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

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: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.
Title: CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.
essential for early B cell proliferation and development
Title: CtIP is essential for early B cell proliferation and development in mice.
CtIP enhances long-range resection by BLM-DNA2-RPA. CtIP interacts with and stimulates the activity of the BLM helicase and upregulates DNA2 activity.
Title: Enhancement of BLM-DNA2-Mediated Long-Range DNA End Resection by CtIP.
CtIP is not a tumor suppressor, but has oncogenic properties that can promote tumorigenesis, consistent with its ability to facilitate MMEJ-dependent chromosomal instability.
Title: The DNA resection protein CtIP promotes mammary tumorigenesis.
we reveal that reprogramming is associated with high levels of DNA end resection, a critical step in homologous recombination. Moreover, the resection factor CtIP is essential for cell reprogramming and establishment of iPSCs, probably to repair reprogramming-induced DNA damage.
Title: CtIP-Specific Roles during Cell Reprogramming Have Long-Term Consequences in the Survival and Fitness of Induced Pluripotent Stem Cells.
Q418P nsSNP influences the efficiency of CTIP function in HR repair of DNA DSBs
Title: The Influence of the CTIP Polymorphism, Q418P, on Homologous Recombination and Predisposition to Radiation-Induced Tumorigenesis (mainly rAML) in Mice.
Ctip1 couples subtype and area specification, enabling specific functional areas to organize precise ratios of appropriate output projections.
Title: Ctip1 Regulates the Balance between Specification of Distinct Projection Neuron Subtypes in Deep Cortical Layers.
work therefore ascribes novel roles for BRCA1 and CtIP in end-processing and fusion reactions at uncapped telomeres
Title: BRCA1 and CtIP promote alternative non-homologous end-joining at uncapped telomeres.
Data indicate that loss of the CtIP-BRCA1 interaction does not detectably affect resection, maintenance of genomic stability or viability.
Title: CtIP-mediated resection is essential for viability and can operate independently of BRCA1.
The phospho-dependent BRCA1-CtIP interaction is not essential for HDR-mediated DSB repair or for tumor suppression.
Title: The interaction between CtIP and BRCA1 is not essential for resection-mediated DNA repair or tumor suppression.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (7) 1 citation
Endonuclease-mediated (3)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

NoName (e-PCR)
- UniSTS:237740

NoName (e-PCR)
- UniSTS:237744

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	ISO Inferred from Sequence Orthology 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
is_active_in site of double-strand break	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

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)

Go to the top of the page Help

NEW Try the new Transcript table

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)

NM_001081223.2 → NP_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:793 → 853

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

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
NM_001252495.1 → NP_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:793 → 853

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

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain

RNA

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
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

NC_000084.7 Reference GRCm39 C57BL/6J

Range

11766333..11876264

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006525812.4 → XP_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:793 → 853

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

pfam10482
Location:20 → 138

CtIP_N; tumor-suppressor protein CtIP N-terminal domain
XM_030250421.2 → XP_030106281.1 DNA endonuclease RBBP8 isoform X2

Conserved Domains (1) summary

pfam08573
Location:519 → 579

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

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.