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

    Gene ID: 5932, updated on 17-Jun-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RBBP8 in Genome Data Viewer
    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

      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
      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

      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)
      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

      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)
      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
      UniProtKB/TrEMBL
      I6L8A6
    2. XM_006722519.3XP_006722582.1  DNA endonuclease RBBP8 isoform X1

      See identical proteins and their annotated locations for XP_006722582.1

      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

      See identical proteins and their annotated locations for XP_011524434.1

      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

      See identical proteins and their annotated locations for XP_006722583.1

      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

      See identical proteins and their annotated locations for XP_006722584.1

      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

      UniProtKB/TrEMBL
      I6L8A6
    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
      UniProtKB/TrEMBL
      I6L8A6
    9. XM_047437731.1XP_047293687.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    10. XM_047437730.1XP_047293686.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    11. XM_047437732.1XP_047293688.1  DNA endonuclease RBBP8 isoform X3

      UniProtKB/TrEMBL
      I6L8A6

    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
      UniProtKB/TrEMBL
      I6L8A6
    2. XM_054318958.1XP_054174933.1  DNA endonuclease RBBP8 isoform X1

      UniProtKB/Swiss-Prot
      A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
      UniProtKB/TrEMBL
      I6L8A6
    3. XM_054318959.1XP_054174934.1  DNA endonuclease RBBP8 isoform X1

      UniProtKB/Swiss-Prot
      A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
      UniProtKB/TrEMBL
      I6L8A6
    4. XM_054318961.1XP_054174936.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    5. XM_054318956.1XP_054174931.1  DNA endonuclease RBBP8 isoform X1

      UniProtKB/Swiss-Prot
      A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
      UniProtKB/TrEMBL
      I6L8A6
    6. XM_054318962.1XP_054174937.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    7. XM_054318957.1XP_054174932.1  DNA endonuclease RBBP8 isoform X1

      UniProtKB/Swiss-Prot
      A6NKN2, A8K8W6, E7ETY1, O75371, Q8NHQ3, Q99708
      UniProtKB/TrEMBL
      I6L8A6
    8. XM_054318964.1XP_054174939.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    9. XM_054318963.1XP_054174938.1  DNA endonuclease RBBP8 isoform X2

      UniProtKB/TrEMBL
      I6L8A6
    10. XM_054318965.1XP_054174940.1  DNA endonuclease RBBP8 isoform X3

      UniProtKB/TrEMBL
      I6L8A6