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

Gene ID: 65056, updated on 29-Mar-2020

Summary

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
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

Genomic context

See GPBP1 in Genome Data Viewer
Location:
5q11.2
Exon count:
14
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (57173948..57264679)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56469676..56560506)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9364 Neighboring gene chromosome 12 open reading frame 29 pseudogene Neighboring gene Sharpr-MPRA regulatory region 13785 Neighboring gene uncharacterized LOC107986381 Neighboring gene TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) pseudogene

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC126339, DKFZp761C169

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
vasculin
Names
vascular wall-linked 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.

Genomic

  1. NG_029503.2 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001127235.2NP_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:369449
    Vasculin; Vascular protein family Vasculin-like 1
  2. NM_001127236.2NP_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:384463
    Vasculin; Vascular protein family Vasculin-like 1
  3. NM_001203246.1NP_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:206285
    Vasculin; Vascular protein family Vasculin-like 1
  4. NM_001331037.1NP_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:397476
    Vasculin; Vascular protein family Vasculin-like 1
  5. NM_022913.4NP_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
    Q86WP2
    Related
    ENSP00000421202.2, ENST00000506184.7
    Conserved Domains (1) summary
    pfam15337
    Location:377456
    Vasculin; Vascular protein family Vasculin-like 1

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_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    57173948..57264679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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