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Aliases for RNF40 Gene

Aliases for RNF40 Gene

  • Ring Finger Protein 40 2 3
  • Ring Finger Protein 40, E3 Ubiquitin Protein Ligase 2 3 5
  • 95 KDa Retinoblastoma-Associated Protein 3 4
  • BRE1-B 3 4
  • BRE1B 3 4
  • RBP95 3 4
  • 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 6.3.2.- 4
  • KIAA0661 4
  • EC 6.3.2 63
  • 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 Chromatin Regulation / Acetylation. 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 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNF40 Gene

Genomics for RNF40 Gene

Regulatory Elements for RNF40 Gene

Enhancers for RNF40 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around RNF40 on UCSC Golden Path with GeneCards custom track

Promoters for RNF40 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RNF40 on UCSC Golden Path with GeneCards custom track

Genomic Location for RNF40 Gene

Chromosome:
16
Start:
30,761,612 bp from pter
End:
30,802,340 bp from pter
Size:
40,729 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:
    • Q6AHZ6
    • Q6N005
    • Q7L3T6
    • Q8N615
    • Q96T18
    • Q9BSV9
    • Q9HC82

    Protein attributes for RNF40 Gene

    Size:
    1001 amino acids
    Molecular mass:
    113650 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=Translation N-terminally shortened.; 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

Proteomics data for RNF40 Gene at MOPED

Post-translational modifications for RNF40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for RNF40 Gene

Gene Families for RNF40 Gene

Protein Domains for RNF40 Gene

Graphical View of Domain Structure for InterPro Entry

O75150

UniProtKB/Swiss-Prot:

BRE1B_HUMAN :
  • Belongs to the BRE1 family.
  • Contains 1 RING-type zinc finger.
Family:
  • Belongs to the BRE1 family.
Similarity:
  • Contains 1 RING-type zinc finger.
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.

Enzyme Numbers (IUBMB) for RNF40 Gene

Gene Ontology (GO) - Molecular Function for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016874 ligase activity IEA --
GO:0031625 ubiquitin protein ligase binding IPI 16307923
GO:0042803 protein homodimerization activity IPI 10944455
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

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
Jensen Localization Image for RNF40 Gene COMPARTMENTS Subcellular localization image for RNF40 gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0016020 membrane IDA 19946888
GO:0019898 extrinsic component of membrane IEA --
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 GeneTex pathway for RNF40 Gene
1 Cell Signaling Technology 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:0007346 NOT regulation of mitotic cell cycle IMP 19575011
GO:0010390 histone monoubiquitination IDA 16307923
GO:0033523 histone H2B ubiquitination IDA 16307923
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

Unigene Clusters for RNF40 Gene

Ring finger protein 40, E3 ubiquitin protein ligase:
Representative Sequences:

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
ECgene alternative splicing isoforms for
RNF40

Expression for RNF40 Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for RNF40 Gene



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.
genes like me logo Genes that share expression patterns with RNF40: view

Protein tissue co-expression partners for RNF40 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues 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
cow
(Bos Taurus)
Mammalia RNF40 35
  • 90.04 (n)
  • 95.6 (a)
RNF40 36
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RNF40 35
  • 91.48 (n)
  • 96.4 (a)
RNF40 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf40 35
  • 87.05 (n)
  • 92.51 (a)
Rnf40 16
Rnf40 36
  • 92 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RNF40 35
  • 99.51 (n)
  • 99.33 (a)
RNF40 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rnf40 35
  • 87.05 (n)
  • 92.61 (a)
oppossum
(Monodelphis domestica)
Mammalia RNF40 36
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF40 36
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RNF40 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf40 35
  • 68.19 (n)
  • 72.1 (a)
African clawed frog
(Xenopus laevis)
Amphibia LOC398536 35
zebrafish
(Danio rerio)
Actinopterygii wufk48a06 35
rnf40 36
  • 67 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG10542 37
  • 47 (a)
Bre1 35
  • 57.4 (n)
  • 49.58 (a)
Bre1 36
  • 43 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007335 35
  • 57.63 (n)
  • 50.11 (a)
worm
(Caenorhabditis elegans)
Secernentea R05D3.4 37
  • 30 (a)
rfp-1 35
  • 41.32 (n)
  • 28.37 (a)
rfp-1 36
  • 23 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BRE1 36
  • 20 (a)
OneToMany
BRE1 38
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4379 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10524 36
  • 42 (a)
OneToMany
Species with no ortholog for RNF40:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RNF40 Gene

ENSEMBL:
Gene Tree for RNF40 (if available)
TreeFam:
Gene Tree for RNF40 (if available)

Paralogs for RNF40 Gene

Paralogs for RNF40 Gene

(1) SIMAP similar genes for RNF40 Gene using alignment to 8 proteins:

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

Variants for RNF40 Gene

Sequence variations from dbSNP and Humsavar for RNF40 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs11556801 - 30,766,835(+) GCTGC(A/G)CATCG reference, missense
rs7195142 - 30,768,395(+) GCTTC(A/G)GGAAC reference, missense
rs9921630 -- 30,772,656(+) TGGAC(A/G)CTTGA intron-variant
rs9921835 -- 30,800,570(+) tcccg(A/G)gttca intron-variant, downstream-variant-500B
rs61754473 -- 30,772,145(+) GTCTA(C/T)GCAGA reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for RNF40 Gene

Variant ID Type Subtype PubMed ID
nsv469724 CNV Loss 16826518
nsv833188 CNV Loss 17160897
nsv905728 CNV Loss 21882294
nsv905729 CNV Loss 21882294
nsv9438 CNV Gain 18304495

Variation tolerance for RNF40 Gene

Residual Variation Intolerance Score: 3.95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.12; 22.77% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for RNF40 Gene

Disorders for RNF40 Gene

Relevant External Links for RNF40

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RNF40

No disorders were found for RNF40 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF40 Gene

Publications for RNF40 Gene

  1. RBP95, a novel leucine zipper protein, binds to the retinoblastoma protein. (PMID: 10944455) Wen H. … Ao S. (Biochem. Biophys. Res. Commun. 2000) 2 3 4 67
  2. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. (PMID: 16307923) Zhu B. … Reinberg D. (Mol. Cell 2005) 3 23
  3. Staring, a novel E3 ubiquitin-protein ligase that targets syntaxin 1 for degradation. (PMID: 12121982) Chin L.S. … Li L. (J. Biol. Chem. 2002) 2 3
  4. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9734811) Ishikawa K. … Ohara O. (DNA Res. 1998) 2 3
  5. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. (PMID: 26871637) Yang X. … Vidal M. (Cell 2016) 3

Products for RNF40 Gene

Sources for RNF40 Gene

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