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RBBP5 RB binding protein 5, histone lysine methyltransferase complex subunit [ Homo sapiens (human) ]

Gene ID: 5929, updated on 8-Jan-2023

Summary

Official Symbol
RBBP5provided by HGNC
Official Full Name
RB binding protein 5, histone lysine methyltransferase complex subunitprovided by HGNC
Primary source
HGNC:HGNC:9888
See related
Ensembl:ENSG00000117222 MIM:600697; AllianceGenome:HGNC:9888
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
RBQ3; SWD1
Summary
This gene encodes a ubiquitously expressed nuclear protein which belongs to a highly conserved subfamily of WD-repeat proteins. The encoded protein binds directly to retinoblastoma protein, which regulates cell proliferation. It interacts preferentially with the underphosphorylated retinoblastoma protein via the E1A-binding pocket B. Three alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2010]
Expression
Ubiquitous expression in thyroid (RPKM 6.5), lymph node (RPKM 6.0) and 25 other tissues See more
Orthologs
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Genomic context

See RBBP5 in Genome Data Viewer
Location:
1q32.1
Exon count:
14
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (205086142..205121978, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (204350529..204386358, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (205055270..205091106, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene contactin 2 Neighboring gene transmembrane protein 81 Neighboring gene Sharpr-MPRA regulatory region 1805 Neighboring gene glycogenin 2 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 3970 Neighboring gene signal peptidase complex subunit 1-like

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

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
EBI GWAS 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
enables histone binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
part_of MLL1 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of MLL1 complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of MLL1/2 complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of MLL3/4 complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of MLL3/4 complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of Set1C/COMPASS complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
PubMed 
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus 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 IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
retinoblastoma-binding protein 5
Names
RBBP-5
SWD1, Set1c WD40 repeat protein, homolog
retinoblastoma-binding protein RBQ-3

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_001193272.2NP_001180201.1  retinoblastoma-binding protein 5 isoform 2

    See identical proteins and their annotated locations for NP_001180201.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different splice site in the 3' coding region, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AK290137, AL583832, BC037284, BQ020418, DA797022
    Consensus CDS
    CCDS53463.1
    UniProtKB/Swiss-Prot
    Q15291
    Related
    ENSP00000356132.1, ENST00000367164.1
    Conserved Domains (2) summary
    sd00039
    Location:2964
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30322
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001193273.2NP_001180202.1  retinoblastoma-binding protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001180202.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two different splice sites in the coding region which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 3) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AK296978, AL583832, BC075059, BQ020418, DA797022
    UniProtKB/Swiss-Prot
    Q15291
    UniProtKB/TrEMBL
    B4DLF8
    Conserved Domains (2) summary
    COG2319
    Location:10194
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:75120
    7WD40; WD40 repeat [structural motif]
  3. NM_005057.4NP_005048.2  retinoblastoma-binding protein 5 isoform 1

    See identical proteins and their annotated locations for NP_005048.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest protein (isoform 1).
    Source sequence(s)
    AL583832, BC075059, BQ020418, DA797022
    Consensus CDS
    CCDS30983.1
    UniProtKB/Swiss-Prot
    Q15291, Q8NDZ7
    UniProtKB/TrEMBL
    A0A024R9B5
    Related
    ENSP00000264515.6, ENST00000264515.11
    Conserved Domains (2) summary
    sd00039
    Location:2964
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30322
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    205086142..205121978 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426902.1XP_047282858.1  retinoblastoma-binding protein 5 isoform X3

  2. XM_047426907.1XP_047282863.1  retinoblastoma-binding protein 5 isoform X5

  3. XM_047426905.1XP_047282861.1  retinoblastoma-binding protein 5 isoform X4

  4. XM_011509833.4XP_011508135.1  retinoblastoma-binding protein 5 isoform X2

    See identical proteins and their annotated locations for XP_011508135.1

    Conserved Domains (2) summary
    sd00039
    Location:2964
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:30322
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. XM_047426894.1XP_047282850.1  retinoblastoma-binding protein 5 isoform X1

  6. XM_047426912.1XP_047282868.1  retinoblastoma-binding protein 5 isoform X7

  7. XM_047426908.1XP_047282864.1  retinoblastoma-binding protein 5 isoform X6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    204350529..204386358 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)