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

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Integrated profiling identifies ITGB3BP as prognostic biomarker for hepatocellular carcinoma.
Title: Integrated profiling identifies ITGB3BP as prognostic biomarker for hepatocellular carcinoma.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74928 (e-PCR)
- UniSTS:48678

SHGC-74935 (e-PCR)
- UniSTS:4218

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

NG_030011.2 RefSeqGene

Range

10962..93417

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AA873717, BU853146, CN364268, U37139
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
NM_001347148.2 → NP_001334077.1 centromere protein R isoform 5

Status: REVIEWED

Source sequence(s)

AA873717, AL592218, BG548447, U37139
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

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

63440770..63529187 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416577.1 → XP_047272533.1 centromere protein R isoform X5
XM_047416576.1 → XP_047272532.1 centromere protein R isoform X2

Related

ENSP00000432904.1, ENST00000489099.5
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
XM_047416579.1 → XP_047272535.1 centromere protein R isoform X7
XM_024446041.2 → XP_024301809.2 centromere protein R isoform X4
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
XM_047416578.1 → XP_047272534.1 centromere protein R isoform X6
XM_017000854.3 → XP_016856343.3 centromere protein R isoform X3