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Rbbp8 retinoblastoma binding protein 8, endonuclease [ Mus musculus (house mouse) ]

Gene ID: 225182, updated on 8-Feb-2024

Summary

Official Symbol
Rbbp8provided by MGI
Official Full Name
retinoblastoma binding protein 8, endonucleaseprovided by MGI
Primary source
MGI:MGI:2442995
See related
Ensembl:ENSMUSG00000041238 AllianceGenome:MGI:2442995
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
RIM; CtIP; SAE2; RBBP-8; 9930104E21Rik
Summary
Predicted to enable several functions, including DNA binding activity; identical protein binding activity; and single-stranded DNA endodeoxyribonuclease activity. Acts upstream of or within G1/S transition of mitotic cell cycle and blastocyst hatching. Predicted to be located in nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in site of double-strand break. Human ortholog(s) of this gene implicated in Seckel syndrome 2. Orthologous to human RBBP8 (RB binding protein 8, endonuclease). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 6.2), placenta adult (RPKM 5.1) and 23 other tissues See more
Orthologs
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Genomic context

See Rbbp8 in Genome Data Viewer
Location:
18 A1; 18 5.85 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 18 NC_000084.7 (11766333..11876264)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 18 NC_000084.6 (11633276..11743207)

Chromosome 18 - NC_000084.7Genomic Context describing neighboring genes Neighboring gene GATA binding protein 6, opposite strand Neighboring gene GATA binding protein 6 Neighboring gene VISTA enhancer mm138 Neighboring gene predicted gene, 35918 Neighboring gene STARR-positive B cell enhancer ABC_E8703 Neighboring gene CapStarr-seq enhancer MGSCv37_chr18:11816567-11816720 Neighboring gene STARR-seq mESC enhancer starr_43816 Neighboring gene predicted gene, 54029 Neighboring gene ring finger and WD repeat domain 2 pseudogene Neighboring gene predicted gene, 41665

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (7)  1 citation
  • Endonuclease-mediated (3) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables damaged DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables endonuclease activity IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
 
enables single-stranded DNA endodeoxyribonuclease activity ISO
Inferred from Sequence Orthology
more info
 
enables transcription corepressor activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
 
involved_in DNA strand resection involved in replication fork processing NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within G1/S transition of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within blastocyst hatching IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell division IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair via homologous recombination ISO
Inferred from Sequence Orthology
more info
 
involved_in homologous recombination NAS
Non-traceable Author Statement
more info
PubMed 
acts_upstream_of_or_within 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 
Component Evidence Code Pubs
part_of BRCA1-C complex ISO
Inferred from Sequence Orthology
more info
 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus NAS
Non-traceable Author Statement
more info
PubMed 
part_of transcription repressor complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
DNA endonuclease RBBP8
Names
ctBP-interacting protein
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.

mRNA and Protein(s)

  1. NM_001081223.2NP_001074692.1  DNA endonuclease RBBP8

    See identical proteins and their annotated locations for NP_001074692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC090479, AC115894, AK037049
    Consensus CDS
    CCDS37738.1
    UniProtKB/Swiss-Prot
    Q80YR6
    UniProtKB/TrEMBL
    Q8VE67
    Related
    ENSMUSP00000046255.7, ENSMUST00000047322.8
    Conserved Domains (2) summary
    pfam08573
    Location:793853
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  2. NM_001252495.1NP_001239424.1  DNA endonuclease RBBP8

    See identical proteins and their annotated locations for NP_001239424.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC090479, AC115894
    Consensus CDS
    CCDS37738.1
    UniProtKB/Swiss-Prot
    Q80YR6
    UniProtKB/TrEMBL
    Q8VE67
    Related
    ENSMUSP00000111527.3, ENSMUST00000115861.9
    Conserved Domains (2) summary
    pfam08573
    Location:793853
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain

RNA

  1. NR_045526.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks 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)
    AC090479, AC115894, AK163908, CD352622, CX567593
  2. NR_045527.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences 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)
    AC090479, AC115894, AK041384
    Related
    ENSMUST00000235039.2

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000084.7 Reference GRCm39 C57BL/6J

    Range
    11766333..11876264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006525812.4XP_006525875.1  DNA endonuclease RBBP8 isoform X1

    See identical proteins and their annotated locations for XP_006525875.1

    UniProtKB/Swiss-Prot
    Q80YR6
    UniProtKB/TrEMBL
    Q8VE67
    Conserved Domains (2) summary
    pfam08573
    Location:793853
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus
    pfam10482
    Location:20138
    CtIP_N; tumor-suppressor protein CtIP N-terminal domain
  2. XM_030250421.2XP_030106281.1  DNA endonuclease RBBP8 isoform X2

    Conserved Domains (1) summary
    pfam08573
    Location:519579
    SAE2; DNA repair protein endonuclease SAE2/CtIP C-terminus

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_175458.2: Suppressed sequence

    Description
    NM_175458.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.