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RWDD3 Gene

protein-coding   GIFtS: 48
GCID: GC01P095699

RWD Domain Containing 3

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(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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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:         

Export aliases for RWDD3 gene to outside databases

Previous GC identifers: GC01P095090 GC01P095171 GC01P095411 GC01P093821


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for RWDD3 Gene:
RWDD3 (RWD domain containing 3) is a protein-coding gene.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   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 Chromatin IP Primers for RWDD3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: RWDD3_HUMAN, Q9Y3V2 (See protein sequence)
Recommended Name: RWD domain-containing protein 3  
Size: 267 amino acids; 30543 Da
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RWDD3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    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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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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


    Find genes that share domains with RWDD3           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: 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:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI17956732
         
    Find genes that share ontologies with RWDD3           About GenesLikeMe


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

         1 MGI phenotypic allele for Rwdd3 (no phenotypes)

    Find genes that share phenotypes with RWDD3           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RWDD3
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    (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
    RWDD3_HUMAN, Q9Y3V2: Nucleus. Cytoplasm. Note=Colocalizes with UBC9/UBE2I in nuclear spots
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton1
    cytosol1
    endoplasmic reticulum1
    extracellular1
    mitochondrion1
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

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

    Find genes that share ontologies with RWDD3           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RWDD3
    Interactions:

        Search GeneGlobe Interaction Network 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, 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
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      Browse compounds at ApexBio 

    Browse Tocris compounds for 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,
    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 RWDD3 gene (5 alternative transcripts): 
    NM_001128142.1  NM_001199682.1  NM_001278247.1  NM_001278248.1  NM_015485.4  

    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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      QuantiTect SYBR Green Assays in human, mouse, rat RWDD3
      QuantiFast Probe-based Assays in human, mouse, rat RWDD3

    Selected AceView cDNA sequences (see all 211):

    BX281301 R93816 AA336662 AA328801 CA390928 BQ894820 BX093145 AA825527 
    BX352440 CD676564 AI187083 AA934062 AA452629 N77031 AW613686 AI198536 
    AI969585 AA935999 AK126344 AI033223 CK430207 BE326625 AL598818 AW518933 

    GeneLoc Exon Structure

    Selected 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™, 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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    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

    RWDD3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RWDD3 Protein Expression

    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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for RWDD3 gene from Selected 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 76.19(n)
    69.55(a)
      424481  NM_001277556.1  NP_001264485.1 
    lizard
    (Anolis carolinensis)
    Reptilia RWDD36
    RWD domain containing 3
    65(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)
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      --

    (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 RWDD3 (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
    ----------
    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
    rs1391537921,2
    C--95712462(+) CAGTG-/TTTTTT 4 -- ut31 nc-transcript-variant0--------
    rs1925607851,2
    --95712590(+) ATGAAA/GTATTA 4 -- ut31 nc-transcript-variant0--------

    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

    Site Specific Mutation Identification with PCR Assays
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    (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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    Find genes that share disorders with RWDD3           About GenesLikeMe

    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)
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    PubMed articles for RWDD3 gene, integrated from 10 sources (see all 24):
    (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. (Genome Res. 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. (Cell 2007)
    3. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (Nature 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. (Genome Res. 2004)
    5. Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium. (PubMed id 23362303)1 Wu J.H....Mozaffarian D. (Circ Cardiovasc Genet 2013)
    6. In silico structural and functional characterization of the RSUME splice variants. (PubMed id 23469069)1 Gerez J....Arzt E. (PLoS ONE 2013)
    7. GWAS-based association between RWDD3 and TECTA variants and paclitaxel induced neuropathy could not be confirmed in Scandinavian ovarian cancer patients. (PubMed id 22877241)1 Bergmann T.K....Brosen K. (Acta Oncol 2013)
    8. RSUME enhances glucocorticoid receptor SUMOylation and transcriptional activity. (PubMed id 23508108)1 Druker J....Arzt E. (Mol. Cell. Biol. 2013)
    9. RSUME is implicated in HIF-1-induced VEGF-A production in pituitary tumour cells. (PubMed id 22009797)1 Shan B....Renner U. (Endocr. Relat. Cancer 2012)
    10. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 25950 HGNC: 21393 AceView: RWDD3andFLJ31842 Ensembl:ENSG00000122481 euGenes: HUgn25950
    ECgene: RWDD3 H-InvDB: RWDD3

    (According to HUGE)
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    (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 RWDD3 Pharmacogenomics, SNPs, Pathways

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