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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
  • 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
  • E3 Ubiquitin-Protein Ligase BRE1B 3
  • RING Finger Protein 40 4
  • Rb-Associated Protein 3
  • EC 2.3.2.27 4
  • KIAA0661 4
  • 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. Diseases associated with RNF40 include Phosphorylase Kinase Deficiency. 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 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 , fRNAdb sequence ontologies and piRNA Summary for RNF40 Gene

Genomics for RNF40 Gene

GeneHancer (GH) Regulatory Elements for RNF40 Gene

Promoters and enhancers for RNF40 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J030760 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +0.5 482 3.5 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 CCDC189 RNF40 PIR45630 ZNF747 ZNF785 PRRT2 SETD1A FUS ZNF720 LOC647086
GH16J030566 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 82 -191.7 -191738 6 ZFP64 FEZF1 DMAP1 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 ZNF688 SETD1A SRCAP ENSG00000260267 NPIPB13 INO80E ZNF764 ZNF747 SMG1P5 SMG1P2
GH16J030052 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 80 -707.4 -707407 3.1 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ALDOA FAM57B ENSG00000285043 SETD1A SRCAP INO80E NPIPB12 ZNF764 SMG1P5 SMG1P2
GH16J029803 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 64.5 -953.2 -953169 10.3 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 PRRT2 ENSG00000280607 ENSG00000259952 GC16P029807 GC16P029809 GC16P029961 MAZ PIR38319 PIR43581 PIR52049
GH16J030872 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE 78.2 +113.3 113273 5.3 MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D MIR762HG MIR4519 RNF40 INO80E SETD1A SRCAP ENSG00000260267 FBRS BCL7C ZNF764
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNF40 on UCSC Golden Path with GeneCards custom track

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

Post-translational modifications for RNF40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RNF40 Gene

Domains & Families for RNF40 Gene

Gene Families for RNF40 Gene

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

Protein Domains for RNF40 Gene

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:
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.

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 IDA,IEA 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

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 GeneTex pathway for RNF40 Gene
1 BioSystems 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 IDA,IEA 16307923
GO:0016567 protein ubiquitination 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

Unigene Clusters for RNF40 Gene

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

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
ECgene alternative splicing isoforms for
RNF40

Expression for RNF40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of RNF40 Gene:

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 34 33
  • 99.51 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RNF40 34 33
  • 91.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RNF40 34 33
  • 90.04 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf40 16 34 33
  • 87.05 (n)
rat
(Rattus norvegicus)
Mammalia Rnf40 33
  • 87.05 (n)
oppossum
(Monodelphis domestica)
Mammalia RNF40 34
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNF40 34
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RNF40 34
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf40 33
  • 68.19 (n)
African clawed frog
(Xenopus laevis)
Amphibia LOC398536 33
zebrafish
(Danio rerio)
Actinopterygii rnf40 34
  • 67 (a)
OneToOne
wufk48a06 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007335 33
  • 57.63 (n)
fruit fly
(Drosophila melanogaster)
Insecta Bre1 34 33
  • 57.4 (n)
OneToMany
CG10542 35
  • 47 (a)
worm
(Caenorhabditis elegans)
Secernentea rfp-1 34 33
  • 41.32 (n)
OneToMany
R05D3.4 35
  • 30 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BRE1 36 34
  • 20 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10524 34
  • 42 (a)
OneToMany
Cin.4379 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4379 33
Species where no ortholog for RNF40 was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RNF40: view image

Paralogs for RNF40 Gene

Paralogs for RNF40 Gene

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

  • BRE1B_HUMAN
  • F8W8Z4_HUMAN
  • H3BP71_HUMAN
  • H3BQ99_HUMAN
  • H3BS50_HUMAN
  • H3BUL6_HUMAN
  • I3L332_HUMAN
  • R4GN66_HUMAN
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 Variation AA Info Type
rs886051919 likely-benign, Glycogen phosphorylase kinase deficiency 30,759,636(+) T/C upstream_transcript_variant
rs886051920 uncertain-significance, Glycogen phosphorylase kinase deficiency 30,759,682(+) G/A upstream_transcript_variant
rs886051921 uncertain-significance, Glycogen phosphorylase kinase deficiency 30,760,976(+) A/G upstream_transcript_variant
rs886051922 uncertain-significance, Glycogen phosphorylase kinase deficiency 30,761,085(+) T/C upstream_transcript_variant
rs1000129251 -- 30,776,333(+) C/CC downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant

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

Variant ID Type Subtype PubMed ID
nsv9438 CNV gain 18304495
nsv833188 CNV loss 17160897
nsv469724 CNV loss 16826518

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)

Additional Variant Information for RNF40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF40

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF40 Gene

Disorders for RNF40 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RNF40 Gene - From: GeneCards

Disorder Aliases PubMed IDs
phosphorylase kinase deficiency
  • glycogen storage disease type ix
- elite association - COSMIC cancer census association via MalaCards
Search RNF40 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RNF40

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

No data available for UniProtKB/Swiss-Prot and Genatlas 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 (Molecular cell 2005) 3 4 22 58
  2. RBP95, a novel leucine zipper protein, binds to the retinoblastoma protein. (PMID: 10944455) Wen H … Ao S (Biochemical and biophysical research communications 2000) 2 3 4 58
  3. 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 research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4 58
  4. WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. (PMID: 21329877) Zhang F … Yu X (Molecular cell 2011) 3 4 58
  5. RAD6-Mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. (PMID: 19410543) Kim J … Roeder RG (Cell 2009) 3 4 58

Products for RNF40 Gene