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... See more...

Aliases for RNF40 Gene

Aliases for RNF40 Gene

  • Ring Finger Protein 40 2 3 5
  • 95 KDa Retinoblastoma-Associated Protein 3 4
  • RING-Type E3 Ubiquitin Transferase BRE1B 3 4
  • E3 Ubiquitin-Protein Ligase BRE1B 3 4
  • BRE1-B 3 4
  • BRE1B 3 4
  • RBP95 3 4
  • Ring Finger Protein 40, E3 Ubiquitin Protein Ligase 3
  • BRE1 E3 Ubiquitin Ligase Homolog B (S. Cerevisiae) 2
  • 95 KDa Retinoblastoma Protein Binding Protein 3
  • BRE1 E3 Ubiquitin Ligase Homolog B 3
  • RING Finger Protein 40 4
  • Rb-Associated Protein 3
  • EC 2.3.2.27 4
  • KIAA0661 4
  • EC 6.3.2 52
  • STARING 3

External Ids for RNF40 Gene

Previous GeneCards Identifiers for RNF40 Gene

  • GC16P030056
  • GC16P031262
  • GC16P030770
  • GC16P030809
  • GC16P030681
  • GC16P030773
  • GC16P028337

Summaries for RNF40 Gene

Entrez Gene Summary for RNF40 Gene

  • 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]

GeneCards Summary for RNF40 Gene

RNF40 (Ring Finger Protein 40) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Protein ubiquitination. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and ubiquitin-protein transferase activity. An important paralog of this gene is RNF20.

UniProtKB/Swiss-Prot Summary for RNF40 Gene

  • Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes.

Gene Wiki entry for RNF40 Gene

Additional gene information for RNF40 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RNF40 Gene

Genomics for RNF40 Gene

GeneHancer (GH) Regulatory Elements for RNF40 Gene

Promoters and enhancers for RNF40 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF40 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RNF40

Top Transcription factor binding sites by QIAGEN in the RNF40 gene promoter:
  • ATF-2
  • c-Ets-1
  • c-Jun
  • Cdc5
  • Ik-2
  • Lmo2
  • Nkx2-5
  • Pax-3
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for RNF40 Gene

Genomic Locations for RNF40 Gene
chr16:30,761,612-30,802,340
(GRCh38/hg38)
Size:
40,729 bases
Orientation:
Plus strand
chr16:30,772,933-30,787,628
(GRCh37/hg19)
Size:
14,696 bases
Orientation:
Plus strand

Genomic View for RNF40 Gene

Genes around RNF40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF40 Gene

Proteins for RNF40 Gene

  • Protein details for RNF40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75150-BRE1B_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase BRE1B
    Protein Accession:
    O75150
    Secondary Accessions:
    • A0A024QZG0
    • Q6AHZ6
    • Q6N005
    • Q7L3T6
    • Q8N615
    • Q96T18
    • Q9BSV9
    • Q9HC82

    Protein attributes for RNF40 Gene

    Size:
    1001 amino acids
    Molecular mass:
    113678 Da
    Quaternary structure:
    • Component of the RNF20/40 complex (also known as BRE1 complex) probably composed of 2 copies of RNF20/BRE1A and 2 copies of RNF40/BRE1B. Interacts with UBE2E1/UBCH6. Interacts with RB1 and WAC.
    SequenceCaution:
    • Sequence=BAA31636.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305}; Sequence=CAE45869.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305};

    Alternative splice isoforms for RNF40 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF40 Gene

Selected DME Specific Peptides for RNF40 Gene

O75150:
  • DFHRIYI
  • RKESELLKGLRAELKKAQESQKEMKLLLDMYKSAPKEQRD
  • RKKDAVLTKCFHVFCFECV
  • KKLRTEV
  • PINREMRHLI
  • LLIVNRYW
  • ETKVLEMETTVEDLQWDIEKLRKREQKLNKHLAEALEQLN
  • VTGQAFEDMQEQN
  • YKARLTCPCCN
  • EDISRLRRKLE
  • LSRADREKAK
  • KVLQFKNKKLAERLEQRQACEDELRERIEKLEKRQATDDA
  • RQRKCPKCN
  • PLSEPALAFVVALGASS
  • VEELCQRVYSRGDSE
  • QLEDTLAQVRKEYEMLRIEFEQ
  • QQLREKDDANFKLMSERIK
  • QRDKVQLMA

Post-translational modifications for RNF40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for RNF40 Gene

Gene Families for RNF40 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for RNF40 Gene

Blocks:
  • Zn-finger, RING
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RNF40 Gene

GenScript: Design optimal peptide antigens:
  • cDNA PSEC0225 fis, clone HEMBA1005766, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (B3KQV1_HUMAN)
  • RING finger protein 40 (BRE1B_HUMAN)
  • cDNA FLJ16291 fis, clone OCBBF2020048, moderately similar to Homo sapiens 95 kDa retinoblastoma protein binding protein (Q6ZN99_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75150

UniProtKB/Swiss-Prot:

BRE1B_HUMAN :
  • Belongs to the BRE1 family.
Family:
  • Belongs to the BRE1 family.
genes like me logo Genes that share domains with RNF40: view

Function for RNF40 Gene

Molecular function for RNF40 Gene

UniProtKB/Swiss-Prot Function:
Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27; Evidence={ECO:0000269 PubMed:16307923, ECO:0000269 PubMed:19410543};.

Enzyme Numbers (IUBMB) for RNF40 Gene

Phenotypes From GWAS Catalog for RNF40 Gene

Gene Ontology (GO) - Molecular Function for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003730 mRNA 3'-UTR binding IDA 19575011
GO:0004842 contributes_to ubiquitin-protein transferase activity IEA,IDA 16307923
GO:0005515 protein binding IPI 10944455
GO:0016740 transferase activity IEA --
GO:0017075 syntaxin-1 binding IEA --
genes like me logo Genes that share ontologies with RNF40: view
genes like me logo Genes that share phenotypes with RNF40: view

Animal Model Products

miRNA for RNF40 Gene

miRTarBase miRNAs that target RNF40

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNF40 Gene

Localization for RNF40 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF40 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNF40 gene
Compartment Confidence
nucleus 5
cytosol 3
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000151 ubiquitin ligase complex IDA 16307923
GO:0005634 nucleus IEA,IDA 10944455
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IEA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with RNF40: view

Pathways & Interactions for RNF40 Gene

genes like me logo Genes that share pathways with RNF40: view

Pathways by source for RNF40 Gene

1 Cell Signaling Technology pathway for RNF40 Gene
1 GeneTex pathway for RNF40 Gene

UniProtKB/Swiss-Prot O75150-BRE1B_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for RNF40 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006511 ubiquitin-dependent protein catabolic process ISS --
GO:0007346 NOT regulation of mitotic cell cycle IMP 19575011
GO:0010390 histone monoubiquitination IEA,IDA 16307923
GO:0016567 protein ubiquitination IEA,TAS --
genes like me logo Genes that share ontologies with RNF40: view

Drugs & Compounds for RNF40 Gene

No Compound Related Data Available

Transcripts for RNF40 Gene

mRNA/cDNA for RNF40 Gene

4 REFSEQ mRNAs :
26 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNF40 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d ^ 11 ^ 12a ·
SP1: - -
SP2: - - - - - - - - -
SP3: - -
SP4: - - - - - - - - -
SP5:
SP6: - - - - - - - - - - - -
SP7:
SP8:
SP9: - - - - - - - - - - - - - - - - - - -
SP10: -
SP11: - -
SP12: - -
SP13:

ExUns: 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9: - - - - - - - - -
SP10:
SP11:
SP12:
SP13:

Relevant External Links for RNF40 Gene

GeneLoc Exon Structure for
RNF40

Expression for RNF40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RNF40 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RNF40 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.5), Lymph node (10.3), and Liver (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNF40 Gene



Protein tissue co-expression partners for RNF40 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RNF40

SOURCE GeneReport for Unigene cluster for RNF40 Gene:

Hs.65238

mRNA Expression by UniProt/SwissProt for RNF40 Gene:

O75150-BRE1B_HUMAN
Tissue specificity: Ubiquitously expressed. Expressed at higher level in testis, heart and pancreas, while it is only weakly expressed in lung, skeletal muscle and small intestine.

Evidence on tissue expression from TISSUES for RNF40 Gene

  • Nervous system(5)
  • Skin(4.4)
  • Liver(4.2)
  • Lung(2.7)
  • Intestine(2.4)
genes like me logo Genes that share expression patterns with RNF40: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF40 Gene

Orthologs for RNF40 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RNF40 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNF40 31 30
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RNF40 31 30
  • 91.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RNF40 31 30
  • 90.04 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf40 17 31 30
  • 87.05 (n)
rat
(Rattus norvegicus)
Mammalia Rnf40 30
  • 87.05 (n)
oppossum
(Monodelphis domestica)
Mammalia RNF40 31
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF40 31
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RNF40 31
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf40 30
  • 68.19 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398536 30
zebrafish
(Danio rerio)
Actinopterygii rnf40 31
  • 67 (a)
OneToOne
wufk48a06 30