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GPBP1 GC-rich promoter binding protein 1 [ Homo sapiens (human) ]

Gene ID: 65056, updated on 5-Mar-2024

Summary

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Official Symbol
GPBP1provided by HGNC
Official Full Name
GC-rich promoter binding protein 1provided by HGNC
Primary source
HGNC:HGNC:29520
See related
Ensembl:ENSG00000062194 MIM:608412; AllianceGenome:HGNC:29520
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
GPBP; SSH6; VASCULIN
Summary
This gene was originally isolated by subtractive hybridization of cDNAs expressed in atherosclerotic plaques with a thrombus, and was found to be expressed only in vascular smooth muscle cells. However, a shorter splice variant was found to be more ubiquitously expressed. This protein is suggested to play a role in the development of atherosclerosis. Studies in mice suggest that it may also function as a GC-rich promoter-specific trans-activating transcription factor. Several alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in testis (RPKM 33.9), ovary (RPKM 22.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
5q11.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57174059..57264679)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58002364..58093366)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56469886..56560506)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22576 Neighboring gene Sharpr-MPRA regulatory region 9364 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56389593-56390094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56391121-56391620 Neighboring gene MPRA-validated peak5252 silencer Neighboring gene RLIG1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22577 Neighboring gene Sharpr-MPRA regulatory region 13785 Neighboring gene Sharpr-MPRA regulatory region 13834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56498073-56498573 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:56507443-56507608 Neighboring gene uncharacterized LOC107986381 Neighboring gene TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Vasculin, a novel vascular protein differentially expressed in human atherogenesis. Bijnens AP, et al. Blood, 2003 Oct 15. PMID 12842993
  2. Legionella effector AnkX interacts with host nuclear protein PLEKHN1. Yu X, et al. BMC Microbiol, 2018 Jan 5. PMID 29433439, Free PMC Article
  3. The murine G+C-rich promoter binding protein mGPBP is required for promoter-specific transcription. Hsu LC, et al. Mol Cell Biol, 2003 Dec. PMID 14612417, Free PMC Article
  4. Yeast two-hybrid screening identified WDR77 as a novel interacting partner of TSC22D2. Li Q, et al. Tumour Biol, 2016 Sep. PMID 27337956
  5. TRIP12 ubiquitination of glucocerebrosidase contributes to neurodegeneration in Parkinson's disease. Seo BA, et al. Neuron, 2021 Dec 1. PMID 34644545, Free PMC Article

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This publication discusses both human and mouse GC-rich promoter binding protein.
    Title: Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing.
  2. occurrence of an unusual TG 3' splice site in intron 9
    Title: Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns.
  3. Vasculin is a novel vascular protein differentially expressed in human atherogenesis
    Title: Vasculin, a novel vascular protein differentially expressed in human atherogenesis.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC126339, DKFZp761C169

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
vasculin
Names
vascular wall-linked protein

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.

Genomic

  1. NG_029503.2 RefSeqGene

    Range
    5112..95726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001127235.2 → NP_001120707.2  vasculin isoform 3

    See identical proteins and their annotated locations for NP_001120707.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an additional in-frame coding exon, and uses an alternate in-frame acceptor splice site at another coding exon compared to variant 1. This results in a shorter isoform (3) compared to isoform 1.
    Source sequence(s)
    AC008435, AI200911, BC000267, BC113004, BQ023353, CN358821
    Consensus CDS
    CCDS47212.2
    UniProtKB/Swiss-Prot
    Q86WP2
    Related
    ENSP00000422337.1, ENST00000511209.5
    Conserved Domains (1) summary
    pfam15337
    Location:369 → 449
    Vasculin; Vascular protein family Vasculin-like 1

  2. NM_001127236.2 → NP_001120708.1  vasculin isoform 2

    See identical proteins and their annotated locations for NP_001120708.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional in-frame coding exon compared to variant 1, resulting in a longer isoform (2) with a 7 aa peptide fragment not found in isoform 1.
    Source sequence(s)
    AC008435, AI200911, AL136844, AY226828, BQ023353, CN358821
    Consensus CDS
    CCDS47211.1
    UniProtKB/Swiss-Prot
    Q86WP2
    Related
    ENSP00000264779.6, ENST00000264779.6
    Conserved Domains (1) summary
    pfam15337
    Location:384 → 463
    Vasculin; Vascular protein family Vasculin-like 1

  3. NM_001203246.2 → NP_001190175.1  vasculin isoform 4

    See identical proteins and their annotated locations for NP_001190175.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) is missing an exon in the 5' region compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and a much shorter isoform (4, also known as SSH6-beta) compared to isoform 1. This isoform has been reported to be more ubiquitously expressed compared to the vascular wall specific expression pattern of the longer isoforms (PMID:12842993).
    Source sequence(s)
    AC008435, AI200911, AK311625, AL161991, BQ023353, BU682723, CD657101, CN358821
    Consensus CDS
    CCDS56368.1
    UniProtKB/Swiss-Prot
    Q86WP2
    Related
    ENSP00000421709.2, ENST00000514387.6
    Conserved Domains (1) summary
    pfam15337
    Location:206 → 285
    Vasculin; Vascular protein family Vasculin-like 1

  4. NM_001331037.2 → NP_001317966.1  vasculin isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and contains an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (5) is longer than isoform 1.
    Source sequence(s)
    AC008435, AC034244, KF457923
    Consensus CDS
    CCDS82998.1
    UniProtKB/TrEMBL
    D4PHA4
    Related
    ENSP00000401596.2, ENST00000424459.7
    Conserved Domains (1) summary
    pfam15337
    Location:397 → 477
    Vasculin; Vascular protein family Vasculin-like 1

  5. NM_022913.4 → NP_075064.1  vasculin isoform 1

    See identical proteins and their annotated locations for NP_075064.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript, and encodes isoform 1.
    Source sequence(s)
    AC008435, AI200911, AL136844, BC113004, BQ023353, CN358821, DB271841
    Consensus CDS
    CCDS34162.1
    UniProtKB/Swiss-Prot
    A6NKW3, Q6NSH6, Q86WP2, Q9H0D4, Q9H785, Q9NSN4
    Related
    ENSP00000421202.2, ENST00000506184.7
    Conserved Domains (1) summary
    pfam15337
    Location:377 → 457
    Vasculin; Vascular protein family Vasculin-like 1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    57174059..57264679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    58002364..58093366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86WP2.1 GenPept UniProtKB/Swiss-Prot:Q86WP2

Gene LinkOut

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