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

Gene ID: 5932, updated on 13-May-2024

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; AllianceGenome:HGNC:9891
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; JAWAD; 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
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Genomic context

Location:
18q11.2
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (22914139..23026486)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (22991142..23219842)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (20513291..20606449)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:20494481-20495088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13142 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:20513021-20513861 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr18:20531824-20532512 Neighboring gene microRNA 4741 Neighboring gene MPRA-validated peak3069 silencer Neighboring gene RNA, 7SL, cytoplasmic 745, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20664224-20664724 Neighboring gene Sharpr-MPRA regulatory region 2761 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20685239-20685740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20685741-20686240 Neighboring gene uncharacterized LOC124904266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20701091-20701590 Neighboring gene NANOG hESC enhancer GRCh37_chr18:20702454-20703005 Neighboring gene Sharpr-MPRA regulatory region 2996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20738534-20739053 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20749225-20750158 Neighboring gene Cdk5 and Abl enzyme substrate 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:20762837-20763336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20768869-20769375 Neighboring gene MPRA-validated peak3070 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20776067-20776663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13150 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:20829775-20830276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:20839263-20839926 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

Associated conditions

Description Tests
Jawad syndrome
MedGen: C0796063 OMIM: 251255 GeneReviews: Not available
Compare labs
Seckel syndrome 2
MedGen: C1847572 OMIM: 606744 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.
EBI GWAS Catalog
Genome-wide association study of intracranial aneurysm identifies three new risk loci.
EBI GWAS Catalog
Many sequence variants affecting diversity of adult human height.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
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
 
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 DNA strand resection involved in replication fork processing IDA
Inferred from Direct Assay
more info
PubMed 
involved_in DNA strand resection involved in replication fork processing NAS
Non-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 IDA
Inferred from Direct Assay
more info
PubMed 
involved_in double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in homologous recombination NAS
Non-traceable Author Statement
more info
PubMed 
involved_in 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 
involved_in negative regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
part_of BRCA1-C complex IPI
Inferred from Physical Interaction
more info
PubMed 
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 NAS
Non-traceable Author Statement
more info
PubMed 
is_active_in site of double-strand break IDA
Inferred from Direct Assay
more info
PubMed 
part_of transcription 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)

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.

Genomic

  1. NG_012121.2 RefSeqGene

    Range
    24191..117349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002894.3NP_002885.1  DNA endonuclease RBBP8 isoform a

    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
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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_203291.2NP_976036.1  DNA endonuclease RBBP8 isoform a

    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
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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_203292.2NP_976037.1  DNA endonuclease RBBP8 isoform b

    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/TrEMBL
    I6L8A6
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    22914139..23026486
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437728.1XP_047293684.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  2. XM_006722519.3XP_006722582.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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_011526132.3XP_011524434.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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_006722520.3XP_006722583.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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
  5. XM_006722521.3XP_006722584.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
    UniProtKB/TrEMBL
    I6L8A6
    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
  6. XM_047437729.1XP_047293685.1  DNA endonuclease RBBP8 isoform X2

  7. XM_005258325.4XP_005258382.1  DNA endonuclease RBBP8 isoform X2

    UniProtKB/TrEMBL
    I6L8A6
    Conserved Domains (1) summary
    pfam10482
    Location:20138
    CtIP_N; Tumour-suppressor protein CtIP N-terminal domain
  8. XM_047437727.1XP_047293683.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  9. XM_047437731.1XP_047293687.1  DNA endonuclease RBBP8 isoform X2

  10. XM_047437730.1XP_047293686.1  DNA endonuclease RBBP8 isoform X2

  11. XM_047437732.1XP_047293688.1  DNA endonuclease RBBP8 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    22991142..23219842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318960.1XP_054174935.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  2. XM_054318958.1XP_054174933.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  3. XM_054318959.1XP_054174934.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  4. XM_054318961.1XP_054174936.1  DNA endonuclease RBBP8 isoform X2

  5. XM_054318956.1XP_054174931.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  6. XM_054318962.1XP_054174937.1  DNA endonuclease RBBP8 isoform X2

  7. XM_054318957.1XP_054174932.1  DNA endonuclease RBBP8 isoform X1

    UniProtKB/Swiss-Prot
    A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
  8. XM_054318964.1XP_054174939.1  DNA endonuclease RBBP8 isoform X2

  9. XM_054318963.1XP_054174938.1  DNA endonuclease RBBP8 isoform X2

  10. XM_054318965.1XP_054174940.1  DNA endonuclease RBBP8 isoform X3