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RNF40 Gene

protein-coding   GIFtS: 62
GCID: GC16P030775

Ring Finger Protein 40, E3 Ubiquitin Protein Ligase

(Previous name: ring finger protein 40)
  See RNF40-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ring Finger Protein 40, E3 Ubiquitin Protein Ligase1 2     STARING2
RING Finger Protein 401 3     BRE1 E3 Ubiquitin Ligase Homolog B2
95 KDa Retinoblastoma-Associated Protein2 3     E3 Ubiquitin-Protein Ligase BRE1B2
BRE1-B2 3     Rb-Associated Protein2
BRE1B2 3     EC 6.3.2.-3
RBP952 3     KIAA06613
BRE1 E3 Ubiquitin Ligase Homolog B (S. Cerevisiae)1     EC 6.3.28
95 KDa Retinoblastoma Protein Binding Protein2     

External Ids:    HGNC: 168671   Entrez Gene: 98102   Ensembl: ENSG000001035497   OMIM: 6077005   UniProtKB: O751503   

Export aliases for RNF40 gene to outside databases

Previous GC identifers: GC16P030056 GC16P031262 GC16P030770 GC16P030809 GC16P030681 GC16P030773 GC16P028337


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. 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: BRE1B_HUMAN, O75150
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

Gene Wiki entry for RNF40 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000016.9  NC_018927.2  NT_187260.1  
Regulatory elements:
   Regulatory transcription factor binding sites in the RNF40 gene promoter:
         ATF-2   Lmo2   Nkx2-5   Cdc5   c-Ets-1   Pax-3   PPAR-gamma1   Ik-2   PPAR-gamma2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRNF40 promoter sequence
   Search Chromatin IP Primers for RNF40

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNF40


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 16p11.2-p11.1   Ensembl cytogenetic band:  16p11.2   HGNC cytogenetic band: 16p11.2-p11.1

RNF40 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNF40 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P030775:  view genomic region     (about GC identifiers)

Start:
30,772,933 bp from pter      End:
30,787,628 bp from pter
Size:
14,696 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: BRE1B_HUMAN, O75150 (See protein sequence)
Recommended Name: E3 ubiquitin-protein ligase BRE1B  
Size: 1001 amino acids; 113650 Da
Subunit: 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
Sequence caution: Sequence=BAA31636.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=CAE45869.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;
Secondary accessions: Q6AHZ6 Q6N005 Q7L3T6 Q8N615 Q96T18 Q9BSV9 Q9HC82
Alternative splicing: 3 isoforms:  O75150-1   O75150-3   O75150-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RNF40: NX_O75150

Explore proteomics data for RNF40 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys788
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for RNF40 (O75150) (see all 18)
     DFHRIYI  KKLRTEV  LLIVNRYW  RQRKCPKCN 


    See RNF40 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001193962.1  NP_001193963.1  NP_001273501.1  NP_055586.1  

    ENSEMBL proteins: 
     ENSP00000455678   ENSP00000325677   ENSP00000457697   ENSP00000456538   ENSP00000455180  
     ENSP00000350563   ENSP00000460142   ENSP00000473507   ENSP00000384942  

    RNF40 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for RNF40

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    RNF: RING-type (C3HC4) zinc fingers

    4 InterPro protein domains:
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR018957 Znf_C3HC4_RING-type
     IPR013083 Znf_RING/FYVE/PHD

    Graphical View of Domain Structure for InterPro Entry O75150

    ProtoNet protein and cluster: O75150

    1 Blocks protein domain: IPB001841 Zn-finger

    UniProtKB/Swiss-Prot: BRE1B_HUMAN, O75150
    Similarity: Belongs to the BRE1 family
    Similarity: Contains 1 RING-type zinc finger


    Find genes that share domains with RNF40           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: BRE1B_HUMAN, O75150
    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): EC 6.3.2.-1 EC 6.3.22

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0004842contributes to ubiquitin-protein ligase activity IDA16307923
    GO:0005515protein binding IPI10944455
    GO:0008270zinc ion binding IEA--
    GO:0017075syntaxin-1 binding IEA--
    GO:0031625ubiquitin protein ligase binding IPI16307923
         
    Find genes that share ontologies with RNF40           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for RNF40:
     Decreased POU5F1-GFP protein e  Increased cell death HMECs cel  Synthetic lethal with Ras 

    Animal Models:
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RNF40
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RNF40

    miRNA
    Products:
        
    miRTarBase miRNAs that target RNF40:
    hsa-mir-92a-3p (MIRT049341), hsa-mir-331-3p (MIRT043403), hsa-mir-186-5p (MIRT045027), hsa-let-7b-5p (MIRT032413), hsa-mir-34a-5p (MIRT025228), hsa-mir-769-5p (MIRT039167), hsa-mir-1229-3p (MIRT036354)

    Block miRNA regulation of human, mouse, rat RNF40 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RNF40 (see all 27):
    hsa-miR-3673 hsa-miR-328 hsa-miR-125a-5p hsa-miR-185* hsa-miR-300 hsa-miR-3193 hsa-miR-331-3p hsa-miR-3150a-3p
    SwitchGear 3'UTR luciferase reporter plasmidRNF40 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat RNF40

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: RNF40 (NM_014771)
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF40


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    BRE1B_HUMAN, O75150: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane4
    cytosol3

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000151ubiquitin ligase complex IDA16307923
    GO:0005634nucleus IDA10944455
    GO:0005737cytoplasm ----
    GO:0005886plasma membrane ----
    GO:0033503HULC complex IDA19410543

    Find genes that share ontologies with RNF40           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for RNF40 About    
    See pathways by source

    SuperPathContained pathways About
    1Cell Cycle / Checkpoint Control
    Cell Cycle / Checkpoint Control0.32
    DNA Damage0.32
    2Protein Stability
    Protein Stability
    3Chromatin Regulation / Acetylation
    Chromatin Regulation / Acetylation


    Find genes that share SuperPaths with RNF40           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    4 Cell Signaling Technology (CST) Pathways for RNF40
        Chromatin Regulation / Acetylation
    Cell Cycle / Checkpoint Control
    DNA Damage
    Protein Stability


    UniProtKB/Swiss-Prot: BRE1B_HUMAN, O75150
    Pathway: Protein modification; protein ubiquitination

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RNF40: 

              Ubiquitination (Ubiquitylation) Pathway in human mouse rat
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Ubiquitin Ligases in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for RNF40

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for RNF40 (O751501, 2, 3 ENSP000003256774) via UniProtKB, MINT, STRING, and/or I2D (see all 240)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RNF20Q5VTR21, 2, 3, ENSP000003737724EBI-744408,EBI-2372238 MINT-8387176 I2D: score=2 STRING: ENSP00000373772
    ZNF451Q9Y4E52, 3, ENSP000003597404MINT-68396 I2D: score=5 STRING: ENSP00000359740
    TRIM51Q9BSJ12, 3MINT-66497 I2D: score=5 
    RB1P064001, 3, ENSP000002671634EBI-744408,EBI-491274 I2D: score=2 STRING: ENSP00000267163
    NCBP1Q091613, ENSP000003642894I2D: score=4 STRING: ENSP00000364289
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006511ubiquitin-dependent protein catabolic process ISS--
    GO:0010390histone monoubiquitination IDA16307923
    GO:0033523histone H2B ubiquitination IDA16307923

    Find genes that share ontologies with RNF40           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RNF40 (BRE1B)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RNF40 gene (4 alternative transcripts): 
    NM_001207033.1  NM_001207034.1  NM_001286572.2  NM_014771.3  

    Unigene Cluster for RNF40:

    Ring finger protein 40, E3 ubiquitin protein ligase
    Hs.65238  [show with all ESTs]
    Unigene Representative Sequence: NM_014771
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000563909 ENST00000324685(uc010caa.3 uc002dzq.3 uc010cab.3 uc010vfa.2 uc002dzr.3 uc010vfb.2)
    ENST00000566811 ENST00000565995 ENST00000563683 ENST00000357890 ENST00000565931
    ENST00000493683 ENST00000566703 ENST00000564260 ENST00000567365 ENST00000602784
    ENST00000402121(uc010vfc.1)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate RNF40 (see all 27):
    hsa-miR-3673 hsa-miR-328 hsa-miR-125a-5p hsa-miR-185* hsa-miR-300 hsa-miR-3193 hsa-miR-331-3p hsa-miR-3150a-3p
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    GenScript: all cDNA clones in your preferred vector: RNF40 (NM_014771)
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat RNF40
      QuantiFast Probe-based Assays in human, mouse, rat RNF40

    Additional mRNA sequence: 

    AB014561.1 AK027406.1 AK291666.1 AK297531.1 BC004527.2 BC006133.1 BC011769.2 BC018647.2 
    BC030802.1 BC113827.1 CR627431.1 

    Selected DOTS entries (see all 34):

    DT.97794528  DT.86853373  DT.100887020  DT.100887027  DT.102845511  DT.101985549  DT.97855945  DT.100887043 
    DT.445993  DT.120714173  DT.99933784  DT.120714140  DT.100060379  DT.95266484  DT.99933835  DT.100887040 
    DT.102838763  DT.120714007  DT.91802974  DT.100765701  DT.100772308  DT.100832268  DT.101985550  DT.120714034 

    Selected AceView cDNA sequences (see all 415):

    CB156733 AA911731 AI056228 AK057076 T15512 BC004527 NM_014771 AB014561 
    BC011769 F02347 AK075526 BU157598 BM802383 BC030802 AF122819 BU931202 
    BQ691549 BQ010157 CA455415 BM013880 BQ688446 AW248501 BM705224 BP366381 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RNF40 (see all 13)    About this scheme

    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:                                                                                                                                                            

    ExUns: 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c
    SP1:                                                                    -                           
    SP2:                                                                    -                           
    SP3:                                                                    -                           
    SP4:                                                                                                
    SP5:                                                                                                


    ECgene alternative splicing isoforms for RNF40

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RNF40 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTCCATCGGC
    RNF40 Expression
    About this image


    RNF40 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Testis (Reproductive System)
     
     Umbilical Cord (Extraembryonic Tissues)
    RNF40 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RNF40 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.65238

    UniProtKB/Swiss-Prot: BRE1B_HUMAN, O75150
    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

        Pathway & Disease-focused RT2 Profiler PCR Arrays including RNF40: 
              Ubiquitination (Ubiquitylation) Pathway in human mouse rat
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Ubiquitin Ligases in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals and fungi.

    Orthologs for RNF40 gene from Selected species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rnf401 , 5 ring finger protein 401, 5 87.05(n)1
    92.51(a)1
      7 (69.61 cM)5
    2339001  NM_172281.21  NP_758485.21 
     1275886985 
    lizard
    (Anolis carolinensis)
    Reptilia RNF406
    ring finger protein 40, E3 ubiquitin protein ligas...
    74(a)
    1 ↔ 1
    GL343516.1(65389-79938)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3985362 similar to ring finger protein 40 75.77(n)    BC042342.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufk48a062 Transcribed sequence with moderate similarity to protein more 81.28(n)    CF996002.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG105423
    Bre11
    Bre11 47(a)3
    57.4(n)1
    49.58(a)1
      64E83
    386521  NM_139732.31  NP_647989.21 
    worm
    (Caenorhabditis elegans)
    Secernentea R05D3.43
    rfp-11
    rfp-11 30(a)3
    41.32(n)1
    28.37(a)1
      III(8430362-8433823)3
    1761801  NM_001027529.31  NP_001022700.11 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes BRE1(YDL074C)4 E3 ubiquitin ligase, forms heterodimer with Rad6p to more   --   4(326149-324047) 851485  NP_010209.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RNF40 gene
    RNF202  
    1 SIMAP similar gene for RNF40 using alignment to 8 protein entries:     BRE1B_HUMAN (see all proteins):
    RNF20

    Find genes that share paralogs with RNF40           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RNF40 (see all 334)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 16 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3701990751,2
    C--30775658(+) CAGACC/TGCCTA 6 R C mis10--------
    rs2007795441,2
    C--30775671(+) GCGCCA/GGGTGG 6 Q R mis10--------
    rs1403503311,2
    C--30775684(+) GAACTC/TTGTCA 6 L syn11Minor allele frequency- T:0.00NA 4522
    rs1503025611,2
    C--30775692(+) TCAGCA/GAGTGT 6 Q R mis10--------
    rs1426103481,2
    F--30775699(+) GTGTAC/TAGCCG 6 Y syn11Minor allele frequency- T:0.00NA 4510
    rs2016317271,2
    --30775746(+) ATCCCC/TACCTG 3 -- int10--------
    rs1378760431,2
    --30775801(+) AAGGGC/TGGCCA 3 -- int10--------
    rs1426919201,2
    --30775987(+) ATCCAC/TAAGGC 3 -- int10--------
    rs1869303351,2
    C--30776301(+) CACCCA/GAGAGC 6 Q R mis10--------
    rs1901640261,2
    --30776314(+) GGCCGC/TGAGAA 6 R syn10--------

    HapMap Linkage Disequilibrium report for RNF40 (30772933 - 30787628 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for RNF40:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv905729CNV Loss21882294
    nsv469724CNV Loss16826518
    nsv905728CNV Loss21882294
    nsv833188CNV Loss17160897
    nsv9438CNV Gain18304495

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RNF40
    DNA2.0 Custom Variant and Variant Library Synthesis for RNF40

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607700    OMIM disorders: --

    1 disease for RNF40:    
    About MalaCards
    retinoblastoma


    Find genes that share disorders with RNF40           About GenesLikeMe


    Export disorders for RNF40 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RNF40 gene, integrated from 10 sources (see all 33):
    (articles sorted by number of sources associating them with RNF40)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. RBP95, a novel leucine zipper protein, binds to the retinoblastoma protein. (PubMed id 10944455)1, 2, 3 Wen H. and Ao S. (Biochem. Biophys. Res. Commun. 2000)
    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. (PubMed id 9734811)1, 2, 3 Ishikawa K.... Ohara O. (DNA Res. 1998)
    3. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. (PubMed id 16307923)1, 2, 9 Zhu B.... Reinberg D. (Mol. Cell 2005)
    4. WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. (PubMed id 21329877)1, 2 Zhang F. and Yu X. (Mol. Cell 2011)
    5. RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. (PubMed id 19410543)1, 2 Kim J.... Roeder R.G. (Cell 2009)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Staring, a novel E3 ubiquitin-protein ligase that targets syntaxin 1 for degradation. (PubMed id 12121982)1, 3 Chin L.S....Li L. (J. Biol. Chem. 2002)
    9. The tumor suppressor CDC73 interacts with the ring finger proteins RNF20 and RNF40 and is required for the maintenance of histone 2B monoubiquitination. (PubMed id 22021426)1 Hahn M.A....Marsh D.J. (Hum. Mol. Genet. 2012)
    10. Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability. (PubMed id 22354749)1 Chernikova S.B....Brown J.M. (Cancer Res. 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9810 HGNC: 16867 AceView: RNF40 Ensembl:ENSG00000103549 euGenes: HUgn9810
    ECgene: RNF40 H-InvDB: RNF40

    (According to HUGE)
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    HUGE: KIAA0661

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RNF40 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RNF40 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RNF40 gene:
    Search GeneIP for patents involving RNF40

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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