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

Gene ID: 9810, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:16867
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
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Genomic context

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See RNF40 in Genome Data Viewer
Location:
16p11.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30761612..30776307)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (31149033..31163750)
RS_2024_09 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 MED14-independent group 3 enhancer GRCh37_chr16:30752251-30753450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7392 Neighboring gene transmembrane protein 265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10722 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr16:30771308-30772507 Neighboring gene phosphorylase kinase catalytic subunit gamma 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30772706-30772935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10724 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:30773347-30773984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30775098-30775598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30775599-30776099 Neighboring gene cilia and flagella associated protein 119 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30780568-30780764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30785886-30786564 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30786565-30787241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10728 Neighboring gene zinc finger protein 629 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:30807171-30807374 Neighboring gene uncharacterized LOC124903679 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7394 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30824465-30825020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30825021-30825575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7396 Neighboring gene adipose secreted signaling protein pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming. Xie W, et al. Cell Death Dis, 2020 Apr 27. PMID 32341358, Free PMC Article
  2. The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells. Schneider D, et al. Clin Epigenetics, 2019 Jul 2. PMID 31266541, Free PMC Article
  3. RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer. Prokakis E, et al. Cell Death Dis, 2023 Sep 28. PMID 37770435, Free PMC Article
  4. The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis. Wegwitz F, et al. Cell Death Dis, 2020 Oct 17. PMID 33070155, Free PMC Article
  5. Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis. Fu J, et al. Oncogene, 2021 Jan. PMID 33199825, Free PMC Article

See all (134) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes.
    Title: Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes.
  2. RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer.
    Title: RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer.
  3. Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis.
    Title: Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis.
  4. The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
    Title: The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
  5. The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming.
    Title: The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming.
  6. The RNF20/40 complex regulates p53-dependent gene transcription and mRNA splicing.
    Title: The RNF20/40 complex regulates p53-dependent gene transcription and mRNA splicing.
  7. Findings reveal that RNF40 is essential for maintaining tumorigenic features of colorectal cancer cells in vitro by controlling the expression of genes encoding central apoptotic regulators.
    Title: The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells.
  8. Cooperative physical interactions among eEF1BdeltaL, RNF20/40, and HSF1 synergistically promote expression of heat shock-responsive genes. In addition, eEF1BdeltaL is a novel ubiquitylation target of RNF20/40 and elucidating its function. This provides a molecular mechanism for the cooperative function of distinct transcription factors in heat shock-responsive gene transcription.
    Title: RNF20/40-mediated eEF1BδL monoubiquitylation stimulates transcription of heat shock-responsive genes.
  9. Our findings suggest that RNF40 plays a central role in the maintenance of tumorigenic features and inflammatory signaling by promoting nuclear NF-kappaB activity.
    Title: Loss of RNF40 Decreases NF-κB Activity in Colorectal Cancer Cells and Reduces Colitis Burden in Mice.
  10. the RNF20/40 complex, a major ubiquitin ligase catalysing histone H2B monoubiquitination, interacts with the motor protein Eg5 during mitosis and participates in spindle assembly.
    Title: Ubiquitin ligase RNF20/40 facilitates spindle assembly and promotes breast carcinogenesis through stabilizing motor protein Eg5.
Submit: New GeneRIF Correction See all GeneRIFs (19)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0661, MGC13051, DKFZp686K191

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables mRNA 3'-UTR binding IDA
Inferred from Direct Assay
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 protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 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
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
NOT involved_in regulation of mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of HULC complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of HULC complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ubiquitin ligase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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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

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_001207033.1 → NP_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/TrEMBL
    A0A0S2Z537, A8K6K1
    Conserved Domains (3) summary
    cd00162
    Location:946 → 989
    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:231 → 945
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam08647
    Location:754 → 848
    BRE1; BRE1 E3 ubiquitin ligase

  2. NM_001207034.1 → NP_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/TrEMBL
    H3BP71
    Related
    ENSP00000350563.5, ENST00000357890.9
    Conserved Domains (3) summary
    COG1196
    Location:193 → 844
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd00162
    Location:847 → 890
    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:654 → 748
    BRE1; BRE1 E3 ubiquitin ligase

  3. NM_001286572.3 → NP_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
    A0A024QZG0, O75150, Q6AHZ6, Q6N005, Q7L3T6, Q8N615, Q96T18, Q9BSV9, Q9HC82
    UniProtKB/TrEMBL
    A0A0S2Z537
    Conserved Domains (2) summary
    cd16815
    Location:945 → 999
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)
    cl25732
    Location:231 → 920
    SMC_N; RecF/RecN/SMC N terminal domain

  4. NM_014771.4 → NP_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)
    AC106886, KF456183
    Consensus CDS
    CCDS10691.1
    UniProtKB/Swiss-Prot
    A0A024QZG0, O75150, Q6AHZ6, Q6N005, Q7L3T6, Q8N615, Q96T18, Q9BSV9, Q9HC82
    UniProtKB/TrEMBL
    A0A0S2Z537
    Related
    ENSP00000325677.6, ENST00000324685.11
    Conserved Domains (2) summary
    cd16815
    Location:945 → 999
    RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)
    cl25732
    Location:231 → 920
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    30761612..30776307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_007064931.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    31149033..31163750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008484755.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_194352.1: Suppressed sequence

    Description
    NM_194352.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75150.5 GenPept UniProtKB/Swiss-Prot:O75150

Gene LinkOut

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