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VGLL3 vestigial like family member 3 [ Homo sapiens (human) ]

Gene ID: 389136, updated on 12-Oct-2019

Summary

Official Symbol
VGLL3provided by HGNC
Official Full Name
vestigial like family member 3provided by HGNC
Primary source
HGNC:HGNC:24327
See related
Ensembl:ENSG00000206538 MIM:609980
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
VGL3; VGL-3
Expression
Biased expression in placenta (RPKM 19.8), fat (RPKM 7.7) and 12 other tissues See more
Orthologs

Genomic context

See VGLL3 in Genome Data Viewer
Location:
3p12.1
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (86937973..86991149, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (86987123..87040412, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927518 Neighboring gene uncharacterized LOC105377196 Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene 1 Neighboring gene long intergenic non-protein coding RNA 506

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

NHGRI GWAS Catalog

Description
A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
NHGRI GWA Catalog
Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ38507, DKFZp686O1845

Gene Ontology Provided by GOA

Process Evidence Code Pubs
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
transcription cofactor vestigial-like protein 3
Names
colon carcinoma related protein

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.

mRNA and Protein(s)

  1. NM_001320493.2NP_001307422.1  transcription cofactor vestigial-like protein 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate 3' terminal exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC108709, BC094780, DA828655
    Consensus CDS
    CCDS82807.1
    UniProtKB/Swiss-Prot
    A8MV65
    Related
    ENSP00000373199.3, ENST00000383698.3
    Conserved Domains (1) summary
    pfam07545
    Location:82112
    Vg_Tdu; Vestigial/Tondu family
  2. NM_001320494.2NP_001307423.1  transcription cofactor vestigial-like protein 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC108709
    Conserved Domains (1) summary
    pfam07545
    Location:4259
    Vg_Tdu; Vestigial/Tondu family
  3. NM_016206.4NP_057290.2  transcription cofactor vestigial-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_057290.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA455617, AC108709, AI379920, BC094780, DA828655, DB319377
    Consensus CDS
    CCDS43110.1
    UniProtKB/Swiss-Prot
    A8MV65
    Related
    ENSP00000381436.2, ENST00000398399.7
    Conserved Domains (1) summary
    pfam07545
    Location:82112
    Vg_Tdu; Vestigial/Tondu family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    86937973..86991149 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713138.4XP_006713201.1  transcription cofactor vestigial-like protein 3 isoform X1

    See identical proteins and their annotated locations for XP_006713201.1

    Conserved Domains (1) summary
    pfam07545
    Location:81111
    Vg_Tdu; Vestigial/Tondu family
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