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

Gene ID: 5932, updated on 9-Feb-2020

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
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

Genomic context

See RBBP8 in Genome Data Viewer
Location:
18q11.2
Exon count:
24
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (22914121..23026486)
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 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 
Y-form DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-strand/single-strand DNA junction binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
flap-structured DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single-stranded DNA endodeoxyribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single-stranded DNA endodeoxyribonuclease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription corepressor activity IDA
Inferred from Direct Assay
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
G1/S transition of mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
blastocyst hatching IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair via homologous recombination IBA
Inferred from Biological aspect of Ancestor
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
 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
negative regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
nucleotide-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
intracellular membrane-bounded organelle 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 
site of double-strand break IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcriptional repressor complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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_002894.3NP_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:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    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
    ENSP00000382628.2, ENST00000399722.6
    Conserved Domains (2) summary
    pfam08573
    Location:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    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
    ENSP00000382630.2, ENST00000399725.6
    Conserved Domains (1) summary
    pfam10482
    Location:20138
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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_011526132.2XP_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:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  2. XM_006722520.2XP_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:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  3. XM_006722519.2XP_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:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  4. XM_005258325.3XP_005258382.1  DNA endonuclease RBBP8 isoform X2

    Conserved Domains (1) summary
    pfam10482
    Location:20138
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
  5. XM_024451233.1XP_024307001.1  DNA endonuclease RBBP8 isoform X3

    Conserved Domains (2) summary
    pfam08573
    Location:699759
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:140
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  6. XM_017025916.1XP_016881405.1  DNA endonuclease RBBP8 isoform X5

  7. XM_006722521.2XP_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:797857
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  8. XM_005258326.4XP_005258383.1  DNA endonuclease RBBP8 isoform X4

    Conserved Domains (1) summary
    pfam08573
    Location:523583
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
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