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

Gene ID: 5932, updated on 22-Aug-2021

Summary

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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
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; 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

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See RBBP8 in Genome Data Viewer
Location:
18q11.2
Exon count:
24
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (22914121..23026486)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (20513291..20606449)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927571 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 2 Neighboring gene microRNA 4741 Neighboring gene RNA, 7SL, cytoplasmic 745, pseudogene Neighboring gene Sharpr-MPRA regulatory region 2761 Neighboring gene Cdk5 and Abl enzyme substrate 1 Neighboring gene transmembrane protein 241

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. CtIP suppresses primary microRNA maturation and promotes metastasis of colon cancer cells in a xenograft mouse model. Ren J, et al. J Biol Chem, 2021 Jan-Jun. PMID 33901493, Free PMC Article
  2. SUMOylation mediates CtIP's functions in DNA end resection and replication fork protection. Locke AJ, et al. Nucleic Acids Res, 2021 Jan 25. PMID 33406258, Free PMC Article
  3. Phosphorylated CtIP bridges DNA to promote annealing of broken ends. Öz R, et al. Proc Natl Acad Sci U S A, 2020 Sep 1. PMID 32817418, Free PMC Article
  4. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability. Zarrizi R, et al. J Clin Invest, 2020 Aug 3. PMID 32379725, Free PMC Article
  5. The internal region of CtIP negatively regulates DNA end resection. Howard SM, et al. Nucleic Acids Res, 2020 Jun 4. PMID 32347940, Free PMC Article

See all (179) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Prognosis value of RBBP8 expression in plasma cell myeloma.
    Title: Prognosis value of RBBP8 expression in plasma cell myeloma.
  3. SCF(SKP2) regulates APC/C(CDH1)-mediated degradation of CTIP to adjust DNA-end resection in G2-phase.
    Title: SCF<sup>SKP2</sup> regulates APC/C<sup>CDH1</sup>-mediated degradation of CTIP to adjust DNA-end resection in G<sub>2</sub>-phase.
  4. SUMOylation mediates CtIP's functions in DNA end resection and replication fork protection.
    Title: SUMOylation mediates CtIP's functions in DNA end resection and replication fork protection.
  5. Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.
    Title: Germline RBBP8 variants associated with early-onset breast cancer compromise replication fork stability.
  6. RBBP8/CtIP suppresses P21 expression by interacting with CtBP and BRCA1 in gastric cancer.
    Title: RBBP8/CtIP suppresses P21 expression by interacting with CtBP and BRCA1 in gastric cancer.
  7. Phosphorylated CtIP bridges DNA to promote annealing of broken ends.
    Title: Phosphorylated CtIP bridges DNA to promote annealing of broken ends.
  8. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP.
    Title: DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP.
  9. The internal region of CtIP negatively regulates DNA end resection.
    Title: The internal region of CtIP negatively regulates DNA end resection.
  10. CtIP contributes to non-homologous end joining formation through interacting with ligase IV and promotion of TMZ resistance in glioma cells.
    Title: CtIP contributes to non-homologous end joining formation through interacting with ligase IV and promotion of TMZ resistance in glioma cells.
Submit: New GeneRIF Correction See all GeneRIFs (83)

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

Associated conditions

Description Tests
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.
GeneReviews: Not available
Genome-wide association study of intracranial aneurysm identifies three new risk loci.
GeneReviews: Not available
Many sequence variants affecting diversity of adult human height.
GeneReviews: Not available
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
GeneReviews: Not available
Microcephaly with mental retardation and digital anomalies
MedGen: C0796063 OMIM: 251255 GeneReviews: Not available
Compare labs
Seckel syndrome 2
MedGen: C1847572 OMIM: 606744 GeneReviews: Not available
Compare labs

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 RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables Y-form DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-strand/single-strand DNA junction binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables flap-structured DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
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
 PubMed 
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 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 IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in response to estradiol IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
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 TAS
Traceable Author Statement
more info
 PubMed 
is_active_in site of double-strand break IBA
Inferred from Biological aspect of Ancestor
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

  1. NG_012121.1 RefSeqGene

    Range
    4997..98155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  2. 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
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  3. 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/Swiss-Prot
    Q99708
    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: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    22914121..23026486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526132.2 → XP_011524434.1  DNA endonuclease RBBP8 isoform X1

    See identical proteins and their annotated locations for XP_011524434.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  2. XM_006722520.2 → XP_006722583.1  DNA endonuclease RBBP8 isoform X1

    See identical proteins and their annotated locations for XP_006722583.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  3. XM_006722519.2 → XP_006722582.1  DNA endonuclease RBBP8 isoform X1

    See identical proteins and their annotated locations for XP_006722582.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  4. XM_005258325.3 → XP_005258382.1  DNA endonuclease RBBP8 isoform X2

    Conserved Domains (1) summary
    pfam10482
    Location:20 → 138
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

  5. XM_024451233.1 → XP_024307001.1  DNA endonuclease RBBP8 isoform X3

    Conserved Domains (2) summary
    pfam08573
    Location:699 → 759
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:1 → 40
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain

  6. XM_017025916.1 → XP_016881405.1  DNA endonuclease RBBP8 isoform X5

  7. XM_006722521.2 → XP_006722584.1  DNA endonuclease RBBP8 isoform X1

    See identical proteins and their annotated locations for XP_006722584.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    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

  8. XM_005258326.4 → XP_005258383.1  DNA endonuclease RBBP8 isoform X4

    Conserved Domains (1) summary
    pfam08573
    Location:523 → 583
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99708.2 GenPept UniProtKB/Swiss-Prot:Q99708

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