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

Gene ID: 5932, updated on 29-May-2016
Official Symbol
RBBP8provided by HGNC
Official Full Name
RB binding protein 8, endonucleaseprovided by HGNC
Primary source
HGNC:HGNC:9891
See related
Ensembl:ENSG00000101773 HPRD:04990; MIM:604124; Vega:OTTHUMG00000131769
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]
Orthologs
Location:
18q11.2
Exon count:
24
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 18 NC_000018.10 (22914121..23026488)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (20513295..20606451)

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 uncharacterized LOC105372022 Neighboring gene Cdk5 and Abl enzyme substrate 1 Neighboring gene transmembrane protein 241

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Microcephaly with mental retardation and digital anomalies
MedGen: C2673414 OMIM: 251255 GeneReviews: Not available
Compare labs
Seckel syndrome 2
MedGen: C1847572 OMIM: 606744 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.
NHGRI GWA Catalog
Genome-wide association study of intracranial aneurysm identifies three new risk loci.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog
  • BARD1 signaling events, organism-specific biosystem (from Pathway Interaction Database)
    BARD1 signaling events, organism-specific biosystem
    BARD1 signaling events
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle Checkpoints, organism-specific biosystem (from REACTOME)
    Cell Cycle Checkpoints, organism-specific biosystemA hallmark of the human cell cycle in normal somatic cells is its precision. This remarkable fidelity is achieved by a number of signal transduction pathways, known as checkpoints, which monitor cell...
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    E2F transcription factor network, organism-specific biosystem
    E2F transcription factor network
  • G2/M Checkpoints, organism-specific biosystem (from REACTOME)
    G2/M Checkpoints, organism-specific biosystemG2/M checkpoints include the checks for damaged DNA, unreplicated DNA, and checks that ensure that the genome is replicated once and only once per cell cycle. If cells pass these checkpoints, they f...
  • G2/M DNA damage checkpoint, organism-specific biosystem (from REACTOME)
    G2/M DNA damage checkpoint, organism-specific biosystemThroughout the cell cycle, the genome is constantly monitored for damage, resulting either from errors of replication, by-products of metabolism or through extrinsic sources such as ultra-violet or i...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
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    Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
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    HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA), organism-specific biosystemHomology directed repair (HDR) of replication-independent DNA double strand breaks (DSBs) via homologous recombination repair (HRR) or single strand annealing (SSA) requires the activation of ATM fol...
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    HDR through Homologous Recombination (HRR), organism-specific biosystemHomology directed repair (HDR) through homologous recombination is known as homologous recombination repair (HRR). HRR occurs after extensive resection of DNA double strand break (DSB) ends, which cr...
  • HDR through MMEJ (alt-NHEJ), organism-specific biosystem (from REACTOME)
    HDR through MMEJ (alt-NHEJ), organism-specific biosystemHomology directed repair (HDR) through microhomology-mediated end joining (MMEJ) is an error prone process also known as alternative nonhomologous end joining (alt-NHEJ), although it does not involve...
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    HDR through Single Strand Annealing (SSA), organism-specific biosystemHomology directed repair (HDR) through single strand annealing (SSA), similar to HDR through homologous recombination repair (HRR), involves extensive resection of DNA double strand break ends (DSBs)...
  • Homologous DNA Pairing and Strand Exchange, organism-specific biosystem (from REACTOME)
    Homologous DNA Pairing and Strand Exchange, organism-specific biosystemThe presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from 3'-ssDNA overhangs created by extensive resection of DNA double strand break (DSB) ends. R...
  • Homology Directed Repair, organism-specific biosystem (from REACTOME)
    Homology Directed Repair, organism-specific biosystemHomology directed repair (HDR) of DNA double strand breaks (DSBs) requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homol...
  • Meiosis, organism-specific biosystem (from REACTOME)
    Meiosis, organism-specific biosystemDuring meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing...
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    Meiotic recombination, organism-specific biosystemMeiotic recombination exchanges segments of duplex DNA between chromosomal homologs, generating genetic diversity (reviewed in Handel and Schimenti 2010, Inagaki et al. 2010, Cohen et al. 2006). Ther...
  • Notch signaling pathway, organism-specific biosystem (from Pathway Interaction Database)
    Notch signaling pathway, organism-specific biosystem
    Notch signaling pathway
  • Notch-mediated HES/HEY network, organism-specific biosystem (from Pathway Interaction Database)
    Notch-mediated HES/HEY network, organism-specific biosystem
    Notch-mediated HES/HEY network
  • Presynaptic phase of homologous DNA pairing and strand exchange, organism-specific biosystem (from REACTOME)
    Presynaptic phase of homologous DNA pairing and strand exchange, organism-specific biosystemThe presynaptic phase of homologous DNA pairing and strand exchange during homologous recombination repair (HRR) begins with the displacement of RPA from ssDNA (Thompson and Limoli 2003) by the joint...
  • Processing of DNA double-strand break ends, organism-specific biosystem (from REACTOME)
    Processing of DNA double-strand break ends, organism-specific biosystemHomology directed repair (HDR) through homologous recombination (HRR) or single strand annealing (SSA) requires extensive resection of DNA double strand break (DSB) ends (Thompson and Limoli 2003, Ci...
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Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II repressing transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA polymerase II transcription corepressor activity IDA
Inferred from Direct Assay
more info
PubMed 
damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA endodeoxyribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
DNA double-strand break processing TAS
Traceable Author Statement
more info
 
DNA double-strand break processing involved in repair via single-strand annealing IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA repair TAS
Traceable Author Statement
more info
PubMed 
DNA replication TAS
Traceable Author Statement
more info
 
DNA synthesis involved in DNA repair TAS
Traceable Author Statement
more info
 
G1/S transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
G2 DNA damage checkpoint IDA
Inferred from Direct Assay
more info
PubMed 
blastocyst hatching IEA
Inferred from Electronic Annotation
more info
 
cell cycle checkpoint TAS
Traceable Author Statement
more info
PubMed 
cell division IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
PubMed 
double-strand break repair via homologous recombination TAS
Traceable Author Statement
more info
 
meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
mitotic nuclear division IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
nucleotide-excision repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
regulation of transcription from RNA polymerase II promoter TAS
Traceable Author Statement
more info
PubMed 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
strand displacement TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
chromosome IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus TAS
Traceable Author Statement
more info
PubMed 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
DNA endonuclease RBBP8
Names
CTBP-interacting protein
RBBP-8
retinoblastoma binding protein 8
sporulation in the absence of SPO11 protein 2 homolog

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
    5001..98155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002894.2NP_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)
    AF043431, BG723261
    Consensus CDS
    CCDS11875.1
    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Related
    ENSP00000323050, OTTHUMP00000162574, ENST00000327155, OTTHUMT00000254699
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  2. NM_203291.1NP_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)
    AF043431, BC001170, BU187672, U72066
    Consensus CDS
    CCDS11875.1
    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Related
    ENSP00000382628, OTTHUMP00000261461, ENST00000399722, OTTHUMT00000446387
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  3. NM_203292.1NP_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)
    BC001170, BX648221, U72066
    Consensus CDS
    CCDS11874.1
    UniProtKB/Swiss-Prot
    Q99708
    Related
    ENSP00000382630, OTTHUMP00000162575, ENST00000399725, OTTHUMT00000254700
    Conserved Domains (1) summary
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p2 Primary Assembly

    Range
    22914121..23026488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011526132.1XP_011524434.1  

    See identical proteins and their annotated locations for XP_011524434.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  2. XM_006722520.1XP_006722583.1  

    See identical proteins and their annotated locations for XP_006722583.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  3. XM_006722519.1XP_006722582.1  

    See identical proteins and their annotated locations for XP_006722582.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  4. XM_005258325.1XP_005258382.1  

    Conserved Domains (1) summary
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  5. XM_006722521.1XP_006722584.1  

    See identical proteins and their annotated locations for XP_006722584.1

    UniProtKB/Swiss-Prot
    Q99708
    UniProtKB/TrEMBL
    A0A024RC34
    Conserved Domains (2) summary
    pfam08573
    Location:795858
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20139
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  6. XM_005258326.2XP_005258383.1  

    Conserved Domains (1) summary
    pfam08573
    Location:521584
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

Alternate CHM1_1.1

Genomic

  1. NC_018929.2 Alternate CHM1_1.1

    Range
    20440466..20533636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)