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ITGB3BP integrin subunit beta 3 binding protein [ Homo sapiens (human) ]

Gene ID: 23421, updated on 5-Mar-2024

Summary

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Official Symbol
ITGB3BPprovided by HGNC
Official Full Name
integrin subunit beta 3 binding proteinprovided by HGNC
Primary source
HGNC:HGNC:6157
See related
Ensembl:ENSG00000142856 MIM:605494; AllianceGenome:HGNC:6157
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
CENPR; NRIF3; TAP20; CENP-R; HSU37139
Summary
This gene encodes a transcriptional coregulator that binds to and enhances the activity of members of the nuclear receptor families, thyroid hormone receptors and retinoid X receptors. This protein also acts as a corepressor of NF-kappaB-dependent signaling. This protein induces apoptosis in breast cancer cells through a caspase 2-mediated signaling pathway. This protein is also a component of the centromere-specific histone H3 variant nucleosome associated complex (CENP-NAC) and may be involved in mitotic progression by recruiting the histone H3 variant CENP-A to the centromere. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
Expression
Ubiquitous expression in testis (RPKM 5.3), adrenal (RPKM 3.4) and 25 other tissues See more
Orthologs
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Genomic context

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See ITGB3BP in Genome Data Viewer
Location:
1p31.3
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (63440770..63529187, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (63316450..63404983, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (63906441..63988896, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1124 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 950 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1125 Neighboring gene DnaJ heat shock protein family (Hsp40) member C7 pseudogene Neighboring gene ALG6 alpha-1,3-glucosyltransferase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:63939727-63940644 Neighboring gene uncharacterized LOC102724319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:63988295-63988918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1126 Neighboring gene RNA, 7SL, cytoplasmic 488, pseudogene Neighboring gene EF-hand calcium binding domain 7 Neighboring gene RNA, U7 small nuclear 123 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. Integrated profiling identifies ITGB3BP as prognostic biomarker for hepatocellular carcinoma. Liang Q, et al. Bosn J Basic Med Sci, 2021 Dec 1. PMID 33974527, Free PMC Article
  2. Serine 28 phosphorylation of NRIF3 confers its co-activator function for estrogen receptor-alpha transactivation. Talukder AH, et al. Oncogene, 2008 Sep 4. PMID 18521086, Free PMC Article
  3. The NRIF3 family of transcriptional coregulators induces rapid and profound apoptosis in breast cancer cells. Li D, et al. Mol Cell Biol, 2004 May. PMID 15082778, Free PMC Article
  4. Affinity modulation of platelet integrin alphaIIbbeta3 by beta3-endonexin, a selective binding partner of the beta3 integrin cytoplasmic tail. Kashiwagi H, et al. J Cell Biol, 1997 Jun 16. PMID 9182673, Free PMC Article
  5. β3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis. Cao Z, et al. Biochem Biophys Res Commun, 2021 Aug 20. PMID 34118594

See all (47) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Integrated profiling identifies ITGB3BP as prognostic biomarker for hepatocellular carcinoma.
    Title: Integrated profiling identifies ITGB3BP as prognostic biomarker for hepatocellular carcinoma.
  2. beta3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis.
    Title: β3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis.
  3. Identification of genes in hepatocellular carcinoma induced by non-alcoholic fatty liver disease.
    Title: Identification of genes in hepatocellular carcinoma induced by non-alcoholic fatty liver disease.
  4. The beta3-endonexin can act as a novel anti-angiogenic factor specifically in the response to hypoxia due to its negative impact on the activation of HIF-1.
    Title: The β3-integrin binding protein β3-endonexin is a novel negative regulator of hypoxia-inducible factor-1.
  5. Data propose that CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step that could be important for kinetochores switching into the correct conformation for microtubule-attachment.
    Title: Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. findings suggest that NRIF3-Ser28 is a physiologic target of Pak1 signaling and contributes to the enhanced NRIF3 co-activator activity, leading to coordinated potentiation of ERalpha transactivation
    Title: Serine 28 phosphorylation of NRIF3 confers its co-activator function for estrogen receptor-alpha transactivation.
  8. Results suggest that breast cancer cells contain a novel "death switch" that can be specifically triggered by NRIF3 or death domain 1.
    Title: The NRIF3 family of transcriptional coregulators induces rapid and profound apoptosis in breast cancer cells.
  9. This protein downregulates urokinase-type plasminogen activator receptor promoter activity.
    Title: Role of beta(3)-endonexin in the regulation of NF-kappaB-dependent expression of urokinase-type plasminogen activator receptor.
  10. Metastasis-associated protein 1 interacts with NRIF3, an estrogen-inducible nuclear receptor coregulator
    Title: Metastasis-associated protein 1 interacts with NRIF3, an estrogen-inducible nuclear receptor coregulator.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 CENP-A containing chromatin assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in chromosome segregation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of epithelial cell apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in signal transduction TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm TAS
Traceable Author Statement
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of inner kinetochore IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
centromere protein R
Names
beta 3 endonexin
beta3-endonexin
integrin beta 3 binding protein (beta3-endonexin)
integrin beta-3-binding protein
nuclear receptor-interacting factor 3

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_030011.2 RefSeqGene

    Range
    10962..93417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206739.2 → NP_001193668.1  centromere protein R isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA873717, BC014385, BU853146, BX004807
    Consensus CDS
    CCDS55603.1
    UniProtKB/Swiss-Prot
    Q13352
    Related
    ENSP00000360133.3, ENST00000371092.7
    Conserved Domains (2) summary
    pfam06729
    Location:66 → 200
    CENP-R; Kinetochore component, CENP-R
    pfam13900
    Location:6 → 40
    GVQW; Putative domain of unknown function

  2. NM_001347145.2 → NP_001334074.1  centromere protein R isoform 3

    Status: REVIEWED

    Source sequence(s)
    AA873717, BU853146, CN364268, U37139

  3. NM_001347147.2 → NP_001334076.1  centromere protein R isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592218, BU633831, BX004807
    Conserved Domains (1) summary
    pfam06729
    Location:27 → 162
    CENP-R; Kinetochore component, CENP-R

  4. NM_001347148.2 → NP_001334077.1  centromere protein R isoform 5

    Status: REVIEWED

    Source sequence(s)
    AA873717, AL592218, BG548447, U37139

  5. NM_014288.5 → NP_055103.3  centromere protein R isoform 2

    See identical proteins and their annotated locations for NP_055103.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. Isoform 2 is shorter, compared to isoform 1.
    Source sequence(s)
    AA873717, BC009929, BU853146
    Consensus CDS
    CCDS30736.1
    UniProtKB/Swiss-Prot
    B2R7D8, Q13352, Q13353, Q5RJ42, Q5RJ44, Q5RJ45, Q7KYX2, Q96CD5, Q9UKB6
    Related
    ENSP00000271002.10, ENST00000271002.15
    Conserved Domains (1) summary
    pfam06729
    Location:27 → 161
    CENP-R; Kinetochore component, CENP-R

RNA

  1. NR_045147.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an additional exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA873717, BU853146, U37139

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    63440770..63529187 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416577.1 → XP_047272533.1  centromere protein R isoform X5

  2. XM_047416576.1 → XP_047272532.1  centromere protein R isoform X2

    Related
    ENSP00000432904.1, ENST00000489099.5

  3. XM_024446042.2 → XP_024301810.1  centromere protein R isoform X4

    Conserved Domains (1) summary
    pfam06729
    Location:1 → 122
    CENP-R; Kinetochore component, CENP-R

  4. XM_047416579.1 → XP_047272535.1  centromere protein R isoform X7

  5. XM_024446041.2 → XP_024301809.2  centromere protein R isoform X4

  6. XM_017000853.3 → XP_016856342.2  centromere protein R isoform X1

    Conserved Domains (1) summary
    pfam06729
    Location:27 → 162
    CENP-R; Kinetochore component, CENP-R

  7. XM_047416578.1 → XP_047272534.1  centromere protein R isoform X6

  8. XM_017000854.3 → XP_016856343.3  centromere protein R isoform X3

RNA

  1. XR_007058557.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    63316450..63404983 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335681.1 → XP_054191656.1  centromere protein R isoform X5

  2. XM_054335678.1 → XP_054191653.1  centromere protein R isoform X2

  3. XM_054335684.1 → XP_054191659.1  centromere protein R isoform X4

  4. XM_054335679.1 → XP_054191654.1  centromere protein R isoform X3

  5. XM_054335682.1 → XP_054191657.1  centromere protein R isoform X6

  6. XM_054335683.1 → XP_054191658.1  centromere protein R isoform X7

  7. XM_054335680.1 → XP_054191655.1  centromere protein R isoform X4

  8. XM_054335677.1 → XP_054191652.1  centromere protein R isoform X1

  9. XM_054335685.1 → XP_054191660.1  centromere protein R isoform X8

RNA

  1. XR_008485969.1 RNA Sequence

  2. XR_008485968.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13352.2 GenPept UniProtKB/Swiss-Prot:Q13352

Gene LinkOut

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