Human Gene RNF40 (uc002dzq.3) Description and Page Index
  Description: Homo sapiens ring finger protein 40, E3 ubiquitin protein ligase (RNF40), transcript variant 1, mRNA.
RefSeq Summary (NM_014771): 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].
Transcript (Including UTRs)
   Position: hg19 chr16:30,772,933-30,787,628 Size: 14,696 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr16:30,773,867-30,785,435 Size: 11,569 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:30,772,933-30,787,628)mRNA (may differ from genome)Protein (1001 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: BRE1B_HUMAN
DESCRIPTION: RecName: Full=E3 ubiquitin-protein ligase BRE1B; Short=BRE1-B; EC=6.3.2.-; AltName: Full=95 kDa retinoblastoma-associated protein; Short=RBP95; AltName: Full=RING finger protein 40;
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.
PATHWAY: Protein modification; protein ubiquitination.
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.
INTERACTION: P06400:RB1; NbExp=3; IntAct=EBI-744408, EBI-491274; Q5VTR2:RNF20; NbExp=10; IntAct=EBI-744408, EBI-2372238;
SUBCELLULAR LOCATION: Nucleus.
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.
SIMILARITY: Belongs to the BRE1 family.
SIMILARITY: Contains 1 RING-type zinc finger.
SEQUENCE CAUTION: Sequence=BAA31636.2; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=CAE45869.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 38.60 RPKM in Testis
Total median expression: 839.04 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -371.63820-0.453 Picture PostScript Text
3' UTR -967.832193-0.441 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD
IPR017907 - Znf_RING_CS

Pfam Domains:
PF00097 - Zinc finger, C3HC4 type (RING finger)
PF13920 - Zinc finger, C3HC4 type (RING finger)

SCOP Domains:
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on O75150
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003730 mRNA 3'-UTR binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0017075 syntaxin-1 binding
GO:0031624 ubiquitin conjugating enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0042803 protein homodimerization activity
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding

Biological Process:
GO:0006325 chromatin organization
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0010390 histone monoubiquitination
GO:0016567 protein ubiquitination
GO:0033523 histone H2B ubiquitination
GO:0043434 response to peptide hormone
GO:1900364 negative regulation of mRNA polyadenylation
GO:1901800 positive regulation of proteasomal protein catabolic process
GO:1902916 positive regulation of protein polyubiquitination
GO:2001168 positive regulation of histone H2B ubiquitination
GO:0007346 regulation of mitotic cell cycle

Cellular Component:
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0019898 extrinsic component of membrane
GO:0032991 macromolecular complex
GO:0033503 HULC complex
GO:0043005 neuron projection
GO:0043679 axon terminus


-  Descriptions from all associated GenBank mRNAs
  LF207918 - JP 2014500723-A/15421: Polycomb-Associated Non-Coding RNAs.
LF383552 - JP 2014500723-A/191055: Polycomb-Associated Non-Coding RNAs.
AK297531 - Homo sapiens cDNA FLJ58265 complete cds, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-).
AK304521 - Homo sapiens cDNA FLJ59150 complete cds, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-).
AK293710 - Homo sapiens cDNA FLJ58523 complete cds, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-).
AK027406 - Homo sapiens cDNA FLJ14500 fis, clone NT2RM1000086.
CR627431 - Homo sapiens mRNA; cDNA DKFZp686K191 (from clone DKFZp686K191).
BX640763 - Homo sapiens mRNA; cDNA DKFZp686I01210 (from clone DKFZp686I01210).
AK291666 - Homo sapiens cDNA FLJ78667 complete cds, highly similar to Homo sapiens ring finger protein 40 (RNF40), transcript variant 1, mRNA.
AK131310 - Homo sapiens cDNA FLJ16291 fis, clone OCBBF2020048, moderately similar to Homo sapiens 95 kDa retinoblastoma protein binding protein.
LF213929 - JP 2014500723-A/21432: Polycomb-Associated Non-Coding RNAs.
AK294258 - Homo sapiens cDNA FLJ58158 complete cds, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-).
AF122819 - Homo sapiens Rb-associated protein mRNA, complete cds.
AB014561 - Homo sapiens KIAA0661 mRNA for KIAA0661 protein.
JD479400 - Sequence 460424 from Patent EP1572962.
BC006133 - Homo sapiens ring finger protein 40, mRNA (cDNA clone MGC:13051 IMAGE:3628183), complete cds.
BC011769 - Homo sapiens ring finger protein 40, mRNA (cDNA clone MGC:19735 IMAGE:3607432), complete cds.
BC018647 - Homo sapiens ring finger protein 40, mRNA (cDNA clone MGC:1973 IMAGE:2967275), complete cds.
JD055727 - Sequence 36751 from Patent EP1572962.
JD406978 - Sequence 388002 from Patent EP1572962.
DQ896794 - Synthetic construct Homo sapiens clone IMAGE:100011254; FLH199441.01L; RZPDo839H0781D ring finger protein 40 (RNF40) gene, encodes complete protein.
AB383945 - Synthetic construct DNA, clone: pF1KSDA0661, Homo sapiens RNF40 gene for E3 ubiquitin-protein ligase BRE1B, complete cds, without stop codon, in Flexi system.
DQ893443 - Synthetic construct clone IMAGE:100006073; FLH199534.01X; RZPDo839H0782D ring finger protein 40 (RNF40) gene, encodes complete protein.
CU675265 - Synthetic construct Homo sapiens gateway clone IMAGE:100017877 5' read RNF40 mRNA.
KU178492 - Homo sapiens ring finger protein 40 isoform 1 (RNF40) mRNA, partial cds.
KU178493 - Homo sapiens ring finger protein 40 isoform 2 (RNF40) mRNA, complete cds, alternatively spliced.
KJ892854 - Synthetic construct Homo sapiens clone ccsbBroadEn_02248 RNF40 gene, encodes complete protein.
AK075526 - Homo sapiens cDNA PSEC0225 fis, clone HEMBA1005766, highly similar to Ubiquitin-protein ligase BRE1B (EC 6.3.2.-).
DQ584519 - Homo sapiens piRNA piR-51631, complete sequence.
LF207919 - JP 2014500723-A/15422: Polycomb-Associated Non-Coding RNAs.
LF370024 - JP 2014500723-A/177527: Polycomb-Associated Non-Coding RNAs.
LF370025 - JP 2014500723-A/177528: Polycomb-Associated Non-Coding RNAs.
BC030802 - Homo sapiens, Similar to ring finger protein 40, clone IMAGE:4404152, mRNA, partial cds.
BC113827 - Homo sapiens cDNA clone IMAGE:40024160.
BC004527 - Homo sapiens ring finger protein 40, mRNA (cDNA clone IMAGE:3603934), partial cds.
AK054773 - Homo sapiens cDNA FLJ30211 fis, clone BRACE2001607.
JD122618 - Sequence 103642 from Patent EP1572962.
JD212315 - Sequence 193339 from Patent EP1572962.
JD330284 - Sequence 311308 from Patent EP1572962.
JD556003 - Sequence 537027 from Patent EP1572962.
JD374216 - Sequence 355240 from Patent EP1572962.
JD107165 - Sequence 88189 from Patent EP1572962.
JD210534 - Sequence 191558 from Patent EP1572962.
JD381063 - Sequence 362087 from Patent EP1572962.
JD381064 - Sequence 362088 from Patent EP1572962.
JD541084 - Sequence 522108 from Patent EP1572962.
JD222474 - Sequence 203498 from Patent EP1572962.
JD468324 - Sequence 449348 from Patent EP1572962.
JD380408 - Sequence 361432 from Patent EP1572962.
JD506945 - Sequence 487969 from Patent EP1572962.
JD531302 - Sequence 512326 from Patent EP1572962.
JD495631 - Sequence 476655 from Patent EP1572962.
JD532507 - Sequence 513531 from Patent EP1572962.
JD493944 - Sequence 474968 from Patent EP1572962.
MA619129 - JP 2018138019-A/191055: Polycomb-Associated Non-Coding RNAs.
MA449506 - JP 2018138019-A/21432: Polycomb-Associated Non-Coding RNAs.
MA605601 - JP 2018138019-A/177527: Polycomb-Associated Non-Coding RNAs.
MA605602 - JP 2018138019-A/177528: Polycomb-Associated Non-Coding RNAs.
MA443495 - JP 2018138019-A/15421: Polycomb-Associated Non-Coding RNAs.
MA443496 - JP 2018138019-A/15422: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O75150 (Reactome details) participates in the following event(s):

R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-8852135 Protein ubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: BRE1B, BRE1B_HUMAN, KIAA0661, NM_014771, NP_055586, O75150, Q6AHZ6, Q6N005, Q7L3T6, Q8N615, Q96T18, Q9BSV9, Q9HC82
UCSC ID: uc002dzq.3
RefSeq Accession: NM_014771
Protein: O75150 (aka BRE1B_HUMAN)
CCDS: CCDS10691.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014771.3
exon count: 20CDS single in 3' UTR: no RNA size: 6022
ORF size: 3006CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 5973.50frame shift in genome: no % Coverage: 99.95
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.