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

    Gene ID: 65056, updated on 3-Nov-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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    See GPBP1 in Genome Data Viewer
    Location:
    5q11.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57174059..57264679)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58002364..58093366)
    RS_2024_09 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 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. Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns. Szafranski K, et al. Genome Biol, 2007. PMID 17672918, Free PMC Article

    See all (39) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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