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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RWDD3 Gene

protein-coding   GIFtS: 51
GCID: GC01P095699

RWD Domain Containing 3

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
RWD Domain Containing 31 2
RSUME2 3
RWD-Containing Sumoylation Enhancer2 3
RWD Domain-Containing Protein 32

External Ids:    HGNC: 213931   Entrez Gene: 259502   Ensembl: ENSG000001224817   UniProtKB: Q9Y3V23   
ORGUL members:         
NONCODE14:n410501      

Export aliases for RWDD3 gene to outside databases

Previous GC identifers: GC01P095090 GC01P095171 GC01P095411 GC01P093821


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for RWDD3 Gene: 
RWDD3 (RWD domain containing 3) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with RWDD3 include hypoxia, and prostatitis. GO annotations related to this gene include protein binding.

UniProtKB/Swiss-Prot: RWDD3_HUMAN, Q9Y3V2
Function: Enhances the sumoylation of a number of proteins including HIF1A, PIAS and I-kappa-B, through direct
interaction with UBC9. Has no effect on ubiquitination

Gene Wiki entry for RWDD3 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000001.10  NC_018912.2  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RWDD3 gene promoter:
         NF-YA   CBF-C   NF-YB   CBF-A   CBF-B   FOXO4   CP1A   CP1C   NF-Y   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRWDD3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RWDD3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RWDD3


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

Entrez Gene cytogenetic band: 1p21.3   Ensembl cytogenetic band:  1p21.3   HGNC cytogenetic band: 1p22.1

RWDD3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RWDD3 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P095699:  view genomic region     (about GC identifiers)

Start:
95,699,711 bp from pter      End:
95,712,781 bp from pter
Size:
13,071 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RWDD3_HUMAN, Q9Y3V2 (See protein sequence)
Recommended Name: RWD domain-containing protein 3  
Size: 267 amino acids; 30543 Da
Subcellular location: Nucleus. Cytoplasm. Note=Colocalizes with UBC9/UBE2I in nuclear spots
1 PDB 3D structure from and Proteopedia for RWDD3:
2EBK (3D)    
Secondary accessions: A6NP44 A8K9F0 C9J9L7 C9JI45 Q08AJ7 Q6FID3 Q9BX35
Alternative splicing: 3 isoforms:  Q9Y3V2-1   Q9Y3V2-2   Q9Y3V2-3   

Explore the universe of human proteins at neXtProt for RWDD3: NX_Q9Y3V2

Explore proteomics data for RWDD3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y3V2

  • RWDD3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RWDD3 Protein Expression
    REFSEQ proteins (5 alternative transcripts): 
    NP_001121614.1  NP_001186611.1  NP_001265176.1  NP_001265177.1  NP_056300.2  

    ENSEMBL proteins: 
     ENSP00000359221   ENSP00000263893   ENSP00000397398  

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    Cloud-Clone Corp. Proteins for RWDD3 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    RWDD3 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR016135 UBQ-conjugating_enzyme/RWD
     IPR006575 RWD-domain

    Graphical View of Domain Structure for InterPro Entry Q9Y3V2

    ProtoNet protein and cluster: Q9Y3V2

    2 Blocks protein domains:
    IPB000608 Ubiquitin-conjugating enzymes
    IPB006575 RWD


    UniProtKB/Swiss-Prot: RWDD3_HUMAN, Q9Y3V2
    Domain: The RWD domain is required for the sumoylation enhancement activity (By similarity)
    Similarity: Contains 1 RWD domain


    RWDD3 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RWDD3_HUMAN, Q9Y3V2
    Function: Enhances the sumoylation of a number of proteins including HIF1A, PIAS and I-kappa-B, through direct
    interaction with UBC9. Has no effect on ubiquitination
    Induction: By hypoxia

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17956732
         
    RWDD3 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for RWDD3:
     Increased S DNA content 

    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RWDD3

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

    5 Interacting proteins for RWDD3 (Q9Y3V21, 3 ENSP000003592214) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBE2IP632791, 3, ENSP000003248974EBI-1549885,EBI-80168 I2D: score=1 STRING: ENSP00000324897
    SUMO1P631651, 3, ENSP000003760764EBI-1549885,EBI-80140 I2D: score=1 STRING: ENSP00000376076
    HIF1AQ166653, ENSP000003380184I2D: score=1 STRING: ENSP00000338018
    NFKBIAP259633, ENSP000002167974I2D: score=1 STRING: ENSP00000216797
    SENP2ENSP000002962574STRING: ENSP00000296257
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RWDD3

    Search CenterWatch for drugs/clinical trials and news about RWDD3

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RWDD3 gene (5 alternative transcripts): 
    NM_001128142.1  NM_001199682.1  NM_001278247.1  NM_001278248.1  NM_015485.4  

    Unigene Cluster for RWDD3:

    RWD domain containing 3
    Hs.709591  [show with all ESTs]
    Unigene Representative Sequence: BF693971
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370202(uc001dri.4 uc009wdu.3 uc001drf.4 uc009wdv.3 uc001drg.4)
    ENST00000263893 ENST00000492639 ENST00000495272(uc001drh.4) ENST00000497058
    ENST00000473397 ENST00000460571 ENST00000429514(uc001drd.4 uc010oty.2 uc009wdt.3)

    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AK292665.1 AK292699.1 AK296476.1 AL050062.1 BC010936.2 BC016307.1 BC065813.1 BC125142.1 
    CR533493.1 NR_037643.1 

    7 DOTS entries:

    DT.95368674  DT.100024370  DT.100778956  DT.100024371  DT.121397179  DT.212473  DT.100778957 

    24/211 AceView cDNA sequences (see all 211):

    AI457123 CD676564 CB163758 BQ575814 BU782509 BX956929 AK126344 BQ045393 
    CK430207 AA699431 AA328801 AA825527 BX352440 BU683936 BG566223 BX096742 
    AL598818 R93816 AI198536 BF589280 AI033223 CB163159 AA961117 AA336662 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for RWDD3 (see all 10)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d · 5e ^ 6a · 6b · 6c ^ 7a · 7b · 7c
    SP1:                                                                                                      
    SP2:                    -     -                 -     -     -     -     -                                 
    SP3:                    -     -                                   -     -                                 
    SP4:                    -                                   -     -     -                                 
    SP5:                                                        -     -     -                                 


    ECgene alternative splicing isoforms for RWDD3

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RWDD3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAGAAAACTT
    RWDD3 Expression
    About this image


    See RWDD3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RWDD3

    SOURCE GeneReport for Unigene cluster: Hs.709591

    UniProtKB/Swiss-Prot: RWDD3_HUMAN, Q9Y3V2
    Tissue specificity: Expressed in a wide number of tissues with highest expression in cerebellum, pituitary, heart,
    kidney, liver, stomach, pancreas, prostate and spleen. Low levels in thalamus, spinal cord, esophagus, thymus,
    lung and peripheral blood leukocytes

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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for RWDD3 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rwdd31 , 5 RWD domain containing 31, 5 84.14(n)1
    78.65(a)1
      3 (52.94 cM)5
    665681  NM_028456.31  NP_082732.21 
     1211554005 
    chicken
    (Gallus gallus)
    Aves RWDD31 RWD domain containing 3 76.07(n)
    69.17(a)
      424481  XM_422323.3  XP_422323.3 
    lizard
    (Anolis carolinensis)
    Reptilia RWDD36
    Uncharacterized protein
    64(a)
    1 ↔ 1
    4(89558017-89580587)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.174392 Transcribed sequence with weak similarity to protein more 78.29(n)    BX711078.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC059571.12   -- 70.98(n)   393729  BC059571.1 


    ENSEMBL Gene Tree for RWDD3 (if available)
    TreeFam Gene Tree for RWDD3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/39 SNPs in RWDD3 are shown (see all 39)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0243464
    ----see VAR_0243462 N K mis40--------
    VAR_0344204
    ----see VAR_0344202 V A mis40--------
    rs2593571,2
    C,F,O,A,H--95711478(-) GTATTA/CTTTCT 4 -- int1 trp321Minor allele frequency- C:0.09NS EA NA WA CSA 1050
    rs1834422411,2
    --95711649(+) TTTAGC/GTGCTG 4 -- int10--------
    rs1875599751,2
    --95711651(+) TAGCTC/GCTGAA 4 -- int10--------
    rs1911131821,2
    --95711959(+) CAAGTA/GTATAA 4 -- int10--------
    rs1822131741,2
    --95712014(+) AATAAA/GCCTAC 4 -- int10--------
    rs1483955941,2
    C--95712051(+) ACTTT-/GAG   
       ACTCA
    GAGTA
    4 -- int10--------
    rs1493504151,2
    C--95712385(+) GACTT-/AAGAAGCT 4 -- cds1 nc-transcript-variant0--------
    rs5920971,2
    C,F,A,H--95712458(+) AATAGC/AAGTGT 4 -- ut31 nc-transcript-variant87Minor allele frequency- A:0.13NS EA NA PA EU CA WA 4789

    HapMap Linkage Disequilibrium report for RWDD3 (95699711 - 95712781 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RWDD3:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv830636CNV Loss17160897
    nsv483022CNV Gain15286789
    nsv823620CNV Gain20364138

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for RWDD3:    About MalaCards
    hypoxia    prostatitis


    RWDD3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RWDD3

    Export disorders for RWDD3 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)
    About This Section

    PubMed articles for RWDD3 gene, integrated from 9 sources (see all 23):
    (articles sorted by number of sources associating them with RWDD3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2, 3 Wiemann S.... Poustka A. (2001)
    2. RSUME, a small RWD-containing protein, enhances SUMO conjugation and stabilizes HIF-1alpha during hypoxia. (PubMed id 17956732)1, 2 Carbia-Nagashima A.... Arzt E. (2007)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
    4. 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. (2004)
    5. Genome-wide association study identifies novel loci as sociated with concentrations of four plasma phospholipid fatty acids in the de n ovo lipogenesis pathway: results from the Cohorts for Heart and Aging Research i n Genomic Epidemiology (CHARGE) consortium. (PubMed id 23362303)1 Wu J.H....Mozaffarian D. (2013)
    6. In silico structural and functional characterization o f the RSUME splice variants. (PubMed id 23469069)1 Gerez J....Arzt E. (2013)
    7. RSUME enhances glucocorticoid receptor SUMOylation and transcriptional activity. (PubMed id 23508108)1 Druker J....Arzt E. (2013)
    8. RSUME is implicated in HIF-1-induced VEGF-A production in pituitary tumour cells. (PubMed id 22009797)1 Shan B....Renner U. (2012)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Genome-wide association study of acute post-surgical pain in humans. (PubMed id 19207018)4 Kim H....Dionne R.A. (2009)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 25950 HGNC: 21393 AceView: RWDD3andFLJ31842 Ensembl:ENSG00000122481 euGenes: HUgn25950
    ECgene: RWDD3 H-InvDB: RWDD3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for RWDD3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for RWDD3 gene:
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