12835394). Acts as a transcriptional repressor to regulate multiple, discrete, neuron-specific aspects of terminal differentiation, including cell migration, axonal development and gene expression (PubMed:12835394, PubMed:12835395, PubMed:25474681, PubMed:30291162). Promotes touch receptor neuron differentiation by repressing the expression of egl-44 and egl-46 (PubMed:30291162). As egl-44 and egl-46, probably acting as a heterodimer, repress expression of zag-1 in FLP neurons, together these proteins form a bistable, negative-feedback loop that regulates the choice between neuronal fates (PubMed:30291162). Required for axon guidance (PubMed:12835395). Involved in the proper development of the pharynx (PubMed:12835395). Required for pharynx isthmus peristalsis, probably via a role in the differentiation of the M4 cholinergic motor neuron (PubMed:25474681). Directly represses its own transcription by interacting with conserved E-box sequence motifs 5'-CACCTG-3' in its own promoter (PubMed:12835394, PubMed:12835395). May also act as a transcriptional activator of the homeodomain ceh-28 (PubMed:25474681).
disruption phenotype: Worms exhibit a starved appearance, are unable to swallow food and die at the L1 larval stage (PubMed:12835395). RNAi- mediated knockdown causes significant reduction in expression of mec-17 (PubMed:30291162). - C. elegans ZAG-1, a Zn-finger-homeodomain protein, regulates axonal development and neuronal differentiation.
Clark, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: Data suggest that ZAG-1 acts as a transcriptional repressor to regulate multiple, discrete, neuron-specific aspects of terminal differentiation, including cell migration, axonal development and gene expression.
- zag-1, a Zn-finger homeodomain transcription factor controlling neuronal differentiation and axon outgrowth in C. elegans.
Wacker, Development (Cambridge, England) 2003 (PubMed)- GeneRIF: Data indicate that zag-1 acts as transcriptional repressor controlling important aspects of terminal differentiation of neurons.
Q91574 ALX homeobox protein 1 from Xenopus laevis
53% identity, 16% coverage
UNC42_CAEEL / L8E946 Homeobox protein unc-42; Uncoordinated protein 42 from Caenorhabditis elegans (see 5 papers)
48% identity, 20% 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
48% identity, 21% coverage
3a01F / Q06453 Crystal structure of aristaless and clawless homeodomains bound to dna (see paper)
49% identity, 87% coverage
XP_001340966 homeobox protein aristaless-like 4 from Danio rerio
48% identity, 15% 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...”
LIM7_CAEEL / G5EC36 LIM/homeobox protein lim-7 from Caenorhabditis elegans (see 2 papers)
NP_491668 LIM/homeobox protein lim-7 from Caenorhabditis elegans
41% identity, 12% coverage
XP_001946004 LIM/homeobox protein Lhx9 from Acyrthosiphon pisum
46% identity, 10% coverage
ALX1_GEOFO / P0DMV5 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Geospiza fortis (Medium ground-finch) (see paper)
53% identity, 16% 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_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
53% identity, 16% 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_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
53% identity, 16% 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_RAT / Q63087 ALX homeobox protein 1; Cartilage homeoprotein 1; CART-1 from Rattus norvegicus (Rat) (see 4 papers)
53% identity, 16% 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).
M9PEI5 Arrowhead, isoform C from Drosophila melanogaster
45% identity, 20% coverage
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...UniProt IDs FLY-FISH FlyExpress LIM-type FBgn0263934 Esn A0A0B4KED7 A0A0B4KEK5 N/A N/A LIM protein FBgn0013751 Awh M9PEI5 Brain, Ectoderm, Optic lobes, primordium, Posterior spiracles, Segmentedpattern, lymph glands N/A LIM-homeodomain (LIM-HD) FBgn0259209 Mlp60A B7YZP9 Muscle, Posterior spiracles Muscle system, Dorsal prothoracic, Pharyngeal muscle, LIM-Only FBgn0263346 Smash A0A0B4K615 CNS,...”
NP_726006 retinal homeobox from Drosophila melanogaster
48% identity, 6% coverage
NP_001001263 homeobox protein prophet of Pit-1 from Sus scrofa
46% identity, 24% coverage
P97458 Homeobox protein prophet of Pit-1 from Mus musculus
NP_032962 homeobox protein prophet of Pit-1 from Mus musculus
46% identity, 25% coverage
- Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene
Ward, Mammalian genome : official journal of the International Mammalian Genome Society 2007 - “...sequence for human (NP006252), pig (NP001001263), cow ( Bos taurus ; NP777103), sheep (NP001009767), mouse (P97458), dog (NP001018643), and partial protein sequence for the chicken ( Gallus gallus ; AB037110) was obtained from the NCBI website. Sequence analysis ClustalW alignment for protein and DNA sequences were...”
- PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression.
Cheung, Endocrinology 2020 - GeneRIF: activates the retinoic acid (RA) signaling pathway through the induction of the RA-synthesizing enzyme ALDH1A2
- Search for regulatory factors of the pituitary-specific transcription factor PROP1 gene.
Nishimura, The Journal of reproduction and development 2016 - GeneRIF: SOX2 is a regulatory factor of Prop1 expression
- All Hormone-Producing Cell Types of the Pituitary Intermediate and Anterior Lobes Derive From Prop1-Expressing Progenitors.
Davis, Endocrinology 2016 - GeneRIF: Data show that human paired like homeodomain factor 1 (PROP1) can substitute functionally for mouse Prop1.
- PROP1 triggers epithelial-mesenchymal transition-like process in pituitary stem cells.
Pérez, eLife 2016 - GeneRIF: Genomic profiling reveals that PROP1 binds to genes expressed in epithelial cells like Claudin 23, and to epithelial-mesenchymal transition inducer genes like Zeb2, Notch2 and Gli2. Zeb2 activation appears to be a key step in the epithelial-mesenchymal transition process.
- Genetic background of Prop1(df) mutants provides remarkable protection against hypothyroidism-induced hearing impairment.
Fang, Journal of the Association for Research in Otolaryngology : JARO 2012 - GeneRIF: endocochlear potential and KCNJ10 immunostaining in the stria vascularis are indistinguishable from wild type, and no differences in neurofilament or synaptophysin staining are evident in Prop1(df) mutants
- Candidate genes for panhypopituitarism identified by gene expression profiling.
Mortensen, Physiological genomics 2011 - GeneRIF: Data report the spatial and temporal regulation of Otx2 in normal mice and Prop1 mutant.
- Ames dwarf (Prop1(df)/Prop1(df)) mice display increased sensitivity of the major GH-signaling pathways in liver and skeletal muscle.
Miquet, Growth hormone & IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society 2010 (PubMed)- GeneRIF: Several components of the main GH-signaling pathways exhibit enhanced sensitivity to the hormone in liver and muscle of Ames dwarf mice.
- Corepressors TLE1 and TLE3 interact with HESX1 and PROP1.
Carvalho, Molecular endocrinology (Baltimore, Md.) 2010 - GeneRIF: Studies suggest that TLE1 and TLE3 might also play roles independent of HESX1 by interacting with other transcription factors like PROP1.
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MIXL1_HUMAN / Q9H2W2 Homeobox protein MIXL1; Homeodomain protein MIX; hMix; MIX1 homeobox-like protein 1; Mix.1 homeobox-like protein from Homo sapiens (Human) (see 4 papers)
45% identity, 24% coverage
- function: Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation. Required for efficient differentiation of cells from the primitive streak stage to blood, by acting early in the recruitment and/or expansion of mesodermal progenitors to the hemangioblastic and hematopoietic lineages. Also involved in the morphogenesis of the heart and the gut during embryogenesis. Acts as a negative regulator of brachyury expression (By similarity).
NP_001284898 visual system homeobox 1, isoform B from Drosophila melanogaster
51% identity, 6% coverage
1fjlA / P06601 Homeodomain from the drosophila paired protein bound to a DNA oligonucleotide (see paper)
45% identity, 82% coverage
Q6BDC3 LIM homeobox 8 from Danio rerio
41% identity, 17% coverage
PROP1_HUMAN / O75360 Homeobox protein prophet of Pit-1; PROP-1; Pituitary-specific homeodomain factor from Homo sapiens (Human) (see 7 papers)
NP_006252 homeobox protein prophet of Pit-1 from Homo sapiens
46% identity, 25% coverage
- function: Possibly involved in the ontogenesis of pituitary gonadotropes, as well as somatotropes, lactotropes and caudomedial thyrotropes
- Mutations Within the Transcription Factor PROP1 in a Cohort of Turkish Patients with Combined Pituitary Hormone Deficiency.
Bulut, Journal of clinical research in pediatric endocrinology 2020 - “...Genomic DNA was isolated from peripheral leucocytes. PROP1 gene (transcript ID: ENST00000308304.2 and protein ID: O75360) was screened by polymerase chain reaction (PCR) amplifications of exons and neighbouring intronic regions. The PCR products were purified and directly sequenced using the Big Dye terminator cycle sequencing ready...”
- Comparison of clinical characteristics of a pediatric cohort with combined pituitary hormone deficiency caused by mutation of the PROP1 gene or of other origins.
Zygmunt-Górska, Hormones (Athens, Greece) 2024 - GeneRIF: Comparison of clinical characteristics of a pediatric cohort with combined pituitary hormone deficiency caused by mutation of the PROP1 gene or of other origins.
- Association of Homozygous PROP1 Mutation in a Saudi Family with Combined Pituitary Hormone Deficiency.
Almatrafi, Medicina (Kaunas, Lithuania) 2023 - GeneRIF: Association of Homozygous PROP1 Mutation in a Saudi Family with Combined Pituitary Hormone Deficiency.
- Mutations Within the Transcription Factor PROP1 in a Cohort of Turkish Patients with Combined Pituitary Hormone Deficiency
Bulut, Journal of clinical research in pediatric endocrinology 2020 - GeneRIF: Mutations Within the Transcription Factor PROP1 in a Cohort of Turkish Patients with Combined Pituitary Hormone Deficiency
- Combined pituitary hormone deficiency caused by PROP1 mutations: update 20 years post-discovery.
Correa, Archives of endocrinology and metabolism 2019 - GeneRIF: A summary of phenotypes in patients with combined pituitary hormone deficiency caused by PROP1 mutations (Review).
- Regulation of pituitary stem cells by epithelial to mesenchymal transition events and signaling pathways.
Cheung, Molecular and cellular endocrinology 2017 - GeneRIF: The anterior pituitary gland comprised specialized cell-types that arise from stem cells expressing SOX2 and PROP1, which is necessary to establish the stem cell pool and promote an epithelial to mesenchymal-like transition, releasing progenitors from the niche. [review]
- Combined pituitary hormone deficiency due to gross deletions in the POU1F1 (PIT-1) and PROP1 genes.
Bertko, Journal of human genetics 2017 - GeneRIF: Deletion in the PROP1 gene is associated with Combined pituitary hormone deficiency.
- Molecular analysis of brazilian patients with combined pituitary hormone deficiency and orthotopic posterior pituitary lobe reveals eight different PROP1 alterations with three novel mutations.
Madeira, Clinical endocrinology 2017 (PubMed)- GeneRIF: PROP1 mutations are a prevalent cause of congenital CPHD with OPP, and therefore, PROP1 sequencing must be the first step of molecular investigation in patients with CPHD and OPP, especially in populations with a high frequency of PROP1 mutations.
- Genesis of two most prevalent PROP1 gene variants causing combined pituitary hormone deficiency in 21 populations.
Dusatkova, European journal of human genetics : EJHG 2016 - GeneRIF: the most frequent variants in the PROP1 gene are not a consequence of variant hot spots as previously assumed, but are founder variants.
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LHX6_MOUSE / Q9R1R0 LIM/homeobox protein Lhx6; LIM homeobox protein 6; LIM/homeobox protein Lhx6.1 from Mus musculus (Mouse) (see 8 papers)
41% identity, 15% coverage
- function: Probable transcription factor required for the expression of a subset of genes involved in interneurons migration and development. Functions in the specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex.
subunit: Interacts with LDB1 (via the LIM zinc-binding domains).
disruption phenotype: Mice lacking Lhx6 fail to thrive, develop general weakness and die within the first 2 weeks after birth.
R7TKD0 Transcription factor Pax3/7 (Fragment) from Capitella teleta
47% identity, 21% 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...”
XP_006234128 LIM/homeobox protein Lhx6 isoform X1 from Rattus norvegicus
41% identity, 15% coverage
NP_001098373 retinal homeobox protein Rx2 from Oryzias latipes
48% identity, 17% coverage
RHTO_06229 Homeobox domain containing protein, transcription factor from Rhodotorula toruloides NP11
46% identity, 9% coverage
K1QWY6 Paired box protein Pax-6 from Magallana gigas
45% identity, 16% 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 ]....”
CG9876 uncharacterized protein from Drosophila melanogaster
45% identity, 20% 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...”
LOC658656, NP_001139341 apterous a from Tribolium castaneum
46% identity, 12% coverage
- Insecticidal Activity of Artemisia vulgaris Essential Oil and Transcriptome Analysis of Tribolium castaneum in Response to Oil Exposure
Gao, Frontiers in genetics 2020 - “...LOC664175 1.02 Down Netrin receptor UNC5C 5.56E-156 / LOC663899 1.12 Down Myosin 9 0 / LOC658656 1.13 Down Apterous 9.30E-31 / LOC656430 1.15 Down Fork head domain-containing protein FD4 4.07E-19 / LOC100142549 1.17 Down Targeting protein for xklp2 9.34E-48 80% embryo/egg not developed/not fertilized c LOC641604...”
- Histone Deacetylase 11 Knockdown Blocks Larval Development and Metamorphosis in the Red Flour Beetle, Tribolium castaneum
George, Frontiers in genetics 2020 - “...USP ultraspiracle nuclear receptor 2.08 0.00 LOC664565 CREB-binding protein 7.73 0.00 LOC660626 Hairy 9.33 0.00 LOC658656 Apterous A 4.67 0.00 a Experiment Fold Change (normalized values). b Baggerleys test: normalized values. FIGURE 6 RT-qPCR validation of RNA-seq data in Tribolium larvae and TcA cells. (A) Differentially...”
- 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 - “...NP_665804, ACI69553, XP_002609922, ABO93221, NP_001158468, XP_785118, XP_002609417, 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...”
- De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae)
Van, PloS one 2012 - “...aligned the amino acid sequences of apterous genes from D. melanogaster (NP_724428), T. castaneum (apA: NP_001139341, apB: ACN43342), Apis mellifera (XP_392622) and A. pisum (apA: XP_001946004, apB: XP_001949543) with those retrieved from BLAST hits to the P. chalceus transcriptome ( Figure 6 ). The apterous gene...”
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
51% identity, 13% 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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NP_571635 mix-type homeobox gene 1 from Danio rerio
41% identity, 19% coverage
F2Z897 Apterous A splicing isoform type B from Bombyx mori
46% identity, 14% coverage
NCU03593 homeobox domain-containing protein from Neurospora crassa OR74A
47% identity, 8% coverage
- A Homeodomain-Containing Transcriptional Factor PoHtf1 Regulated the Development and Cellulase Expression in Penicillium oxalicum
Guo, Frontiers in microbiology 2021 - “...Htf in P. anserine , Pah1 (CAC16792.1) and its homolog in N. crassa OR74a, Kal-1 (NCU03593, EAA32084.1), respectively. Htfs from M. oryzae (MGG_00184, XP_003718936) and F. graminearum (FGSG_07097, XP_011326799.1), which are involved in hyphal growth and conidiogenesis ( Liu et al., 2010 ; Zheng et al.,...”
- Cold Shock as a Screen for Genes Involved in Cold Acclimatization in Neurospora crassa
Watters, G3 (Bethesda, Md.) 2018 - “...NCU03489 11095 colonial-21 col-21 Transc Factors NCU03576 13043 conidiophore development protein hymA hym-1 Morph/Hyph Binding NCU03593 11129 homeobox domain-containing protein kal-1 Transc Factors NCU03643 11049 fatty acid regulation-2 far-2 Transc Factors NCU03669 11658 AdoMet-dependent rRNA methyltransferase spb1 rmt-3 E. coli CS Orth Catalytic Activity Cellular Component...”
- Functional Profiling of Transcription Factor Genes in Neurospora crassa
Carrillo, G3 (Bethesda, Md.) 2017 - “...NCU05891 ) did not form any conidia ( Table S1 ), and the kal-1 / NCU03593 homeodomain mutant had an abnormal conidiation pattern ( Colot et al. 2006 ). The mutant lacking the MYB gene rcn-1 / NCU07834 had a conidiation defect as its only phenotype...”
- Alternative Oxidase Transcription Factors AOD2 and AOD5 of Neurospora crassa Control the Expression of Genes Involved in Energy Production and Metabolism
Qi, G3 (Bethesda, Md.) 2017 - “...NCU03466 (hypo) Nd Y Y NCU03548 (hypo) Nd Y Y NCU03549 (hypo) Nd Y Y NCU03593 (kaleidoscope-1) Nd Y Y NCU03651 (NADP-dependent malic enzyme) 2+, 5+ Y Y NCU03749 (hydroxyacyl glutathione hydrolase) 2 N Na NCU04307 (MSF1) No effect Y Y NCU04569 (5-oxoprolinase) 2+, 5+ Y...”
- Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica
Pomraning, BMC genomics 2016 (no snippet) - Exploring the bZIP transcription factor regulatory network in Neurospora crassa
Tian, Microbiology (Reading, England) 2011 - “...defects [ pp-1 (NCU00340), NCU02671, NCU06503, cre-1 (NCU08807), ada-6 (NCU04866), col-26 (NCU07788), vad-3 (NCU06407), kal-1 (NCU03593) and the bZIP TF gene, ada-1 (NCU00499)] ( Colot et al. , 2006 ). Phylogenetic analysis of N. crassa bZIP family members In S. cerevisiae , the bZIP TF family...”
- “...1.5 7075 Conserved hypothetical protein NCU08726 Zn2Cys6 0.2 2025 fl , conidial development protein fluffy NCU03593 1.7 1015 Probable homeoprotein *Significance cut-off ( bagel ) of at least 1.5-fold. Growth data from the Broad Institute ( http://www.broadinstitute.org/annotation/genome/neurospora/MultiHome.html ). Table 2. Summary of expression profiling data for...”
- Temporal and spatial regulation of gene expression during asexual development of Neurospora crassa
Greenwald, Genetics 2010 - “...ID NCU00499 NCU01459 NCU02713 NCU02713 NCU03043 NCU03489 NCU03593 NCU03686 NCU03931 NCU04179 NCU04731 NCU06656 NCU07374 NCU07617 NCU08307 NCU08651 NCU08726 Gene...”
- A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors
Colot, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...CBF CAAT-binding factor (NCU02017), and homeobox (NCU00097 and NCU03593). Genes showing ascospore lethality are shown in the oval. The numbers of transcription...”
XP_011607069 paired box protein Pax-3 isoform X1 from Takifugu rubripes
45% identity, 11% coverage
XP_017213137 paired box protein Pax-3a isoform X1 from Danio rerio
45% identity, 11% 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.
LOC552251 homeobox protein aristaless from Apis mellifera
49% identity, 14% 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...”
P29673 Protein apterous from Drosophila melanogaster
NP_724428 apterous, isoform A from Drosophila melanogaster
46% identity, 12% coverage
- The Roles of the LIM Domain Proteins in Drosophila Cardiac and Hematopoietic Morphogenesis
She, Frontiers in cardiovascular medicine 2021 - “...FBgn0265598 Beadex Q8IQX7 , M9PI02 , M9PHX4 Intestine, Brainlobes, Ovary, Testis N/A LIM-Only FBgn0267978 Ap P29673 Mesoderm, Brain, CNS, Tracheal system, Lymph Glands, Segmented pattern N/A LIM-HD FBgn0050147 Hil Q0E908 N/A N/A LIM protein FBgn0014863 Mlp84B Q24400 N/A Muscle system LIM-Only FBgn0051624 CG31624 Q2XYF8 N/A N/A...”
- Identification of protein related to dietary vitamin B3 deficiency in Mediterranean fruit fly larvae
Cho, Analytical science advances 2021 - “...54 (32) O16844 Imaginal discderived wing morphogenesis Protein apterous ( LHX2 ) 4 32 (30) P29673 Imaginal discderived wing morphogenesis Carboxypeptidase D ( CPD ) 5 34 (31) P42787 Imaginal discderived wing morphogenesis Protein dachsous ( DCHS1 ) 9 53 (32) Q24292 Imaginal discderived leg morphogenesis...”
- The transcription factor optomotor-blind restricts apterous expression through TrxG and PcG genes.
Chen, Developmental biology 2023 (PubMed)- GeneRIF: The transcription factor optomotor-blind restricts apterous expression through TrxG and PcG genes.
- Impact of Drosophila LIM homeodomain protein Apterous on the morphology of the adult mushroom body.
Nakano, Biochemical and biophysical research communications 2023 (PubMed)- GeneRIF: Impact of Drosophila LIM homeodomain protein Apterous on the morphology of the adult mushroom body.
- Consolidation and maintenance of long-term memory involve dual functions of the developmental regulator Apterous in clock neurons and mushroom bodies in the Drosophila brain.
Inami, PLoS biology 2021 - GeneRIF: Consolidation and maintenance of long-term memory involve dual functions of the developmental regulator Apterous in clock neurons and mushroom bodies in the Drosophila brain.
- Cell elimination strategies upon identity switch via modulation of apterous in Drosophila wing disc.
Klipa, PLoS genetics 2019 - GeneRIF: Systematic analysis of apterous mutant clones along with their twin spots shows that they are eliminated from the dorsal compartment via three different mechanisms: relocation to the ventral compartment, basal extrusion, and death, depending on the position of the clone in the wing disc.
- apterous Brain Neurons Control Receptivity to Male Courtship in Drosophila Melanogaster Females.
Aranha, Scientific reports 2017 - GeneRIF: neurons expressing the transcription factor apterous, affect the modulation of female walking speed during courtship.
- Neuronal cell fate specification by the molecular convergence of different spatio-temporal cues on a common initiator terminal selector gene.
Stratmann, PLoS genetics 2017 - GeneRIF: Nplp1 neuropeptide neurons in the developing Drosophila nerve cord belong to two sub-classes; Tv1 and dAp neurons, generated by two distinct progenitors. Nplp1 neurons are specified by spatial cues
- Neuronal Cell Fate Specification by the Convergence of Different Spatiotemporal Cues on a Common Terminal Selector Cascade.
Gabilondo, PLoS biology 2016 - GeneRIF: Ap role in the neuronal cell fate specification
- Modulation of light-driven arousal by LIM-homeodomain transcription factor Apterous in large PDF-positive lateral neurons of the Drosophila brain.
Shimada, Scientific reports 2016 - GeneRIF: These results raise the possibility that the daily oscillation of Ap expression in l-LNvs may contribute to the buffering of light-driven arousal in wild-type flies.
- More
A1JVI8 Homeobox protein from Mus musculus
43% identity, 7% coverage
- Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4.
Eidahl, Human molecular genetics 2016 - “...Needle ( http://www.ebi.ac.uk/Tools/psa/emboss_needle/ ). The following UniProt/Swiss-Prot identifications were used DUX4_HUMAN (Accession Q9UBX2), A1JVI8_MOUSE (Accession A1JVI8), Q7TNE6_MOUSE (Accession Q7TNE6), DUXA_HUMAN (A6NLW8), DUX1_HUMAN (O43812) and DUX5_HUMAN (Q96PT3) for the amino acid sequence alignments of DUX4, Dux, Duxbl, DUXA, DUX1 and DUX5, respectively. Cell culture Human embryonic kidney...”
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
46% identity, 16% 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.
- More
- 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...”
LOC725574 LIM/homeobox protein Awh from Apis mellifera
43% identity, 17% coverage
- Transcriptomic Analysis of Genes Associated with Stinger Development at Different Life Stages of Apis mellifera
Zhou, International journal of molecular sciences 2024 - “...protein Wnt - 1 ( LOC413502 ), tachykinin ( LOC406083 ), LIM/homeobox protein Awh ( LOC725574 and LOC725532 ), BTB/POZ domain protein Ktl ( LOC725415 ), and homeobox protein invected ( LOC100577365 ). Under the same criteria, we screened 186 highly expressed genes in W_S_P_5 d,...”
- “...transcription factors: distal - less ( 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...”
XP_001949543 LIM/homeobox protein Lhx2 from Acyrthosiphon pisum
45% identity, 16% coverage
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
49% identity, 14% 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.
MIXL1_MOUSE / Q9WUI0 Homeobox protein MIXL1; Homeodomain protein MIX; mMix; MIX1 homeobox-like protein 1; Mix.1 homeobox-like protein from Mus musculus (Mouse) (see 11 papers)
43% identity, 24% coverage
- function: Transcription factor that play a central role in proper axial mesendoderm morphogenesis and endoderm formation. Required for efficient differentiation of cells from the primitive streak stage to blood, by acting early in the recruitment and/or expansion of mesodermal progenitors to the hemangioblastic and hematopoietic lineages. Also involved in the morphogenesis of the heart and the gut during embryogenesis. Acts as a negative regulator of brachyury expression.
disruption phenotype: Mice display defects in mesendoderm morphogenesis and patterning during development. Embryos show a marked thickening of the primitive streak. By the early somite stage, embryonic development is arrested, with the formation of abnormal head folds, foreshortened body axis, absence of heart tube and gut, deficient paraxial mesoderm, and an enlarged midline tissue mass that replaces the notochord. Development of extra-embryonic structures is generally normal except that the allantois is often disproportionately large for the size of the mutant embryo.
T1G8F8 Uncharacterized protein from Helobdella robusta
43% identity, 19% 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...”
XP_005167424 LIM/homeobox protein Lhx2b isoform X1 from Danio rerio
45% identity, 13% coverage
XP_012818027 visual system homeobox 1 isoform X1 from Xenopus tropicalis
49% identity, 15% coverage
TRF2_PYRO7 / G4N2B2 Pyriculol/pyriculariol biosynthesis cluster transcription factor 1 from Pyricularia oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (Rice blast fungus) (Magnaporthe oryzae) (see paper)
45% identity, 8% coverage
- function: Transcriptional regulator; part of the gene cluster that mediates the biosynthesis of pyriculol and pyriculariol, two heptaketides that induce lesion formation upon application on rice leaves but are dispensable for pathogenicity (PubMed:27902426). With TRF1, negatively regulates the expression of the gene cluster and the subsequent pyriculol and pyriculariol production (PubMed:27902426).
disruption phenotype: Leads to increased expression of the pyriculol/pyriculariol biosynthesis cluster highly reducing polyketide synthase PKS19.
NP_492586 Homeobox protein ceh-5 from Caenorhabditis elegans
42% identity, 43% coverage
LIM4_CAEEL / G5EEA1 LIM/homeobox protein lim-4 from Caenorhabditis elegans (see 5 papers)
NP_508669 LIM/homeobox protein lim-4 from Caenorhabditis elegans
43% identity, 16% coverage
- function: Transcription factor that binds to the promoter of target genes (PubMed:16168406, PubMed:26305787, PubMed:26341465). Regulates genes involved in serotonin synthesis and release in serotonergic ADF neurons (PubMed:16168406, PubMed:26305787). Involved in specification of neuron cell fate, olfactory receptor expression, locomotion, and foraging behavior (PubMed:10421632, PubMed:26305787). Required in AWB olfactory neurons to repress AWC cell fate and promote the AWB cell fate during early development (PubMed:10421632). Cooperates with additional factors to direct the differentiation of the olfactory neurons, functioning with the transcription factor sox-2 to suppress AWC terminal differentiation and promote AWB neuron differentiation (PubMed:26341465). Involved in regulating terminal specification and maintenance of the SMB sensory/inter/motor neurons (PubMed:26305787). Plays a role in regulation of RID motor neuron differentiation, but is dispensable for motor axon outgrowth in the dorsal nerve cord (PubMed:14568548). May regulate its own expression (PubMed:10421632, PubMed:26305787).
subunit: Interacts with transcription factor sox-2. - The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type.
Kim, PLoS genetics 2015 - GeneRIF: the evolutionarily conserved LIM-4/LHX6 homeodomain proteins function in generation of precise neuronal subtypes.
- Cell-type specific regulation of serotonergic identity by the C. elegans LIM-homeodomain factor LIM-4.
Zheng, Developmental biology 2005 (PubMed)- GeneRIF: cis-element(s) within introns are necessary and sufficient to direct lim-4 to specify serotonergic phenotype, whereas its 5'-upstream sequence directs lim-4 function in olfactory neuron AWB
- LIM homeobox gene-dependent expression of biogenic amine receptors in restricted regions of the C. elegans nervous system.
Tsalik, Developmental biology 2003 - GeneRIF: lim-4 Lhx gene is required for several but not all aspects of RID motor neuron differentiation.
NP_990100 visual system homeobox 1 from Gallus gallus
49% identity, 15% coverage
XP_695330 homeobox protein aristaless-like 3 isoform X2 from Danio rerio
46% identity, 15% coverage
NP_001287047 eyegone, isoform C from Drosophila melanogaster
50% identity, 8% 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.
- More
3cmyA / P23760 Structure of a homeodomain in complex with DNA (see paper)
47% identity, 88% coverage
NP_031467 homeobox protein aristaless-like 3 from Mus musculus
46% identity, 16% 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.
- More
CIMG_09071 homeobox domain-containing protein from Coccidioides immitis RS
44% identity, 9% 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)
46% identity, 15% 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...”
Q5ZNB2 Paired box protein 7 from Salvelinus alpinus
49% identity, 11% coverage
AL_DROME / Q06453 Homeobox protein aristaless from Drosophila melanogaster (Fruit fly) (see paper)
NP_722629 aristaless from Drosophila melanogaster
49% identity, 12% 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...”
NP_477026 reversed polarity from Drosophila melanogaster
47% 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_001245266 paired box protein Pax-7a from Oncorhynchus mykiss
49% identity, 11% coverage
NP_001245265 paired box gene 7b from Oncorhynchus mykiss
49% identity, 11% coverage
NP_006874 short stature homeobox protein isoform SHOXb from Homo sapiens
47% identity, 24% 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
NP_001033832 visual system homeobox 2, isoform A from Drosophila melanogaster
51% identity, 8% coverage
LOC102223853 dorsal root ganglia homeobox protein-like from Xiphophorus maculatus
45% identity, 18% coverage
PAX7_MOUSE / P47239 Paired box protein Pax-7 from Mus musculus (Mouse) (see 3 papers)
49% identity, 11% 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...”
Q683Y9 Paired box protein 7 from Salmo salar
49% identity, 10% coverage
NP_001139621 paired box protein Pax-7b from Danio rerio
49% identity, 10% coverage
NP_001007013 homeobox protein aristaless-like 3 from Rattus norvegicus
46% identity, 16% coverage
XP_066838118 paired box protein Pax-7 isoform X1 from Anser cygnoides
49% identity, 10% coverage
NP_571400 paired box protein Pax-7a isoform PAX7C from Danio rerio
49% identity, 10% 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
49% identity, 11% coverage
XP_006538694 paired box protein Pax-7 isoform X3 from Mus musculus
49% identity, 11% coverage
LOC536229, XP_015316176 paired box protein Pax-7 from Bos taurus
49% identity, 13% 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
XP_006239325 paired box protein Pax-7 isoform X1 from Rattus norvegicus
49% identity, 10% 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_002274194 homeobox-leucine zipper protein REVOLUTA isoform X1 from Vitis vinifera
41% identity, 6% 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
49% identity, 10% 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...”
NP_990396 paired box protein Pax-7 from Gallus gallus
49% identity, 10% 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_001020793 short stature homeobox protein from Canis lupus familiaris
47% identity, 18% coverage
SHOX_HUMAN / O15266 Short stature homeobox protein; Pseudoautosomal homeobox-containing osteogenic protein; Short stature homeobox-containing protein from Homo sapiens (Human) (see 4 papers)
47% identity, 18% 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...”
XP_020951119 paired box protein Pax-7 isoform X3 from Sus scrofa
49% identity, 11% 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.
NP_723721 paired, isoform B from Drosophila melanogaster
P06601 Segmentation protein paired from Drosophila melanogaster
41% identity, 9% 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)
46% identity, 11% 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).
HDG11_ARATH / Q9FX31 Homeobox-leucine zipper protein HDG11; HD-ZIP protein HDG11; Homeodomain GLABRA 2-like protein 11; Homeodomain transcription factor HDG11; Protein ENHANCED DROUGHT TOLERANCE 1; Protein HOMEODOMAIN GLABROUS 11 from Arabidopsis thaliana (Mouse-ear cress) (see 7 papers)
AT1G73360, NP_177479 homeodomain GLABROUS 11 from Arabidopsis thaliana
NP_177479 HDG11 (HOMEODOMAIN GLABROUS 11); DNA binding / transcription factor from Arabidopsis thaliana
45% identity, 7% coverage
- function: Transcription factor which acts as a positive regulator of drought stress tolerance. Can transactivate CIPK3, NCED3 and ERECTA (PubMed:18451323). Transactivates several cell-wall-loosening protein genes by directly binding to HD motifs in their promoters. These target genes play important roles in coordinating cell-wall extensibility with root development and growth (PubMed:24821957). Transactivates CYP74A/AOS, AOC3, OPR3 and 4CLL5/OPCL1 genes by directly binding to HD motifs in their promoters. These target genes are involved in jasmonate (JA) biosynthesis, and JA signaling affects root architecture by activating auxin signaling, which promotes lateral root formation (PubMed:25752924). Acts as a negative regulator of trichome branching (PubMed:16778018, PubMed:24824485). Required for the establishment of giant cell identity on the abaxial side of sepals (PubMed:23095885). Seems to promote cell differentiation (PubMed:25564655). May regulate cell differentiation and proliferation during root and shoot meristem development (PubMed:25564655).
subunit: Interacts with BBM.
disruption phenotype: Plants show excess branching of trichomes (PubMed:16778018, PubMed:24824485). In plants missing HDG3, HDG7, HDG11, PDF2 and ATML1, increased cell division leading to cell overproliferation (PubMed:25564655). - Characterization of promoter elements of isoprene-responsive genes and the ability of isoprene to bind START domain transcription factors
Weraduwage, Plant direct 2023 - “...an atomic model for the START domain within the homeoboxleucine zipper protein HDG11 (uniprot code Q9FX31) (UniProt, 2015 ). In turn, this model was tested for its capacity to bind to isoprene as well as to thylakoid membrane models. The initial protein structure was homology modeled...”
- Involvement of a universal amino acid synthesis impediment in cytoplasmic male sterility in pepper
Fang, Scientific reports 2016 - “...6.79 36.89 * Q56WN1 Glutamine synthetase cytosolic isozyme 1-1 84.22 2 356 5.28 38.98 * Q9FX31 Homeobox-leucine zipper protein HDG11 129.26 3 722 6.23 79.12 * Q9FNX8 Lipoxygenase 4 224.21 4 926 6.37 98.30 * Q9SMU8 Peroxidase 34 128.49 2 353 7.71 35.70 * Q9SZD4 26S...”
- Identification of Quantitative Trait Loci (QTLs) and candidate genes for trichome development in Brassica villosa using genetic, genomic, and transcriptomic approaches
Bergmann, Molecular genetics and genomics : MGG 2025 - “...15.54 1.32 1.38 0.00 BRICK1 TRINITY_DN8124_c0_g2_i1 AT2G22640 23.69 21.85 36.24 0.00 0.00 0.00 EDT1 TRINITY_DN2846_c0_g1_i75 AT1G73360 20.36 28.13 32.25 0.00 0.00 0.00 RBR1 TRINITY_DN4767_c0_g1_i8 AT3G12280 25.54 22.20 21.88 0.00 0.00 0.00 WAVE4 TRINITY_DN25940_c0_g2_i1 AT2G38440 19.86 20.27 24.52 0.00 0.00 0.00 MYB82 Unigene.4850 C2 13,159,285 13,160,362 AT5G52600...”
- “...0.00 SKD1 TRINITY_DN6467_c0_g1_i6 AT2G27600 35.17 31.48 5.92 0.00 0.00 0.00 EDT1 Unigene.19989 C5 37,708,424 37,710,683 AT1G73360 10.61 10.14 13.80 1.33 1.77 1.78 WVD2 TRINITY_DN4022_c0_g3_i5 AT5G28646 19.70 9.25 10.22 0.00 0.00 0.00 ARP2 TRINITY_DN163_c0_g1_i14 AT3G27000 18.51 5.03 9.91 0.00 0.00 0.00 HDG12 Unigene.2953 C1 38,274,278 38,275,721 AT1G17920...”
- The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation
McGuire, The New phytologist 2025 - “....( 2019 ) AT3G20310 ERF7 Represses GCCbox mediated transcription 6.19E05 Nakano etal .( 2006 ) AT1G73360 HDG11 Trichome development 6.49E05 Nakamura etal .( 2006 ) AT5G14340 MYB40 Arsenic resistance 6.64E05 Chen etal .( 2021 ) AT3G50700 IDD2 6.67E05 AT3G53200 MYB27 Anthocyanin repressor 6.97E05 Albert etal .(...”
- QTL mapping for pod quality and yield traits in snap bean (Phaseolus vulgaris L.)
Njau, Frontiers in plant science 2024 - “...orthologs of this gene include HOMEODOMAIN GLABROUS 11 and 12 ( HDG11 and HDG12 ; AT1G73360 and AT1G17920 respectively), and PROTODERMAL FACTOR 2 ( PDF2 , AT4G04890 ). In Arabidopsis, these genes are involved in the maintenance of floral organ identity, cell wall identity, and patterning...”
- HD-ZIP IV genes are essential for embryo initial cell polarization and the radial axis formation in Arabidopsis.
Tanaka, Current biology : CB 2024 (PubMed)- GeneRIF: HD-ZIP IV genes are essential for embryo initial cell polarization and the radial axis formation in Arabidopsis.
- Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton
Wang, Frontiers in plant science 2022 - “...AtHDG4 (At4g17710), AtHDG5 (At5g46880), AtHDG6 (At4g25530), AtHDG7 (At5g52170), AtHDG8 (At3g03260), AtHDG9 (At5g17320), AtHDG10 (At1g34650), AtHDG11 (At1g73360), AtHDG12 (At1g17920), GhHD1 (Gh_A06G1283), GhHOX1 (AF530913), GhHOX3 (Gh_A12G2462). The MBW Regulatory Complex WD40-repeat proteins provide a scaffold in proteinprotein interactions between R2R3-MYB and bHLH proteins. In Arabidopsis , GL1, GL3/EGL3,...”
- Genome-Wide Identification of Direct Targets of the TTG1-bHLH-MYB Complex in Regulating Trichome Formation and Flavonoid Accumulation in Arabidopsis Thaliana
Wei, International journal of molecular sciences 2019 - “..., 53 ] BLT (AT1G64690) 2.10 Promoting trichome branching [ 54 , 55 ] HDG11 (AT1G73360) 1.78 Promoting trichome differentiation [ 56 ] GL2 (AT1G79840) 6.33 Promoting trichome differentiation [ 22 , 23 , 24 ] TTG2 (AT2G37260) 7.89 Promoting trichome formation [ 25 , 57...”
- A gene regulatory network for root hair development
Shibata, Journal of plant research 2019 - “...(maMYB) At5g45420 MYB Hair growth Slabaugh et al. ( 2011 ) HOMEODOMAIN GLABROUS 11 (HDG11) At1g73360 HD-ZIP Hair growth Xu et al. ( 2014 ) OBF BINDING PROTEIN 4 (OBP4) At5g60850 Dof Hair growth Rymen et al. ( 2017 ) GT2-LIKE1 (GTL1) At1g33240 Trihelix Hair growth...”
- A gene expression map of shoot domains reveals regulatory mechanisms
Tian, Nature communications 2019 - “...GLABROUS 2 1.56 4.23E08 AT1G14350 FOUR LIPS 1.63 1.02E09 AT3G62680 PROLINE-RICH PROTEIN 3 5.16 8.14E05 AT1G73360 HOMEODOMAIN GLABROUS 11 1.48 7.83E03 AT1G17920 HOMEODOMAIN GLABROUS 12 2.44 2.72E09 AT2G22640 BRICK1 1.52 1.63E05 AT4G04890 PROTODERMAL FACTOR 2 2.08 7.22E25 AT2G47000 ATP-BINDING CASSETTE B4 1.70 1.64E04 AT2G26650 K +...”
- More
- The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1
Pan, BMC plant biology 2015 - “...HDG4 (NP_193506), HDG5 (NP_199499), HDG6 (NP_567722), HDG7 (NP_200030), HDG8 (NP_186976), HDG9 (NP_197234), HDG10 (NP_174724), HDG11 (NP_177479) and HDG12 (NP_564041) in Arabidopsis ; ZmOCL1 (CAG38614), ZmOCL2 (CAB96422), ZmOCL3 (CAB96423), and ZmOCL4 (CAB96424) for maize; GaHOX1 (ABY41242), GaHOX2 (ABY67263), GhHD1A (AFO11041), and GhHD1D (AFO11042) for cotton; OsRoc1 (BAB85750)...”
- START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Schrick, Genome biology 2004 - “...START 687 207-438 1 - NP_174724 At1g34650 - HD ZLZ START 708 221-454 1 - NP_177479 At1g73360 - HD ZLZ START 722 228-458 1 - NP_565223 At1g79840 GL2 HD ZLZ START 747 253-487 1 - NP_180796 At2g32370 - HD ZLZ START 721 245-472 2 - NP_186976...”
VSX1_CARAU / Q90277 Visual system homeobox 1; Homeobox protein VSX-1; Transcription factor VSX1 from Carassius auratus (Goldfish) (see paper)
45% identity, 16% 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.
NP_001315326 paired box protein Pax-3b from Danio rerio
45% identity, 12% coverage
A6NJT0 Homeobox protein unc-4 homolog from Homo sapiens
NP_001073930 homeobox protein unc-4 homolog from Homo sapiens
46% identity, 11% 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)
48% identity, 29% 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.
XP_004251138 homeobox-leucine zipper protein REVOLUTA from Solanum lycopersicum
41% identity, 6% coverage
XP_008330042 LIM/homeobox protein Lhx9 isoform X1 from Cynoglossus semilaevis
45% identity, 14% coverage
LHX2_MOUSE / Q9Z0S2 LIM/homeobox protein Lhx2; Homeobox protein LH-2; LIM homeobox protein 2 from Mus musculus (Mouse) (see 2 papers)
45% identity, 14% coverage
- function: Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.
subunit: Interacts (via LIM domains) with CITED2 (PubMed:10593900). Interacts with POU4F2 isoform 1 (PubMed:24643061). - Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Azimzadeh, Frontiers in microbiology 2016 - “...lectin-like receptor 3 Down Up GBP2 Q9Z0E6 Guanylate binding protein 2, interferon-inducible Down Up Lhx2 Q9Z0S2 LIM homeobox 2 Down Up Apod P51910 Apolipoprotein D Down Up Arhgap9 Q1HDU4 Rho GTPase activating protein 9 Down Up Gas1 Q01721 Growth arrest-specific 1 Down Up MITD1 Q8VDV8 MIT,...”
- MEF2C and EBF1 Co-regulate B Cell-Specific Transcription.
Kong, PLoS genetics 2016 - “...lineage commitment, we also performed ChIP-seq using cells that over-express the transcription factor LHX2 (UniProt Q9Z0S2) and mimic hematopoietic progenitor cells (HPCs) in vivo and in vitro [ 31 ]. 41% of MEF2C peaks in HPCs overlapped with its peaks in pre-B cells, and vice versa,...”
8ejoA / A0A6I8NF41 Crystal structure of the homeodomain of platypus sdux in complex with DNA (see paper)
44% identity, 93% coverage
XP_012818036 short stature homeobox protein 2 isoform X1 from Xenopus tropicalis
47% identity, 18% coverage
NP_477330 PvuII-PstI homology 13 from Drosophila melanogaster
43% identity, 16% 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
46% identity, 11% 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.
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
48% identity, 16% 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...”
XP_005167911 short stature homeobox protein isoform X1 from Danio rerio
47% identity, 17% coverage
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
48% identity, 29% 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_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
45% identity, 16% coverage
DUX1_HUMAN / O43812 Double homeobox protein 1 from Homo sapiens (Human) (see 2 papers)
TC 1.I.1.1.3 / O43812 Nuclear Pore Complex, NPC with 86 protein components from Homo sapiens
44% identity, 32% coverage
- function: Probable transcription activator. Binds the P5 DNA element sequence 5'-GATCTGAGTCTAATTGAGAATTACTGTAC-3'.
- substrates: RNA, proteins
tcdb comment: NPCs mediate nucleocytoplasmic transport and gain transport selectivity through nucleoporin FG domains.Chug et al. 2015 reported a structural analysis of the frog FG Nup62•58•54 complex. It comprises a ≈13 nanometer-long trimerization interface with an unusual 2W3F coil, a canonical heterotrimeric coiled coil, and a kink that enforces a compact six-helix bundle. Nup54 also contains a ferredoxin-like domain.Chug et al. 2015 further identified a heterotrimeric Nup93-binding module for NPC anchorage. The quaternary structure alternations in the Nup62 complex, which were previously proposed to trigger a general gating of the NPC, are incompatible with the trimer structure.Chug et al. 2015 suggested that the highly elongated Nup62 complex projects barrier-forming FG repeats far into the central NPC channel, supporting a barrier that guards the entire cross section. The Sun1/UNC84A protein and Sun2/UNC84B may function redundantly in early HIV-1 infection steps and therefore influence HIV-1 replication and pathogenesis (Schaller et al. 2017). The integral transmembrane nucleoporin Pom121 functionally links nuclear pore complex assembly to nuclear envelope formation (Antonin et al. 2005) and ensures efficient HIV-1 pre-integration complex nuclear import (Guo et al. 2018). Mechanosensing at the nuclear envelope by nuclear pore complex stretch activation involves cell membrane integrins (TC# 8.A.54) and SUN proteins, SUN1 and SUN2, in the nuclear membrane (Donnaloja et al. 2019). TMX2 is a thioredoxin-like protein that facilitates the transport of proteins across the nuclear membrane (Oguro and Imaoka 2019) - DUX4 is a multifunctional factor priming human embryonic genome activation
Vuoristo, iScience 2022 - “...UniProt A6NLW8 DUXB protein sequence Homo sapiens UniProt A0A1W2PPF3 DUX1 protein sequence Homo sapiens UniProt O43812 DUX3 protein sequence Homo sapiens UniProt Q96PT4 DUX5 protein sequence Homo sapiens UniProt Q96PT3 DUX4 protein sequence Pan troglodytes NCBI XP_024209610.1 DUX4 protein sequence Gorilla gorilla gorilla NCBI XP_018890005.1 DUX4...”
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...contain two homeobox domains and two different penetratin-like peptides (see some examples at UniProt links O43812, Q96PT3, A6NLW8, and P0CJ85). Human Zink finger homeobox protein 3 has four homeobox domains in its long sequence of 3703 residues (see Q15911) with four associated penetratins, which are, however,...”
- Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4.
Eidahl, Human molecular genetics 2016 - “...identifications were used DUX4_HUMAN (Accession Q9UBX2), A1JVI8_MOUSE (Accession A1JVI8), Q7TNE6_MOUSE (Accession Q7TNE6), DUXA_HUMAN (A6NLW8), DUX1_HUMAN (O43812) and DUX5_HUMAN (Q96PT3) for the amino acid sequence alignments of DUX4, Dux, Duxbl, DUXA, DUX1 and DUX5, respectively. Cell culture Human embryonic kidney cells (HEK293) were cultured in DMEM supplemented...”
NP_446130 retinal homeobox protein Rx from Rattus norvegicus
48% identity, 16% coverage
O35602 Retinal homeobox protein Rx from Mus musculus
NP_038861 retinal homeobox protein Rx from Mus musculus
48% identity, 16% 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.
- More
NP_957490 short stature homeobox protein 2 from Danio rerio
47% identity, 18% coverage
AFUA_4G10220, Afu4g10220 homeobox transcription factor (RfeB), putative from Aspergillus fumigatus Af293
44% identity, 9% coverage
- Identification of Homeobox Transcription Factors in a Dimorphic Fungus Talaromyces marneffei and Protein-Protein Interaction Prediction of RfeB
Pongpom, Journal of fungi (Basel, Switzerland) 2024 - “...Pah1 from P. anserine , MoHox1 from M. oryzae , kal-1 from N. crassa , Afu4g10220 (RfeB) from A. fumigatus , and Pho2 from S. cerevisiae . Indeed, the RfeB protein family from Aspergillus spp., Hoy1 from Yallowia lipolytica , Pah1, MoHox1, and kal-1 were previously...”
- Determining Aspergillus fumigatus transcription factor expression and function during invasion of the mammalian lung
Liu, PLoS pathogens 2021 - “...0.9 10221 Afu3g08050 1 0.4 3.9 6.2 4186 Afu3g08520 RlmA 1 2.2 2.1 2.1 4134 Afu4g10220 1 0.9 2.0 1.8 21511 Afu5g01650 1 1.6 2.5 2.3 27841 Afu5g13790 1 29.2 1.9 2.6 815 Afu7g00130 NscR 1 21.3 209.4 308.4 3803 Afu8g05270 1 0.5 2.2 2.0 3969...”
- “...study afu1g15910 Af293; Afu1g15910 :: hph Present study afu3g08050 Af293; Afu3g08050 :: hph Present study afu4g10220 Af293; Afu4g10220 :: hph Present study afu5g01650 Af293; Afu5g01650 :: hph Present study afu5g13790 Af293; Afu5g13790 :: hph Present study afu7g00130 Af293; Afu7g00130 :: hph Present study afu8g05270 Af293; Afu8g05270...”
- RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
Irmer, BMC genomics 2015 - “...AFUA_3G11250 ace2 C2H2 transcription factor (Swi5), role in conidiophore development, pigment production, germination and virulence AFUA_4G10220 homeobox transcription factor (RfeB), ortholog(s) have role in conidiophore development, conidium formation, hyphal growth, regulation nucleotide biosynthesis AFUA_4G11480 C2H2 finger domain protein, S. cerevisiae ortholog is Zinc-regulated transcription facto AFUA_4G12470...”
NP_733401 Zn finger homeodomain 1, isoform E from Drosophila melanogaster
40% identity, 5% coverage
- Expanding the mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets.
Wu, FEBS letters 2019 (PubMed)- GeneRIF: mesodermal transcriptional network by genome-wide identification of Zinc finger homeodomain 1 (Zfh1) targets
- Direct control of somatic stem cell proliferation factors by the Drosophila testis stem cell niche.
Albert, Development (Cambridge, England) 2018 (PubMed)- GeneRIF: Zfh1 binds and downregulates salvador and kibra, two tumour suppressor genes of the Hippo/Wts/Yki pathway, thereby restricting Yki activation and proliferation to the Zfh1(+) stem cells.
- Without children is required for Stat-mediated zfh1 transcription and for germline stem cell differentiation.
Maimon, Development (Cambridge, England) 2014 - GeneRIF: Zfh1 levels are increased in somatic cells that contact germ cells, and Woc is required for a Stat92E-mediated upregulation of zfh1 transcription.
- Transcription factor zfh1 downregulates Drosophila Imd pathway.
Myllymäki, Developmental and comparative immunology 2013 (PubMed)- GeneRIF: zfh1 is an important regulator of the immune response in Drosophila.
- Antagonistic function of Lmd and Zfh1 fine tunes cell fate decisions in the Twi and Tin positive mesoderm of Drosophila melanogaster.
Sellin, Developmental biology 2009 (PubMed)- GeneRIF: Data show that cell fate decisions in the dorsal and lateral Twi- and Tin-positive mesoderm of Drosophila melanogaster depend on the antagonistic action of the transcription factor Lame duck and the zinc finger homeodomain factor Zfh1.
- Zfh1 promotes survival of a peripheral glia subtype by antagonizing a Jun N-terminal kinase-dependent apoptotic pathway.
Ohayon, The EMBO journal 2009 - GeneRIF: Study shows a novel function for Zfh1 as an anti-apoptotic molecule and uncovers a cryptic JNK-dependent apoptotic programme in ePG10, which is normally blocked by Zfh1.
- The transcription factor Zfh1 is involved in the regulation of neuropeptide expression and growth of larval neuromuscular junctions in Drosophila melanogaster.
Vogler, Developmental biology 2008 (PubMed)- GeneRIF: Study shows that Zfh1 cell autonomously regulates motoneuronal outgrowth and larval growth of neuromuscular junctions and that the growth of NMJs is dependent on the dosage of Zfh1.
- Zfh-1 controls somatic stem cell self-renewal in the Drosophila testis and nonautonomously influences germline stem cell self-renewal.
Leatherman, Cell stem cell 2008 - GeneRIF: Zfh-1 is a presumptive somatic target of Jak/STAT signaling, demonstrating that it is necessary and sufficient to maintain somatic stem cells.
- More
HM10_CAEEL / P41935 Homeobox protein ceh-10 from Caenorhabditis elegans (see 7 papers)
45% identity, 15% 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.
XP_003029756 regulator of mushroom development from Schizophyllum commune H4-8
47% identity, 7% coverage
NP_001157150 short stature homeobox protein 2 isoform c from Homo sapiens
47% identity, 17% 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...”
XP_006713790 short stature homeobox protein 2 isoform X1 from Homo sapiens
47% identity, 15% 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.
- More
O60902 Short stature homeobox protein 2 from Homo sapiens
47% identity, 16% 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_001289286 short stature homeobox protein 2 isoform 2 from Mus musculus
47% identity, 17% 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.
- More
NP_037160 short stature homeobox protein 2 from Rattus norvegicus
47% identity, 16% coverage
DUX5_HUMAN / Q96PT3 Double homeobox protein 5 from Homo sapiens (Human) (see paper)
44% identity, 28% coverage
- DUX4 is a multifunctional factor priming human embryonic genome activation
Vuoristo, iScience 2022 - “...UniProt O43812 DUX3 protein sequence Homo sapiens UniProt Q96PT4 DUX5 protein sequence Homo sapiens UniProt Q96PT3 DUX4 protein sequence Pan troglodytes NCBI XP_024209610.1 DUX4 protein sequence Gorilla gorilla gorilla NCBI XP_018890005.1 DUX4 protein sequence Pongo abelii NCBI XP_024097529.1 DUX4 protein sequence Colobus angolensis palliatus NCBI XP_011811800.1...”
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...two homeobox domains and two different penetratin-like peptides (see some examples at UniProt links O43812, Q96PT3, A6NLW8, and P0CJ85). Human Zink finger homeobox protein 3 has four homeobox domains in its long sequence of 3703 residues (see Q15911) with four associated penetratins, which are, however, of...”
- Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4.
Eidahl, Human molecular genetics 2016 - “...DUX4_HUMAN (Accession Q9UBX2), A1JVI8_MOUSE (Accession A1JVI8), Q7TNE6_MOUSE (Accession Q7TNE6), DUXA_HUMAN (A6NLW8), DUX1_HUMAN (O43812) and DUX5_HUMAN (Q96PT3) for the amino acid sequence alignments of DUX4, Dux, Duxbl, DUXA, DUX1 and DUX5, respectively. Cell culture Human embryonic kidney cells (HEK293) were cultured in DMEM supplemented with 10% fetal...”
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)
47% identity, 16% coverage
XP_023014225 paired mesoderm homeobox protein 2A-like from Leptinotarsa decemlineata
43% identity, 16% coverage
NP_001139175 paired like homeobox 2Ba from Danio rerio
47% identity, 34% coverage
NP_571120 homeobox protein engrailed-1a from Danio rerio
43% identity, 24% coverage
LOC100121225 paired mesoderm homeobox protein 2 from Nasonia vitripennis
45% identity, 21% 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_726607 eyeless, isoform B from Drosophila melanogaster
39% identity, 9% 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
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NP_571300 retinal homeobox protein Rx1 from Danio rerio
48% identity, 17% coverage
CC1G_01962 hypothetical protein from Coprinopsis cinerea okayama7#130
44% identity, 8% coverage
NP_001014693 eyeless, isoform D from Drosophila melanogaster
39% identity, 6% 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...”
HOX29_ORYSI / A2WLR5 Homeobox-leucine zipper protein HOX29; HD-ZIP protein HOX29; Homeodomain transcription factor HOX29; OsHox29 from Oryza sativa subsp. indica (Rice) (see paper)
41% identity, 6% coverage
- function: Probable transcription factor.
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
48% identity, 17% coverage
ATHB8_ARATH / Q39123 Homeobox-leucine zipper protein ATHB-8; HD-ZIP protein ATHB-8; Homeodomain transcription factor ATHB-8 from Arabidopsis thaliana (Mouse-ear cress) (see 7 papers)
AT4G32880, NP_195014 homeobox-leucine zipper protein ATHB-8 from Arabidopsis thaliana
NP_195014 ATHB-8 (HOMEOBOX GENE 8); DNA binding / transcription factor from Arabidopsis thaliana
39% identity, 6% coverage
- function: Probable transcription factor involved in the regulation of vascular development. May promote differentiation of precambial and cambial cells.
subunit: Interacts with ESR1 and ESR2 (PubMed:17376809). Interacts with ZPR3 (PubMed:18408069). - Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens
Ryo, Journal of experimental botany 2018 - “...from P. patens ; AtPhyA (P14712), AtPhyB (P14713), AtPhyC (P14714), AtPhyD (P42497), AtPhyE (P42498), ATHB8 (Q39123), AtICU4 (Q9ZU11), AtPHV (O04292), AtREV (Q9SE43), AtMAP3K (AEE84700), AtMAPKKK1 (AEE74423), AtMAPKKK2 (AEE74424), AtMAPKKK3 (AEE74425), AtRAF10 (AED95818), AtRAF11 (AEE34716), AtZTL (Q94BT6), AtFKF1 (Q9C9W9), AtLKP2 (Q8W420), AtPHOT1 (O48963), AtPHOT2 (P93025), and AtTLP...”
- Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity
Barff, The plant genome 2025 - “...OF MAX2 1LIKE5 AT5G57130 Phloem (precursors) (Wallner etal., 2017 ) p ATHB8 HOMEOBOX GENE 8 AT4G32880 Procambium, xylem precursors and columella in RAM (Baima etal., 1995) John Wiley & Sons, Ltd. 2.2 Protoplast extraction Protoplasts were extracted from the abovementioned seedlings following the protocol described by...”
- Damage activates EXG1 and RLP44 to suppress vascular differentiation during regeneration in Arabidopsis
Mazumdar, Plant communications 2025 (no snippet) - Auxin signaling in the cambium promotes tissue adhesion and vascular formation during Arabidopsis graft healing
Serivichyaswat, Plant physiology 2024 - “...AT1G04550 APL Gramene: AT1G79430 APL Araport: AT1G79430 CASP1 Gramene: AT2G36100 CASP1 Araport: AT2G36100 ATHB8 Gramene: AT4G32880 ATHB8 Araport: AT4G32880 LTP1 Gramene: AT2G38540 LTP1 Araport: AT2G38540 ML1 Gramene: AT4G21750 ML1 Araport: AT4G21750 PXY Gramene: AT5G61480 PXY Araport: AT5G61480 SLR1 Gramene: AT4G14550 SLR1 Araport: AT4G14550 TMO5 Gramene: AT3G25710...”
- Advances in understanding the graft healing mechanism: a review of factors and regulatory pathways
Wang, Horticulture research 2024 - “...] HCA2 AT5G62940 Involved in cell wall remodeling and vascular remodeling. [ 58 ] ATHB8 AT4G32880 Regulate xylem differentiation. [ 112 ] IPT3/7 AT3G63110 AT3G23630 Promote cytokinin synthesis. [ 54 ] LBD4 AT1G31320 Define phloem boundaries. [ 107 ] LOG4/5 AT3G53450 AT4G35190 Promote cytokinin synthesis. [...”
- Genetic and molecular mechanisms underlying the parthenocarpic fruit mutation in tomato
Picarella, Frontiers in plant science 2024 - “...by BLASTP at SGN using the Arabidopsis HD-Zip III protein sequences as queries: ATHB8 ( At4g32880 ), ATHB9/PHV ( At1g30490 ), ATHB14/PHB ( At2g34710 ), ATHB15/CNA/ICU4 ( At1g52150 ), and IFL1/REV ( At5g60690 ). The Arabidopsis proteins and the six identified tomato orthologs were aligned by...”
- Auxin signaling in the cambium promotes tissue attachment and vascular development duringArabidopsis thalianagraft formation
Serivichyaswat, 2023 - Identification of new potential downstream transcriptional targets of the strigolactone pathway including glucosinolate biosynthesis
Hellens, Plant direct 2023 - “...AT2G44990, AT3G14370, AT3G15540, AT3G28345, AT3G53480, AT3G59900, AT3G62100, AT3G63300, AT4G00880, AT4G14560, AT4G17980, AT4G22620, AT4G27260, AT4G28640, AT4G30290, AT4G32880, AT4G34760, AT4G36110, AT5G13360, AT5G19530, AT5G20820, AT5G39610, AT5G43700, AT5G47370, AT5G54490, AT5G54510, AT5G55250, AT5G62380, AT5G65670, AT5G67480, AT1G03055, AT2G42620, AT3G21420, AT3G03990. AUTHOR CONTRIBUTIONS Alicia M. Hellens, Franziska Fichtner, Philip B. Brewer, and Christine...”
- WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus
Ogura, Science advances 2023 - “...(5-GGTTCTTCCACTACATCACG-3) and TDR-pro-R (5-CGTAGCTTTTAGAAAGAAATTAAAG-3) for TDR (AT5G61480); and ATHB8-pro-F (5-CTTATCACAGGGGACAATGTCG-3) and ATHB-pro-R (5-CTTTGATCCTCTCCGATCTCTC-3) for ATHB8 (AT4G32880). After verifying the full-length sequence of the cloned fragment, the promoter together with pDONR-L1-GFP-L2 was transferred to the binary vector R4pGWB501 ( 46 ) via an LR reaction (Invitrogen). For...”
- More
- START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Schrick, Genome biology 2004 - “...836 152-366 1 - NP_181018 At2g34710 PHB, ATHB-14 HD ZIP START 852 166-383 2 - NP_195014 At4g32880 ATHB-8 HD ZIP START 833 151-369 4 - NP_200877 At5g60690 REV, IFL1 HD ZIP START 842 153-366 5 - NP_180399 At2g28320 - PH START DUF1336 737 171-364 2 -...”
XP_002936715 retinal homeobox protein Rx from Xenopus tropicalis
48% identity, 17% coverage
ZFH1_DROME / P28166 Zinc finger protein 1; Zinc finger homeodomain protein 1 from Drosophila melanogaster (Fruit fly) (see paper)
40% identity, 6% coverage
- function: Involved in the development of the embryonic central nervous system, embryonic mesoderm and adult musculature.
- A survey of well conserved families of C2H2 zinc-finger genes in Daphnia
Seetharam, BMC genomics 2010 - “...5:1579836-1581770 EGR2 (NP_000390) EGRH2 (NP_500019) EGR3 (NP_004421) EGRH3 (NP_001041062) EGR4 (NP_001956) ZFH1/2 ZEB1 (P37275) ZFH1 (P28166) ZAG1 (Q94196) ZFH1 (Dappu-225224) 31:791001-795287 ZEB2 (O60315) ZFH3/4 ZFHX2 (Q9C0A1) ZFH2 (P28167) ZC123.3 (O45019) ZFH2 (Dappu-233159) 2:1855545-1862285 ZFHX3 (Q15911) ZFHX4 (Q86UP3) SPALT SALL1 (Q9NSC2) SPALTm (P39770) SEM4(NP_491997) SALL (Dappu-111734) 88:97830-103728...”
- Combination of a zinc finger and homeodomain required for protein-interaction
Smith, Molecular biology reports 2003 - “...(NP 035676); 3, hamster BZP (Q60542); 4, Drosophila Zfh-1 (P28166); 5, mosquito (EAA06926); 6, mouse SIP-1 (NP 056568). Figure 3. Zfhep ZHD binds the Oct-1 POU...”
- 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 - “...Q16, Ss +, + 2 0,0,0 D, N Intercellular comm. Zinc-finger 1 (P28166) 1060 Q6, Qs, Q5, Qs +, + 0,2,1 2 D, N, T Embryonic CNS devel. DWNT-3 (P28466) 1010 G6, S14...”
PAX6_DROME / O18381 Paired box protein Pax-6; Protein eyeless from Drosophila melanogaster (Fruit fly) (see paper)
39% identity, 7% 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...”
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)
48% identity, 17% coverage
- function: Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation.
ISX_MOUSE / A1A546 Intestine-specific homeobox from Mus musculus (Mouse) (see 2 papers)
NP_082113 intestine-specific homeobox isoform 2 from Mus musculus
47% identity, 21% coverage
NP_571302 retinal homeobox protein Rx3 from Danio rerio
48% identity, 19% 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
HOX29_ORYSJ / Q5QMZ9 Homeobox-leucine zipper protein HOX29; HD-ZIP protein HOX29; Homeodomain transcription factor HOX29; OSHB5; OsHox29 from Oryza sativa subsp. japonica (Rice) (see 2 papers)
41% identity, 6% coverage
- function: Probable transcription factor that may be necessary for the proper patterning of vascular bundles.
- Overexpression of OsHox32 Results in Pleiotropic Effects on Plant Type Architecture and Leaf Development in Rice
Li, Rice (New York, N.Y.) 2016 - “...and Zea mays (Zm); the protein sequence accession numbers are OsHox9: Q9AV49; OsHox10: Q6TAQ6; OsHox29: Q5QMZ9; OsHox32: NP_001050745; OsHox33: NP_001067260; PHB: BAJ14107.1; PHV: NP_174337.1; REV: AAF42938.1; CNA: NP_175627.1; ATHB8: NP_195014.1; RLD1: NP_001105533.1; and RLD2: NP_001105994.1 Overexpression of OsHox32 Affects the Architecture of the Rice Leaf and...”
Q6FKZ3 Candida glabrata strain CBS138 chromosome L complete sequence from Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)
37% identity, 10% coverage
- Designed Multifunctional Peptides for Intracellular Targets
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...The budding yeast penetratin analog KNVRIWFQNRRAKVRK KGKL extended at its C-terminal (underlined) from the PHO2 (Q6FKZ3) protein has a high positive charge and unknown abilities. Its CPP probability prediction by the MLCPP server is similar (0.93) to pAntp (0.98). Hemolytic activity prediction by the HAPPENN server...”
- “...IWFQNRR A K QRR RRQKARRNQFWIRIVRR 6/1/0.96 7/1/0.96 Candida glabrata/ budding yeast Homeobox containing protein PHO2/ Q6FKZ3 KNVR IWFQNRR A K VR K KNVR IWFQNRR A K VR K KGKL 4/3/0.95 4/5/0.95 Hanseniaspora osmophila/ wine-making yeast Regulatory protein PHO2 with homobox domain 1/A0A1E5RMZ3 T Q V KIWFQNRRMKWK...”
A0A0B7A551 Uncharacterized protein (Fragment) from Arion vulgaris
45% identity, 12% 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_571459 aristaless-related homeobox protein from Danio rerio
49% identity, 12% coverage
LOC103708475 homeobox-leucine zipper protein ATHB-15-like from Phoenix dactylifera
39% identity, 6% coverage
GSB_DROME / P09082 Protein gooseberry; BSH9; Protein gooseberry distal from Drosophila melanogaster (Fruit fly) (see paper)
NP_523863 gooseberry from Drosophila melanogaster
39% identity, 13% 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_001084383 paired like homeobox 2B L homeolog from Xenopus laevis
43% identity, 19% 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...”
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)
47% identity, 11% 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.
REV_ARATH / Q9SE43 Homeobox-leucine zipper protein REVOLUTA; HD-ZIP protein REV; Homeodomain transcription factor REV; Protein AMPHIVASAL VASCULAR BUNDLE 1; Protein INTERFASCICULAR FIBERLESS 1 from Arabidopsis thaliana (Mouse-ear cress) (see 12 papers)
AT5G60690, NP_200877 Homeobox-leucine zipper family protein / lipid-binding START domain-containing protein from Arabidopsis thaliana
NP_200877 REV (REVOLUTA); DNA binding / lipid binding / transcription factor from Arabidopsis thaliana
39% identity, 6% coverage
- function: Probable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212).
subunit: Homodimer (Probable). Heterodimer with ZPR1, ZPR2, ZPR3 or ZPR4 (PubMed:18055602). Interacts with ESR1 and ESR2 (PubMed:17376809). Interacts with ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:18055602, PubMed:18408069). Heterodimerization with ZPR3 prevents DNA binding by REV (PubMed:18055602).
disruption phenotype: Plants display strongly reduced auxin polar transport in inflorescence stems and hypocotyls. This phenotype is probably due to altered cell differentiation and morphology (PubMed:11402186). Repression by miR165 suppresses DOF5.1 over- expression mediated upward-curling phenotype (PubMed:20807212). - Comprehensive mapping of Arabidopsis alternative splicing landscape reveals key insights into plant development and immunity
Barff, The plant genome 2025 - “...ML1 MERISTEM LAYER 1 AT4G21750 L1 Layer epidermis (Session etal., 1999 ) p REV REVOLUTA AT5G60690 Shoot apical meristem (SAM) central zone (Otsuga etal., 2008 ) p UFO UNUSUAL FLORAL ORGANS AT1G30950 SAM peripheral zone (Hepworth etal., 2006 ) p LTP1 LOCALIZED LIPID TRANSFERT PROTEIN1 AT2G38540...”
- Identification of QTLs for early maturity-related traits based on RIL population of two elite cotton cultivars
Wang, BMC plant biology 2024 - “...another candidate gene, was annotated as homeobox-leucine zipper family protein and homologous to REVOLUTA ( AT5G60690 ) of Arabidopsis . REVOLUTA encoded a homeobox-leucine zipper family protein / lipid-binding START domain-containing protein, which functions as a Class III homeodomain-leucine zipper (HD-ZIPIII) transcription factor regulating the normal...”
- “...gene associated with early maturity trait, is found homologous with REV gene in Arabidopsis ( AT5G60690 ). qRT-PCR analysis indicated that the expression of GH_D03G1541 in SCRC21 was significantly high compared to SCRC19 at 1 DPS, 5 DPS and 10 DPS, implying this gene may function...”
- ALTERED MERISTEM PROGRAM1 sustains cellular differentiation by limiting HD-ZIP III transcription factor gene expression
Yang, Plant physiology 2024 - “...under accession numbers AT3G54720 (AMP1), AT5G19740 (LAMP1), AT3G52770 (ZPR3), At2g36307 (ZPR4), AT2G34710 (PHB), At1g30490 (PHV), AT5G60690 (REV), AT2G17950 (WUS), At1g12980 (DRN), AT1G01183 (MIR165A), AT2G46685 (MIR166A), At1g48410 (AGO1), and AT5G25760 (UBC). Supplementary Material kiae300_Supplementary_Data Acknowledgments We thank Yk Helariutta and Michael Prigge for providing seed material. We...”
- Densification of Genetic Map and Stable Quantitative Trait Locus Analysis for Amino Acid Content of Seed in Soybean (Glycine max L.)
Li, Plants (Basel, Switzerland) 2024 - “...AT3G21630 GO:0005515 protein binding Glyma.02g271700 AT5G20930 GO:0005515 protein binding Glyma.11g144900 AT5G45890 GO:0005576 extracellular region Glyma.11g145800 AT5G60690 GO:0003700 sequence-specific DNA binding transcription factor activity Arabidopsis homologs were found in SoyBase ( http://www.soybase.org , accessed on 16 May 2024); Null indicates no homologous genes were found in Arabidopsis....”
- Genetic and molecular mechanisms underlying the parthenocarpic fruit mutation in tomato
Picarella, Frontiers in plant science 2024 - “...ATHB9/PHV ( At1g30490 ), ATHB14/PHB ( At2g34710 ), ATHB15/CNA/ICU4 ( At1g52150 ), and IFL1/REV ( At5g60690 ). The Arabidopsis proteins and the six identified tomato orthologs were aligned by Geneious 5.6.3 ( http://www.geneious.com/ ), and a phylogenetic tree was generated using Jukes-Cantor and neighbor-joining as genetic...”
- The METHYLTRANSFERASE B-SERRATE interaction mediates the reciprocal regulation of microRNA biogenesis and RNA m6A modification
Bai, Journal of integrative plant biology 2024 - “...BPM3 (At2g39760), ESD4 (At4g15880), TSL (At5g20930), SPL5 (At3g15270), SPL10 (At1g27370), MYB33 (At5g06100), CUC1 (At3g15170), REV (At5g60690), MIR159A (At1g73687), MIR159B (At1g18075), MIR160A (At2g39175), MIR163 (At1g66725), MIR164 (At2g47585), MIR167B (At3g63375), MIR162A (At5g08185), MIR172 (At2g28056), MIR319 (At4g23713), MIR398 (At2g03445), MIR156 (At2g25095), MIR166 (At2g46685), U6 (At3g14735), and ACTIN2 (At3g18780). CONFLICTS...”
- GWAS for the identification of introgressed candidate genes of Sinapis alba with increased branching numbers in backcross lines of the allohexaploid Brassica
Singh, Frontiers in plant science 2024 - “...leaves to cotyledons, altered flowering time, and photomorphogenesis. Gene_325747_5, orthologous to REVOLUTA ( REV ) (At5g60690) of A. thaliana , has been shown to regulate meristem initiation at lateral positions and is a member of a small homeodomain-leucine zipper family. Gene_325747_6 was orthologous to AINTEGUMENTA (ANT)...”
- Dissection of the genetic basis and molecular mechanism of ovule number per ovary in oilseed rape (Brassica napus L.)
Qadir, Frontiers in plant science 2024 - “...in specification of organs originating from the shoot apical meristem. qONPO.A10-1 10.483-15.040 73 BnaA10g13520D 2.375 AT5G60690 REV REVOLUTA regulates meristem initiation at lateral positions. a member of a small homeodomain-leucine zipper family. BnaA10g18480D 0.138 AT3G02310 SEP1 MADS-box protein, binds K domain of AG in vivo ....”
- More
- Transcriptome analyses of leaf architecture in Sansevieria support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots
Golenberg, Plant direct 2023 - “...AS2 Asymmetric Leaves2 O04479 1.69E58 1.56e58 5.41e39 PHB Phabulosa O04291 .0 .0 .0 REV Revoluta Q9SE43 .0 .0 .0 PHV Phavoluta O04292 .0 .0 .0 ARF3 Ettin/Auxin Response Factor3 O23661 .0 .0 .0 ARF4 Ettin/Auxin Response Factor4 Q9ZTX9 .0 .0 .0 MP Monopteros P93024 7.05e163 9.56e163...”
- Light-regulated PAS-containing histidine kinases delay gametophore formation in the moss Physcomitrella patens
Ryo, Journal of experimental botany 2018 - “...AtPhyB (P14713), AtPhyC (P14714), AtPhyD (P42497), AtPhyE (P42498), ATHB8 (Q39123), AtICU4 (Q9ZU11), AtPHV (O04292), AtREV (Q9SE43), AtMAP3K (AEE84700), AtMAPKKK1 (AEE74423), AtMAPKKK2 (AEE74424), AtMAPKKK3 (AEE74425), AtRAF10 (AED95818), AtRAF11 (AEE34716), AtZTL (Q94BT6), AtFKF1 (Q9C9W9), AtLKP2 (Q8W420), AtPHOT1 (O48963), AtPHOT2 (P93025), and AtTLP (O64511) from Arabidopsis; SmPHK (405045) from...”
- START lipid/sterol-binding domains are amplified in plants and are predominantly associated with homeodomain transcription factors
Schrick, Genome biology 2004 - “...START 852 166-383 2 - NP_195014 At4g32880 ATHB-8 HD ZIP START 833 151-369 4 - NP_200877 At5g60690 REV, IFL1 HD ZIP START 842 153-366 5 - NP_180399 At2g28320 - PH START DUF1336 737 171-364 2 - NP_191040 At3g54800 - PH START DUF1336 733 176-370 3 -...”
NP_001086450 aristaless related homeobox L homeolog from Xenopus laevis
49% identity, 10% coverage
Q05917 Homeobox protein engrailed-2 from Gallus gallus
NP_001254648 homeobox protein engrailed-2 from Gallus gallus
41% identity, 19% coverage
- A cationic motif upstream Engrailed2 homeodomain controls cell internalization through selective interaction with heparan sulfates.
Cardon, Nature communications 2023 - “...of recombinant proteins Regions 200-259 (HD) and 183-259 (ExtHD) of chicken Engrailed2 (Uniprot accession number Q05917) as well as the full-length protein (residues 1-289) were expressed as (His)6-tagged Cherry fusion proteins using pSCherry1 vectors and the E. coli SE1 strain as expression host (Eurogentec, Seraing, Belgium)....”
- Designed Multifunctional Peptides for Intracellular Targets.
Juretić, Antibiotics (Basel, Switzerland) 2022 - “...is highlighted with bold font. The QSLAQELGLNE Sec peptide is a cryptide in engrailed-2 proteins Q05917 (HME2_CHICK), P52730 (HME2B_XENLA), and P09015 (HME2A_DANRE), to mention only the reviewed Swiss-Prot proteins containing that peptide. The human analog of the QSLAQELGLNE peptide contains glycine to serine substitution. Sec and...”
- “...108 ]. Homeoproteins are rich in multifunctional cryptides. For example, let us examine the UNIPROT Q05917 entry and structurally solved PDB 3ZOB sequence 3ZOB_1 with three -helices [ 109 ] for chicken engrailed 2 homeoprotein. The GAG (glycosaminoglycans at the cell surface)-binding sequence P (186) RSRKPKKKNPN...”
- Role of En2 in the tectal laminar formation of chick embryos.
Omi, Development (Cambridge, England) 2014 (PubMed)- GeneRIF: A potential role of En2 in regulating cell migration and positioning in the tectal laminar formation.
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