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Aliases for RNF40 Gene

Aliases for RNF40 Gene

  • Ring Finger Protein 40, E3 Ubiquitin Protein Ligase 2 3
  • 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
  • E3 Ubiquitin-Protein Ligase BRE1B 3
  • Ring Finger Protein 40 2
  • RING Finger Protein 40 4
  • Rb-Associated Protein 3
  • EC 6.3.2.- 4
  • KIAA0661 4
  • EC 6.3.2 64
  • STARING 3

External Ids for RNF40 Gene

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, E3 Ubiquitin Protein Ligase) is a Protein Coding gene. Diseases associated with RNF40 include retinoblastoma. Among its related pathways are Cell Cycle / Checkpoint Control and Protein Stability. GO annotations related to this gene include protein homodimerization activity and ubiquitin protein ligase binding. 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

Genomic Location for RNF40 Gene

Start:
30,761,612 bp from pter
End:
30,776,307 bp from pter
Size:
14,696 bases
Orientation:
Plus strand

Genomic View for RNF40 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RNF40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF40 Gene

Regulatory Elements 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
  • Ubiquitination at Lys788

Domains for RNF40 Gene

Gene Families for RNF40 Gene

HGNC:
  • RNF :RING-type (C3HC4) zinc fingers

Protein Domains for RNF40 Gene

UniProtKB/Swiss-Prot:

BRE1B_HUMAN
Family:
  • Belongs to the BRE1 family.:
    • O75150
Similarity:
  • Contains 1 RING-type zinc finger.:
    • O75150
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:0003730 mRNA 3-UTR binding IDA 19575011
GO:0004842 contributes_to ubiquitin-protein transferase activity IDA 16307923
GO:0005515 protein binding IPI 10944455
GO:0008270 zinc ion binding IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with RNF40: view

Phenotypes for RNF40 Gene

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

No data available for Animal Models , Transcription Factor Targeting 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
plasma membrane 4
cytosol 3

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 IDA 10944455
GO:0005654 nucleoplasm IDA --
GO:0016020 membrane IDA 19946888
GO:0033503 HULC complex IDA 19410543
genes like me logo Genes that share ontologies with RNF40: view

Pathways for RNF40 Gene

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

Pathways by source for RNF40 Gene

UniProtKB/Swiss-Prot O75150-BRE1B_HUMAN

  • Pathway: Protein modification; protein ubiquitination

Gene Ontology (GO) - Biological Process for RNF40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process ISS --
GO:0007346 NOT regulation of mitotic cell cycle IMP 19575011
GO:0010390 histone monoubiquitination IDA 16307923
GO:0033523 histone H2B ubiquitination IDA 16307923
GO:1900364 negative regulation of mRNA polyadenylation IMP 19575011
genes like me logo Genes that share ontologies with RNF40: view

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

Integrated Proteomics: protein expression 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 expressions with RNF40: view

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 36
  • 99.51 (n)
  • 99.33 (a)
RNF40 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RNF40 36
  • 90.04 (n)
  • 95.6 (a)
RNF40 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RNF40 36
  • 91.48 (n)
  • 96.4 (a)
RNF40 37
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf40 36
  • 87.05 (n)
  • 92.51 (a)
Rnf40 16
Rnf40 37
  • 92 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RNF40 37
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF40 37
  • 75 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rnf40 36
  • 87.05 (n)
  • 92.61 (a)
lizard
(Anolis carolinensis)
Reptilia RNF40 37
  • 74 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC398536 36
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf40 36
  • 68.19 (n)
  • 72.1 (a)
zebrafish
(Danio rerio)
Actinopterygii rnf40 37
  • 67 (a)
OneToOne
wufk48a06 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007335 36
  • 57.63 (n)
  • 50.11 (a)
fruit fly
(Drosophila melanogaster)
Insecta Bre1 36
  • 57.4 (n)
  • 49.58 (a)
Bre1 37
  • 43 (a)
OneToMany
CG10542 38
  • 47 (a)
worm
(Caenorhabditis elegans)
Secernentea rfp-1 36
  • 41.32 (n)
  • 28.37 (a)
rfp-1 37
  • 23 (a)
OneToMany
R05D3.4 38
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BRE1 37
  • 20 (a)
OneToMany
BRE1 39
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4379 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10524 37
  • 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

Selected 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 MAF
rs1048622 -- 30,774,125(+) AAACT(C/T)AGGGG utr-variant-3-prime
rs1057734 -- 30,767,360(+) GAAGT(A/C)TCAGG intron-variant
rs1530201 -- 30,767,324(+) tgaca(A/G)atagg intron-variant
rs3747486 -- 30,775,606(+) CTCAG(C/T)TGGGT utr-variant-3-prime
rs4889507 -- 30,771,399(+) gatca(C/T)gaggt intron-variant

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

Relevant External Links for RNF40 Gene

HapMap Linkage Disequilibrium report
RNF40

Disorders for RNF40 Gene

(1) MalaCards Diseases for RNF40 Gene

Search for RNF40 Gene in MalaCards »
genes like me logo Genes that share disorders with RNF40: view

No data available for UniProtKB/Swiss-Prot for RNF40 Gene

Publications for RNF40 Gene

  1. 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 4 23
  2. 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 4
  3. 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
  4. 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
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for RNF40 Gene

Sources for RNF40 Gene

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