RBBP8 RB binding protein 8, endonuclease [Homo sapiens (human)] - Gene

Summary

Official Symbol: RBBP8provided by HGNC
Official Full Name: RB binding protein 8, endonucleaseprovided by HGNC
Primary source: HGNC:HGNC:9891
See related: Ensembl:ENSG00000101773 MIM:604124; AllianceGenome:HGNC:9891
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: RIM; COM1; CTIP; JWDS; SAE2; JAWAD; SCKL2
Summary: The protein encoded by this gene is a ubiquitously expressed nuclear protein. It is found among several proteins that bind directly to retinoblastoma protein, which regulates cell proliferation. This protein complexes with transcriptional co-repressor CTBP. It is also associated with BRCA1 and is thought to modulate the functions of BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. It is suggested that this gene may itself be a tumor suppressor acting in the same pathway as BRCA1. Three transcript variants encoding two different isoforms have been found for this gene. More transcript variants exist, but their full-length natures have not been determined. [provided by RefSeq, Jul 2008]
Expression: Broad expression in testis (RPKM 11.3), kidney (RPKM 6.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 18q11.2

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (22914139..23026486)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (22991142..23219842)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (20513291..20606449)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

NUDT16 regulates CtIP PARylation to dictate homologous recombination repair.
Title: NUDT16 regulates CtIP PARylation to dictate homologous recombination repair.
A novel RBBP8(p.E281*) germline mutation is a predisposing mutation in familial hereditary cancer syndrome.
Title: A novel RBBP8(p.E281*) germline mutation is a predisposing mutation in familial hereditary cancer syndrome.
Prognostic Significance of mRNA Expression RBBP8 or Its Methylation in Gliomas.
Title: Prognostic Significance of mRNA Expression RBBP8 or Its Methylation in Gliomas.
SIAH2 regulates DNA end resection and replication fork recovery by promoting CtIP ubiquitination.
Title: SIAH2 regulates DNA end resection and replication fork recovery by promoting CtIP ubiquitination.
The mechanism of radiotherapy for lung adenocarcinoma in promoting protein SIRT6-mediated deacetylation of RBBP8 to enhance the sensitivity of targeted therapy.
Title: The mechanism of radiotherapy for lung adenocarcinoma in promoting protein SIRT6-mediated deacetylation of RBBP8 to enhance the sensitivity of targeted therapy.
The Ubiquitin Ligase RNF138 Cooperates with CtIP to Stimulate Resection of Complex DNA Double-Strand Breaks in Human G1-Phase Cells.
Title: The Ubiquitin Ligase RNF138 Cooperates with CtIP to Stimulate Resection of Complex DNA Double-Strand Breaks in Human G1-Phase Cells.
IKZF1 selectively enhances homologous recombination repair by interacting with CtIP and USP7 in multiple myeloma.
Title: IKZF1 selectively enhances homologous recombination repair by interacting with CtIP and USP7 in multiple myeloma.
RNAi Screening Uncovers a Synthetic Sick Interaction between CtIP and the BARD1 Tumor Suppressor.
Title: RNAi Screening Uncovers a Synthetic Sick Interaction between CtIP and the BARD1 Tumor Suppressor.
A 24-generation-old founder mutation impairs splicing of RBBP8 in Pakistani families affected with Jawad syndrome.
Title: A 24-generation-old founder mutation impairs splicing of RBBP8 in Pakistani families affected with Jawad syndrome.
CtIP suppresses primary microRNA maturation and promotes metastasis of colon cancer cells in a xenograft mouse model.
Title: CtIP suppresses primary microRNA maturation and promotes metastasis of colon cancer cells in a xenograft mouse model.

Submit: New GeneRIF Correction See all GeneRIFs (92)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Jawad syndrome MedGen: C0796063 OMIM: 251255 GeneReviews: Not available	not available
Seckel syndrome 2 MedGen: C1847572 OMIM: 606744 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of intracranial aneurysm identifies three new risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. 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

SHGC-57607 (e-PCR)
- UniSTS:72504

D18S78 (e-PCR), detects polymorphism
- UniSTS:147771

D18S866 (e-PCR), detects polymorphism
- UniSTS:60557

SHGC-58091 (e-PCR)
- UniSTS:59073

D7S663 (e-PCR), detects polymorphism
- UniSTS:21462

RH70701 (e-PCR)
- UniSTS:35320

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction 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
enables single-stranded DNA endodeoxyribonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing involved in repair via single-strand annealing	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA double-strand break processing involved in repair via single-strand annealing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	TAS Traceable Author Statement more info	PubMed
involved_in DNA strand resection involved in replication fork processing	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA strand resection involved in replication fork processing	NAS Non-traceable Author Statement more info	PubMed
involved_in G1/S transition of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in blastocyst hatching	IEA Inferred from Electronic Annotation more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via homologous recombination	IDA Inferred from Direct Assay more info	PubMed
involved_in double-strand break repair via homologous recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homologous recombination	NAS Non-traceable Author Statement more info	PubMed
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in mitotic G2/M transition checkpoint	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of BRCA1-C complex	IPI Inferred from Physical Interaction more info	PubMed
located_in intracellular membrane-bounded organelle	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	NAS Non-traceable Author Statement more info	PubMed
is_active_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: DNA endonuclease RBBP8

Names: CTBP-interacting protein; RBBP-8; retinoblastoma binding protein 8; sporulation in the absence of SPO11 protein 2 homolog

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_012121.2 RefSeqGene

Range

24191..117349

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002894.3 → NP_002885.1 DNA endonuclease RBBP8 isoform a

See identical proteins and their annotated locations for NP_002885.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 both encode isoform a.

Source sequence(s)

AC091147, AF043431, BG723261

Consensus CDS

CCDS11875.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Related

ENSP00000323050.5, ENST00000327155.10

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
NM_203291.2 → NP_976036.1 DNA endonuclease RBBP8 isoform a

See identical proteins and their annotated locations for NP_976036.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode isoform a.

Source sequence(s)

AC091147, AF043431, BC001170, BU187672, U72066

Consensus CDS

CCDS11875.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Related

ENSP00000382628.2, ENST00000399722.6

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
NM_203292.2 → NP_976037.1 DNA endonuclease RBBP8 isoform b

See identical proteins and their annotated locations for NP_976037.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.

Source sequence(s)

AC091147, BC001170, BX648221, U72066

Consensus CDS

CCDS11874.1

UniProtKB/TrEMBL

I6L8A6

Related

ENSP00000382630.2, ENST00000399725.6

Conserved Domains (1) summary

pfam10482
Location:20 → 138

CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

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_000018.10 Reference GRCh38.p14 Primary Assembly

Range

22914139..23026486

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047437728.1 → XP_047293684.1 DNA endonuclease RBBP8 isoform X1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
XM_006722519.3 → XP_006722582.1 DNA endonuclease RBBP8 isoform X1

See identical proteins and their annotated locations for XP_006722582.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
XM_011526132.3 → XP_011524434.1 DNA endonuclease RBBP8 isoform X1

See identical proteins and their annotated locations for XP_011524434.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
XM_006722520.3 → XP_006722583.1 DNA endonuclease RBBP8 isoform X1

See identical proteins and their annotated locations for XP_006722583.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
XM_006722521.3 → XP_006722584.1 DNA endonuclease RBBP8 isoform X1

See identical proteins and their annotated locations for XP_006722584.1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708

UniProtKB/TrEMBL

I6L8A6

Conserved Domains (2) summary

pfam08573
Location:797 → 857

SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
XM_047437729.1 → XP_047293685.1 DNA endonuclease RBBP8 isoform X2
XM_005258325.4 → XP_005258382.1 DNA endonuclease RBBP8 isoform X2

UniProtKB/TrEMBL

I6L8A6

Conserved Domains (1) summary

pfam10482
Location:20 → 138

CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
XM_047437727.1 → XP_047293683.1 DNA endonuclease RBBP8 isoform X1

UniProtKB/Swiss-Prot

A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
XM_047437731.1 → XP_047293687.1 DNA endonuclease RBBP8 isoform X2
XM_047437730.1 → XP_047293686.1 DNA endonuclease RBBP8 isoform X2
XM_047437732.1 → XP_047293688.1 DNA endonuclease RBBP8 isoform X3