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RNF40 ring finger protein 40 [ Homo sapiens (human) ]

Gene ID: 9810, updated on 17-Jun-2019

Summary

Official Symbol
RNF40provided by HGNC
Official Full Name
ring finger protein 40provided by HGNC
Primary source
HGNC:HGNC:16867
See related
Ensembl:ENSG00000103549 MIM:607700
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
BRE1B; RBP95; STARING
Summary
The protein encoded by this gene contains a RING finger, a motif known to be involved in protein-protein and protein-DNA interactions. This protein was reported to interact with the tumor suppressor protein RB1. Studies of the rat counterpart suggested that this protein may function as an E3 ubiquitin-protein ligase, and facilitate the ubiquitination and degradation of syntaxin 1, which is an essential component of the neurotransmitter release machinery. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]
Expression
Ubiquitous expression in testis (RPKM 21.6), bone marrow (RPKM 14.4) and 25 other tissues See more
Orthologs

Genomic context

See RNF40 in Genome Data Viewer
Location:
16p11.2
Exon count:
22
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (30761612..30800231)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30772933..30787628)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Snf2 related CREBBP activator protein Neighboring gene transmembrane protein 265 Neighboring gene phosphorylase kinase catalytic subunit gamma 2 Neighboring gene coiled-coil domain containing 189 Neighboring gene zinc finger protein 629 Neighboring gene chromosome 20 open reading frame 27 pseudogene Neighboring gene BAF chromatin remodeling complex subunit BCL7C Neighboring gene microRNA 4519

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • ATM Signaling Network in Development and Disease, organism-specific biosystem (from WikiPathways)
    ATM Signaling Network in Development and Disease, organism-specific biosystemThis pathway is modeled after Figure 4 in the article "The ATM signaling network in development and disease" (See Bibliography). When DNA is damaged, DDR begins to work on recuperating the damage th...
  • E3 ubiquitin ligases ubiquitinate target proteins, organism-specific biosystem (from REACTOME)
    E3 ubiquitin ligases ubiquitinate target proteins, organism-specific biosystemE3 ubiquitin ligases catalyze the transfer of an ubiquitin from an E2-ubiquitin conjugate to a target protein. Generally, ubiquitin is transferred via formation of an amide bond to a particular lysin...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein ubiquitination, organism-specific biosystem (from REACTOME)
    Protein ubiquitination, organism-specific biosystemUbiquitin is a small, 76 amino acid residue protein that is conjugated by E3 ubiquitin ligases to other proteins in order to regulate their function or degradation (enzymatic cascade reviewed in Neut...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0661, MGC13051, DKFZp686K191

Gene Ontology Provided by GOA

Function Evidence Code Pubs
mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
syntaxin-1 binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin conjugating enzyme binding IEA
Inferred from Electronic Annotation
more info
 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
histone H2B ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
histone monoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of mRNA polyadenylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H2B ubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of proteasomal protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein polyubiquitination IEA
Inferred from Electronic Annotation
more info
 
protein ubiquitination TAS
Traceable Author Statement
more info
 
NOT regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to peptide hormone IEA
Inferred from Electronic Annotation
more info
 
ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
HULC complex IDA
Inferred from Direct Assay
more info
PubMed 
axon terminus IEA
Inferred from Electronic Annotation
more info
 
cytosol IEA
Inferred from Electronic Annotation
more info
 
extrinsic component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase BRE1B
Names
95 kDa retinoblastoma protein binding protein
95 kDa retinoblastoma-associated protein
BRE1 E3 ubiquitin ligase homolog B
BRE1-B
RING-type E3 ubiquitin transferase BRE1B
Rb-associated protein
ring finger protein 40, E3 ubiquitin protein ligase
NP_001193962.1
NP_001193963.1
NP_001273501.1
NP_055586.1
XP_011544299.1
XP_024306268.1

NCBI Reference Sequences (RefSeq)

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_001207033.1NP_001193962.1  E3 ubiquitin-protein ligase BRE1B isoform 2

    See identical proteins and their annotated locations for NP_001193962.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate splice site in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.
    Source sequence(s)
    AB014561, AC106886, AI373490, AK291666
    UniProtKB/Swiss-Prot
    O75150
    UniProtKB/TrEMBL
    A8K6K1
    Conserved Domains (3) summary
    cd00162
    Location:946989
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    TIGR02168
    Location:231945
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam08647
    Location:754848
    BRE1; BRE1 E3 ubiquitin ligase
  2. NM_001207034.1NP_001193963.1  E3 ubiquitin-protein ligase BRE1B isoform 3

    See identical proteins and their annotated locations for NP_001193963.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks in-frame two consecutive exons in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC106886, AI373490, AK027406, AK291666, BC018647
    Consensus CDS
    CCDS55994.1
    UniProtKB/Swiss-Prot
    O75150
    UniProtKB/TrEMBL
    A8K6K1
    Related
    ENSP00000350563.5, ENST00000357890.9
    Conserved Domains (3) summary
    COG1196
    Location:193844
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd00162
    Location:847890
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
    pfam08647
    Location:654748
    BRE1; BRE1 E3 ubiquitin ligase
  3. NM_001286572.3NP_001273501.1  E3 ubiquitin-protein ligase BRE1B isoform 1

    See identical proteins and their annotated locations for NP_001273501.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 and 4 both encode the same isoform (1).
    Source sequence(s)
    AC106886, KF456183
    Consensus CDS
    CCDS10691.1
    UniProtKB/Swiss-Prot
    O75150
    UniProtKB/TrEMBL
    A0A024QZG0
    Related
    ENSP00000455180.1, ENST00000563683.5
    Conserved Domains (2) summary
    cd16815
    Location:945999
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)
    cl25732
    Location:231920
    SMC_N; RecF/RecN/SMC N terminal domain
  4. NM_014771.3NP_055586.1  E3 ubiquitin-protein ligase BRE1B isoform 1

    See identical proteins and their annotated locations for NP_055586.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 4 both encode the same isoform (1).
    Source sequence(s)
    AB014561, AC106886, AI373490, BC018647
    Consensus CDS
    CCDS10691.1
    UniProtKB/Swiss-Prot
    O75150
    UniProtKB/TrEMBL
    A0A024QZG0
    Related
    ENSP00000325677.6, ENST00000324685.10
    Conserved Domains (2) summary
    cd16815
    Location:945999
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)
    cl25732
    Location:231920
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    30761612..30800231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545997.2XP_011544299.1  E3 ubiquitin-protein ligase BRE1B isoform X1

    Conserved Domains (2) summary
    TIGR02168
    Location:231920
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam08647
    Location:754848
    BRE1; BRE1 E3 ubiquitin ligase
  2. XM_024450500.1XP_024306268.1  E3 ubiquitin-protein ligase BRE1B isoform X2

    Conserved Domains (1) summary
    cl25732
    Location:231834
    SMC_N; RecF/RecN/SMC N terminal domain
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