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

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: mouse all
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Genomic context

Location:: 1q32.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (205086142..205121978, complement)
RS_2023_10	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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Long noncoding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA1455p/RBBP5 axis.
Title: Long non‑coding RNA AC245100.4 promotes prostate cancer tumorigenesis via the microRNA‑145‑5p/RBBP5 axis.
We used a hybrid methods approach to study the assembly and biochemical function of the minimally active MLL1 complex (MLL1, WDR5 and RbBP5)..We identified a new interaction site between the MLL1 SET domain and the WD40 beta-propeller domain of RbBP5, and demonstrate the susceptibility of the catalytic function of the complex to disruption of individual interaction sites.
Title: The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions.
We identified an internal interaction between the WD40 propeller and the C-terminal distal region in RBBP5, which assisted the maintenance of the compact conformation of the MLL1 complex. We also discovered a vertebrate-specific motif in the C-terminal distal region of RBBP5 that contributed to nucleosome recognition and methylation of nucleosomes by the MLL1 complex.
Title: The internal interaction in RBBP5 regulates assembly and activity of MLL1 methyltransferase complex.
Our nuclear magnetic resonance binding data supports the hypothesis that in addition to the role of RbBP5 in catalytic activation, its beta-propeller domain is a platform for the recruitment of the MLL complexes to chromatin targets through its direct interaction with nucleic acids.
Title: The structure of the RbBP5 β-propeller domain reveals a surface with potential nucleic acid binding sites.
RBBP5 plays an important role in the progression of hepatocellular carcinoma.
Title: Retinoblastoma Binding Protein 5 Correlates with the Progression in Hepatocellular Carcinoma.
Results from a study on gene expression variability markers in early-stage human embryos shows that RBBP5 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
this study shows that during epithelial-mesenchymal transition in the prostate cancer cell line RbBP5 binding is increased in the vicinity of Snail transcription start site
Title: Role of RbBP5 and H3K4me3 in the vicinity of Snail transcription start site during epithelial-mesenchymal transition in prostate cancer cell.
different cancer mutations in MLL1 lead to a loss or increase in activity, illustrating the complex and tumor-specific role of MLL1 in carcinogenesis.
Title: Somatic cancer mutations in the MLL1 histone methyltransferase modulate its enzymatic activity and dependence on the WDR5/RBBP5/ASH2L complex.
role of RBQ3 in the development of multiple myeloma
Title: RBQ3 participates in multiple myeloma cell proliferation, adhesion and chemoresistance.
This study demonstrated that RBQ3 might play an important role in glioma, and RBQ3 inhibitors might be novel anti-tumor agents.
Title: Expression and clinical role of RBQ3 in gliomas.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:482323

AL009343 (e-PCR)
- UniSTS:77601

D8S2279 (e-PCR)
- UniSTS:473907

D11S3114 (e-PCR)
- UniSTS:152207

D16S325 (e-PCR)
- UniSTS:147089

RH120684 (e-PCR)
- UniSTS:132765

RH66579 (e-PCR)
- UniSTS:88739

SHGC-35381 (e-PCR)
- UniSTS:36572

D11S3316 (e-PCR)
- UniSTS:152558

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

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in response to estrogen	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription initiation-coupled chromatin remodeling	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
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

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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)

NM_001193272.2 → NP_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/TrEMBL

B4DMM7

Related

ENSP00000356132.1, ENST00000367164.1

Conserved Domains (2) summary

sd00039
Location:29 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:30 → 322

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 ...
NM_001193273.2 → NP_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/TrEMBL

B4DLF8

Conserved Domains (2) summary

COG2319
Location:10 → 194

WD40; WD40 repeat [General function prediction only]

sd00039
Location:75 → 120

7WD40; WD40 repeat [structural motif]
NM_005057.4 → NP_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

A8K272, Q15291, Q7Z6D8, Q8NDZ7

UniProtKB/TrEMBL

B4DMM7

Related

ENSP00000264515.6, ENST00000264515.11

Conserved Domains (2) summary

sd00039
Location:29 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:30 → 322

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: 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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

205086142..205121978 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B4DMM7
XM_047426907.1 → XP_047282863.1 retinoblastoma-binding protein 5 isoform X5

UniProtKB/TrEMBL

B4DLF8
XM_047426905.1 → XP_047282861.1 retinoblastoma-binding protein 5 isoform X4

UniProtKB/TrEMBL

B4DMM7
XM_011509833.4 → XP_011508135.1 retinoblastoma-binding protein 5 isoform X2

See identical proteins and their annotated locations for XP_011508135.1

UniProtKB/TrEMBL

B4DMM7

Conserved Domains (2) summary

sd00039
Location:29 → 64

7WD40; WD40 repeat [structural motif]

cl29593
Location:30 → 322

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 ...
XM_047426894.1 → XP_047282850.1 retinoblastoma-binding protein 5 isoform X1

UniProtKB/TrEMBL

B4DMM7
XM_047426912.1 → XP_047282868.1 retinoblastoma-binding protein 5 isoform X7
XM_047426908.1 → XP_047282864.1 retinoblastoma-binding protein 5 isoform X6

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

204350529..204386358 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338012.1 → XP_054193987.1 retinoblastoma-binding protein 5 isoform X3

UniProtKB/TrEMBL

B4DMM7
XM_054338014.1 → XP_054193989.1 retinoblastoma-binding protein 5 isoform X5

UniProtKB/TrEMBL

B4DLF8
XM_054338013.1 → XP_054193988.1 retinoblastoma-binding protein 5 isoform X4

UniProtKB/TrEMBL

B4DMM7
XM_054338011.1 → XP_054193986.1 retinoblastoma-binding protein 5 isoform X2

UniProtKB/TrEMBL

B4DMM7
XM_054338010.1 → XP_054193985.1 retinoblastoma-binding protein 5 isoform X1

UniProtKB/TrEMBL

B4DMM7
XM_054338016.1 → XP_054193991.1 retinoblastoma-binding protein 5 isoform X7
XM_054338015.1 → XP_054193990.1 retinoblastoma-binding protein 5 isoform X6