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GRHL3 grainyhead like transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 57822, updated on 7-Jun-2020

Summary

Official Symbol
GRHL3provided by HGNC
Official Full Name
grainyhead like transcription factor 3provided by HGNC
Primary source
HGNC:HGNC:25839
See related
Ensembl:ENSG00000158055 MIM:608317
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SOM; VWS2; TFCP2L4
Summary
This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]
Expression
Biased expression in esophagus (RPKM 31.7), skin (RPKM 14.0) and 1 other tissue See more
Orthologs

Genomic context

See GRHL3 in Genome Data Viewer
Location:
1p36.11
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (24319333..24364482)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (24645812..24690972)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene interferon lambda receptor 1 Neighboring gene long intergenic non-protein coding RNA 2800 Neighboring gene GRHL3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 15224 Neighboring gene sperm tail PG-rich repeat containing 1 Neighboring gene NIPA like domain containing 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Van der Woude syndrome 2
MedGen: C1847604 OMIM: 606713 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC46624

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
central nervous system development IEA
Inferred from Electronic Annotation
more info
 
cochlea morphogenesis IEA
Inferred from Electronic Annotation
more info
 
ectoderm development IEA
Inferred from Electronic Annotation
more info
 
epidermis development ISS
Inferred from Sequence or Structural Similarity
more info
 
establishment of planar polarity IEA
Inferred from Electronic Annotation
more info
 
establishment of skin barrier IEA
Inferred from Electronic Annotation
more info
 
eyelid development in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
neural tube closure ISS
Inferred from Sequence or Structural Similarity
more info
 
pattern specification process IEA
Inferred from Electronic Annotation
more info
 
planar cell polarity pathway involved in neural tube closure IEA
Inferred from Electronic Annotation
more info
 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of actin cytoskeleton organization IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
wound healing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
grainyhead-like protein 3 homolog
Names
sister of mammalian grainyhead
transcription factor CP2-like 4
transcription factor hSOM1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009308.2 RefSeqGene

    Range
    4967..40928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001195010.2NP_001181939.1  grainyhead-like protein 3 homolog isoform 4

    See identical proteins and their annotated locations for NP_001181939.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL138902, BC036890
    Consensus CDS
    CCDS53284.1
    UniProtKB/Swiss-Prot
    Q8TE85
    Related
    ENSP00000348333.2, ENST00000356046.6
    Conserved Domains (1) summary
    pfam04516
    Location:164375
    CP2; CP2 transcription factor
  2. NM_021180.3NP_067003.2  grainyhead-like protein 3 homolog isoform 1

    See identical proteins and their annotated locations for NP_067003.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as SOM1) encodes isoform 1.
    Source sequence(s)
    AK315164, AY231160, BC036890
    Consensus CDS
    CCDS251.1
    UniProtKB/Swiss-Prot
    Q8TE85
    Related
    ENSP00000236255.4, ENST00000236255.4
    Conserved Domains (1) summary
    pfam04516
    Location:215426
    CP2; CP2 transcription factor
  3. NM_198173.3NP_937816.1  grainyhead-like protein 3 homolog isoform 2

    See identical proteins and their annotated locations for NP_937816.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as SOM2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK315164, AY231160, BC036890, DA714132
    Consensus CDS
    CCDS44088.1
    UniProtKB/Swiss-Prot
    Q8TE85
    Related
    ENSP00000354943.4, ENST00000361548.8
    Conserved Domains (1) summary
    pfam04516
    Location:210421
    CP2; CP2 transcription factor
  4. NM_198174.3NP_937817.3  grainyhead-like protein 3 homolog isoform 3

    See identical proteins and their annotated locations for NP_937817.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has distinct N- and C-termini and is longer than isoform 1.
    Source sequence(s)
    AK074386, AK315164, DA714132
    Consensus CDS
    CCDS252.2
    UniProtKB/Swiss-Prot
    Q8TE85
    Related
    ENSP00000288955.5, ENST00000350501.9
    Conserved Domains (1) summary
    pfam04516
    Location:210421
    CP2; CP2 transcription factor

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    24319333..24364482
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541870.2XP_011540172.1  grainyhead-like protein 3 homolog isoform X2

    See identical proteins and their annotated locations for XP_011540172.1

    UniProtKB/Swiss-Prot
    Q8TE85
    Conserved Domains (1) summary
    pfam04516
    Location:117328
    CP2; CP2 transcription factor
  2. XM_011541869.1XP_011540171.1  grainyhead-like protein 3 homolog isoform X1

    See identical proteins and their annotated locations for XP_011540171.1

    UniProtKB/Swiss-Prot
    Q8TE85
    Conserved Domains (1) summary
    pfam04516
    Location:164375
    CP2; CP2 transcription factor
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