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

    Gene ID: 389136, updated on 28-Oct-2024

    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; AllianceGenome:HGNC:24327
    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
    Summary
    Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in placenta (RPKM 19.8), fat (RPKM 7.7) and 12 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See VGLL3 in Genome Data Viewer
    Location:
    3p12.1
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (86937973..86991149, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (87012305..87065510, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (86987123..87040299, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927518 Neighboring gene MPRA-validated peak4735 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:86925274-86925774 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:86940033-86940783 Neighboring gene uncharacterized LOC105377196 Neighboring gene MPRA-validated peak4737 silencer Neighboring gene MPRA-validated peak4738 silencer Neighboring gene phosphoribosyl pyrophosphate amidotransferase pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20109 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 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

    EBI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ38507, DKFZp686O1845

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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, D3DU37, Q504T7
      Related
      ENSP00000381436.2, ENST00000398399.7
      Conserved Domains (1) summary
      pfam07545
      Location:82112
      Vg_Tdu; Vestigial/Tondu family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_006713138.5XP_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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      87012305..87065510 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346475.1XP_054202450.1  transcription cofactor vestigial-like protein 3 isoform X1