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VGLL4 vestigial like family member 4 [ Homo sapiens (human) ]

Gene ID: 9686, updated on 10-Oct-2024

Summary

Official Symbol
VGLL4provided by HGNC
Official Full Name
vestigial like family member 4provided by HGNC
Primary source
HGNC:HGNC:28966
See related
Ensembl:ENSG00000144560 MIM:618692; AllianceGenome:HGNC:28966
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
VGL-4
Summary
Predicted to enable transcription coactivator binding activity. Involved in negative regulation of Wnt signaling pathway; negative regulation of cell growth; and negative regulation of hippo signaling. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 26.1), thyroid (RPKM 18.5) and 25 other tissues See more
Orthologs
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Genomic context

See VGLL4 in Genome Data Viewer
Location:
3p25.3-p25.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (11556067..11721815, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (11551371..11717542, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (11597541..11762013, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19429 Neighboring gene ribosomal protein L13a pseudogene 27 Neighboring gene autophagy related 7 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:11405755-11406954 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:11521898-11522503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11574579-11575079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11586483-11587050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11587827-11588328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11588329-11588828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11616238-11617058 Neighboring gene CSTB pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11624893-11625731 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11634691-11635222 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11635223-11635753 Neighboring gene Sharpr-MPRA regulatory region 8254 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:11642749-11643347 and GRCh37_chr3:11643348-11643945 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11650998-11651770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11680477-11681428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19433 Neighboring gene Sharpr-MPRA regulatory region 9131 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19434 Neighboring gene TAM41 mitochondrial translocator assembly and maintenance homolog Neighboring gene Sharpr-MPRA regulatory region 5418 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:11826643-11827198 Neighboring gene FANCD2 pseudogene 2 Neighboring gene CYCS pseudogene 12

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 association study on common SNPs and rare CNVs in anorexia nervosa.
EBI GWAS Catalog
Common variants in left/right asymmetry genes and pathways are associated with relative hand skill.
EBI GWAS Catalog
Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA0121

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription coactivator binding IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
transcription cofactor vestigial-like protein 4
Names
Vestigial-like 4
vestigial like 4

NCBI Reference Sequences (RefSeq)

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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_001128219.3NP_001121691.1  transcription cofactor vestigial-like protein 4 isoform a

    See identical proteins and their annotated locations for NP_001121691.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    BU682809, D50911, DA383197, DA386938, DR159250
    Consensus CDS
    CCDS46754.1
    Related
    ENSP00000404251.2, ENST00000430365.7
    Conserved Domains (2) summary
    smart00711
    Location:240255
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:14230
    VGLL4; Transcription cofactor vestigial-like protein 4
  2. NM_001128220.3NP_001121692.1  transcription cofactor vestigial-like protein 4 isoform c

    See identical proteins and their annotated locations for NP_001121692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK307708, BU682809, D50911
    Consensus CDS
    CCDS46755.1
    UniProtKB/TrEMBL
    Q0H0I7
    Related
    ENSP00000416615.2, ENST00000451674.6
    Conserved Domains (2) summary
    smart00711
    Location:154169
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:6144
    VGLL4; Transcription cofactor vestigial-like protein 4
  3. NM_001128221.3NP_001121693.1  transcription cofactor vestigial-like protein 4 isoform d

    See identical proteins and their annotated locations for NP_001121693.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK308761, BU682809, D50911
    Consensus CDS
    CCDS46756.1
    UniProtKB/TrEMBL
    Q0H0I7
    Related
    ENSP00000402878.2, ENST00000424529.6
    Conserved Domains (2) summary
    smart00711
    Location:150165
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1140
    VGLL4; Transcription cofactor vestigial-like protein 4
  4. NM_001284390.2NP_001271319.1  transcription cofactor vestigial-like protein 4 isoform e

    See identical proteins and their annotated locations for NP_001271319.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (e) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    BC000763, BU682809, D50911, DA383197
    Consensus CDS
    CCDS68343.1
    UniProtKB/TrEMBL
    A0A0A6YYI5
    Related
    ENSP00000413030.2, ENST00000426568.5
    Conserved Domains (2) summary
    smart00711
    Location:239254
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:27229
    VGLL4; Transcription cofactor vestigial-like protein 4
  5. NM_001284391.1NP_001271320.1  transcription cofactor vestigial-like protein 4 isoform f

    See identical proteins and their annotated locations for NP_001271320.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (f) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC022001, AI809612, AK300344, BU682809, D50911, DA383197
    Consensus CDS
    CCDS68342.1
    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9, Q0H0I7
    Related
    ENSP00000404624.1, ENST00000413604.5
    Conserved Domains (2) summary
    smart00711
    Location:175190
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1165
    VGLL4; Transcription cofactor vestigial-like protein 4
  6. NM_014667.4NP_055482.2  transcription cofactor vestigial-like protein 4 isoform b

    See identical proteins and their annotated locations for NP_055482.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains alternate 5' exon structure and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AK130542, BU682809, D50911, DA383197
    Consensus CDS
    CCDS2606.1
    UniProtKB/Swiss-Prot
    A0A075B6E4, B4DTS7, G5E9M7, J3KN68, Q14135, Q7L5V0, Q9BQ78
    Related
    ENSP00000273038.3, ENST00000273038.7
    Conserved Domains (2) summary
    smart00711
    Location:234249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8223
    VGLL4; Transcription cofactor vestigial-like protein 4

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
    11556067..11721815 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449259.1XP_047305215.1  transcription cofactor vestigial-like protein 4 isoform X1

  2. XM_024453835.2XP_024309603.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/Swiss-Prot
    A0A075B6E4, B4DTS7, G5E9M7, J3KN68, Q14135, Q7L5V0, Q9BQ78
    Conserved Domains (2) summary
    smart00711
    Location:234249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8223
    VGLL4; Transcription cofactor vestigial-like protein 4
  3. XM_024453836.2XP_024309604.1  transcription cofactor vestigial-like protein 4 isoform X3

    UniProtKB/Swiss-Prot
    A0A075B6E4, B4DTS7, G5E9M7, J3KN68, Q14135, Q7L5V0, Q9BQ78
    Conserved Domains (2) summary
    smart00711
    Location:234249
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:8223
    VGLL4; Transcription cofactor vestigial-like protein 4
  4. XM_047449260.1XP_047305216.1  transcription cofactor vestigial-like protein 4 isoform X2

  5. XM_047449261.1XP_047305217.1  transcription cofactor vestigial-like protein 4 isoform X4

    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9
  6. XM_011534269.2XP_011532571.1  transcription cofactor vestigial-like protein 4 isoform X4

    See identical proteins and their annotated locations for XP_011532571.1

    UniProtKB/TrEMBL
    A0A024R2F0, A0A9K3Y712, G5E9M9, Q0H0I7
    Conserved Domains (2) summary
    smart00711
    Location:175190
    TDU; Short repeats in human TONDU, fly vestigial and other proteins
    pfam15245
    Location:1165
    VGLL4; Transcription cofactor vestigial-like protein 4
  7. XM_047449262.1XP_047305218.1  transcription cofactor vestigial-like protein 4 isoform X5

  8. XM_024453837.2XP_024309605.1  transcription cofactor vestigial-like protein 4 isoform X7

    UniProtKB/TrEMBL
    E7EQU6
    Related
    ENSP00000394439.1, ENST00000418000.5
    Conserved Domains (1) summary
    pfam15245
    Location:8204
    VGLL4; Transcription cofactor vestigial-like protein 4
  9. XM_047449263.1XP_047305219.1  transcription cofactor vestigial-like protein 4 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    11551371..11717542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348499.1XP_054204474.1  transcription cofactor vestigial-like protein 4 isoform X1

  2. XM_054348501.1XP_054204476.1  transcription cofactor vestigial-like protein 4 isoform X3

  3. XM_054348502.1XP_054204477.1  transcription cofactor vestigial-like protein 4 isoform X3

  4. XM_054348500.1XP_054204475.1  transcription cofactor vestigial-like protein 4 isoform X2

  5. XM_054348503.1XP_054204478.1  transcription cofactor vestigial-like protein 4 isoform X8

  6. XM_054348507.1XP_054204482.1  transcription cofactor vestigial-like protein 4 isoform X8

  7. XM_054348504.1XP_054204479.1  transcription cofactor vestigial-like protein 4 isoform X5

  8. XM_054348506.1XP_054204481.1  transcription cofactor vestigial-like protein 4 isoform X7

  9. XM_054348505.1XP_054204480.1  transcription cofactor vestigial-like protein 4 isoform X6