UIMC1 ubiquitin interaction motif containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UIMC1provided by HGNC
Official Full Name: ubiquitin interaction motif containing 1provided by HGNC
Primary source: HGNC:HGNC:30298
See related: Ensembl:ENSG00000087206 MIM:609433; AllianceGenome:HGNC:30298
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: RAP80; X2HRIP110
Summary: This gene encodes a nuclear protein that interacts with Brca1 (breast cancer 1) in a complex to recognize and repair DNA lesions. This protein binds ubiquitinated lysine 63 of histone H2A and H2AX. This protein may also function as a repressor of transcription. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
Expression: Broad expression in testis (RPKM 26.7), bone marrow (RPKM 12.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q35.2

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (176905005..177022602, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (177450819..177549966, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (176332006..176433795, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair.
Title: RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair.
BRCA1 poly-ADP ribosylation (PARsylation) and the presence of BRCA1-bound RAP80 are critical for the normal interaction of BRCA1 with some of its partners (e.g., CtIP and BACH1).
Title: RAP80 and BRCA1 PARsylation protect chromosome integrity by preventing retention of BRCA1-B/C complexes in DNA repair foci.
Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2alpha, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains
Title: Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation.
RAP80 positively regulated the stability of USP13 to promote cell proliferation of esophageal cancer cells.
Title: RAP80 is an independent prognosis biomarker for the outcome of patients with esophageal squamous cell carcinoma.
RAP80-BRCA1 complex foci formation is regulated by USP13.USP13 interacts with and deubiquitinates RAP80.RAP80 role in the DNA damage response.
Title: USP13 regulates the RAP80-BRCA1 complex dependent DNA damage response.
The RAP80 deficiency reduces the protein level of p32 and p32 dependent mitochondrial translating proteins such as Rieske and COX1.
Title: RAP80 binds p32 to preserve the functional integrity of mitochondria.
Low RAP80 mRNA expression correlates with sporadic high-grade serous ovarian carcinoma.
Title: Low RAP80 mRNA expression correlates with shorter survival in sporadic high-grade serous ovarian carcinoma.
RAP80 is a critical gatekeeper in impeding epithelial-mesenchymal transition-induced metastasis and malignant phenotypes of cancer as well as preserving DNA integrity.
Title: RAP80 regulates epithelial-mesenchymal transition related with metastasis and malignancy of cancer.
Data suggest that RAP80 SIM (SUMO interacting motif) binds SUMO-2; both specificity and affinity are enhanced through phosphorylation of canonical CK2 (casein kinase 2) site within the SIM.
Title: Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80.
Impaired TIP60-mediated H4K16 acetylation accounts for the aberrant chromatin accumulation of 53BP1 and RAP80 in Fanconi anemia pathway-deficient cells.
Title: Impaired TIP60-mediated H4K16 acetylation accounts for the aberrant chromatin accumulation of 53BP1 and RAP80 in Fanconi anemia pathway-deficient cells.

Submit: New GeneRIF Correction See all GeneRIFs (45)

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

EBI GWAS Catalog

Description
Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH46284 (e-PCR)
- UniSTS:56858

D17S813E (e-PCR)
- UniSTS:92461

WI-14295 (e-PCR)
- UniSTS:867

RH98513 (e-PCR)
- UniSTS:83580

G19848 (e-PCR)
- UniSTS:60028

A002A19 (e-PCR)
- UniSTS:60029

D6S972 (e-PCR)
- UniSTS:149389

SHGC-132904 (e-PCR)
- UniSTS:173975

SHGC-56577 (e-PCR)
- UniSTS:43494

STS_06 (e-PCR)
- UniSTS:257016

Homology

Homologs of the UIMC1 gene: The UIMC1 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and chicken.
Orthologs from Annotation Pipeline: 435 organisms have orthologs with human gene UIMC1
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables K63-linked polyubiquitin modification-dependent protein binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables K63-linked polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables histone binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion 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 chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in histone H2A K63-linked deubiquitination	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in histone H2A K63-linked deubiquitination	IC Inferred by Curator more info	PubMed
involved_in histone H2A K63-linked deubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic G2 DNA damage checkpoint signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic G2/M transition checkpoint	IC Inferred by Curator more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA repair	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA repair	IC Inferred by Curator more info	PubMed
involved_in response to ionizing radiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of BRCA1-A complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
part_of BRCA1-A complex	IC Inferred by Curator more info	PubMed
part_of BRCA1-A complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: BRCA1-A complex subunit RAP80

Names: receptor-associated protein 80; retinoid X receptor-interacting protein 110

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.

mRNA and Protein(s)

NM_001199297.2 → NP_001186226.1 BRCA1-A complex subunit RAP80 isoform 1

See identical proteins and their annotated locations for NP_001186226.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein (isoform 1).

Source sequence(s)

AK023044, BC006078, BP270983, BX537376, CF994701

Consensus CDS

CCDS4408.1

UniProtKB/Swiss-Prot

Q96RL1, Q9UHX7

UniProtKB/TrEMBL

A0A024R7R0
NM_001199298.2 → NP_001186227.1 BRCA1-A complex subunit RAP80 isoform 1

See identical proteins and their annotated locations for NP_001186227.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein (isoform 1).

Source sequence(s)

AC027318, AF349313, BP270983, BX537376

Consensus CDS

CCDS4408.1

UniProtKB/Swiss-Prot

Q96RL1, Q9UHX7

UniProtKB/TrEMBL

A0A024R7R0

Related

ENSP00000421926.1, ENST00000511320.6
NM_001317961.1 → NP_001304890.1 BRCA1-A complex subunit RAP80 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an exon in the 5' UTR and uses an alternate in-frame splice site compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC027318, BC032561, BP270983, BX537376, CF994701

Consensus CDS

CCDS83050.1

UniProtKB/Swiss-Prot

Q96RL1

Related

ENSP00000427480.1, ENST00000506128.5
NM_016290.4 → NP_057374.3 BRCA1-A complex subunit RAP80 isoform 1

See identical proteins and their annotated locations for NP_057374.3

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein (isoform 1).

Source sequence(s)

AC027318, BX537376

Consensus CDS

CCDS4408.1

UniProtKB/Swiss-Prot

Q96RL1, Q9UHX7

UniProtKB/TrEMBL

A0A024R7R0

Related

ENSP00000366434.4, ENST00000377227.8

RNA

NR_146149.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in its 5' exon, lacks an alternate internal exon and contains an alternate internal 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)

AC027318, AF113538, AF349313, BP270983, BX537376, EF077643
NR_146150.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate splice site in its 5' exon and at an internal 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)

AC027318, AK023044, BC006078, BP270983, BX537376, CF994701

Related

ENST00000512031.5