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

    Gene ID: 23421, updated on 28-Oct-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (63440770..63529187, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (63316450..63404983, complement)
    RS_2024_09 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 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. 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
    2. 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
    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. beta3-endonexin as a novel inhibitor of cyclin A-associated kinase. Ohtoshi A, et al. Biochem Biophys Res Commun, 2000 Jan 27. PMID 10673397

    See all (49) 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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    NEW Try the new Transcript table

    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_2024_08

    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

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

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