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

RTTN Gene

protein-coding   GIFtS: 44
GCID: GC18M067730

rotatin

 Explore 2 diseases affiliated with
RTTN via our new
 Human Malady Compendium 
Biological research products
for RTTN
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Rotatin1
DKFZP434G1451

External Ids:    HGNC: 186541   Entrez Gene: 259142   Ensembl: ENSG000001762257   OMIM: 6104365   UniProtKB: Q86VV83   

Export aliases for RTTN gene to outside databases

Previous GC identifers: GC18M067493 GC18M065820 GC18M065822 GC18M064389


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

Entrez Gene summary for RTTN:
This gene encodes a large protein whose specific function is unknown. Absence of the orthologous protein in mouse
results in embryonic lethality with deficient axial rotation, abnormal differentiation of the neural tube, and
randomized looping of the heart tube during development. In human, mutations in this gene are associated with
polymicrogyria with seizures. In human fibroblasts this protein localizes at the ciliary basal bodies. Given the
intracellular localization of this protein and the phenotypic effects of mutations, this gene is suspected of playing
a role in the maintenance of normal ciliary structure which in turn effects the developmental process of left-right
organ specification, axial rotation, and perhaps notochord development. (provided by RefSeq, Jan 2013)

UniProtKB/Swiss-Prot: RTTN_HUMAN, Q86VV8
Function: Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a
normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000018.9  NC_018929.1  NT_025028.14  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RTTN gene promoter:
         AML1a   NF-kappaB   E47   C/EBPalpha   AREB6   POU2F1   POU2F1a   FOXO1a   NF-kappaB1   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRTTN promoter sequence
   Search SABiosciences Chromatin IP Primers for RTTN

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


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

Entrez Gene cytogenetic band: 18q22.2   Ensembl cytogenetic band:  18q22.2   HGNC cytogenetic band: 18q22.1

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

GeneLoc information about chromosome 18         GeneLoc Exon Structure

GeneLoc location for GC18M067730:  view genomic region     (about GC identifiers)

Start:
67,671,029 bp from pter      End:
67,873,181 bp from pter
Size:
202,153 bases      Orientation:
minus strand

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

UniProtKB/Swiss-Prot: RTTN_HUMAN, Q86VV8 (See protein sequence)
Recommended Name: Rotatin  
Size: 2226 amino acids; 248630 Da
Subcellular location: Cytoplasm, cytoskeleton, cilium basal body. Note=Colocalizes with the basal bodies at the primary
cilium
Sequence caution: Sequence=BAC86583.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAC87292.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAC87292.1;
Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=CAH18659.1; Type=Erroneous initiation;
Note=Translation N-terminally extended;
Secondary accessions: Q68CS9 Q6ZRL8 Q6ZTK3 Q86TG4 Q8N8N8 Q8TBQ4 Q96IN9 Q9UFJ4
Alternative splicing: 4 isoforms:  Q86VV8-1   Q86VV8-2   Q86VV8-3   Q86VV8-4   (No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for RTTN: NX_Q86VV8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86VV8

  • RTTN Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_775901.3  
    ENSEMBL proteins: 
     ENSP00000255674   ENSP00000462675   ENSP00000462733   ENSP00000462926   ENSP00000399520  
     ENSP00000402352  

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    Uscn Proteins for RTTN

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0036064cilium basal body IDA--


    RTTN for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for RTTN


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    RTTN for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR011989 ARM-like
     IPR016024 ARM-type_fold

    Graphical View of Domain Structure for InterPro Entry Q86VV8

    ProtoNet protein and cluster: Q86VV8


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: RTTN_HUMAN, Q86VV8
    Function: Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a
    normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2

    miRNA
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    Inhib. RNA
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTTN

    1 GenomeRNAi human phenotype for RTTN:
     Increased gamma-H2AX phosphory 

    Animal Models:
         6 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Rttn):
     cardiovascular system  embryogenesis  growth/size  homeostasis/metabolism  mortality/aging 
     nervous system 

    RTTN for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

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

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for RTTN (Q86VV83 ENSP000002556744) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCP0CG483, ENSP000003448184I2D: score=1 STRING: ENSP00000344818
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007368determination of left/right symmetry IEA--


    RTTN for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 RTTN
    Search CenterWatch for drugs/clinical trials and news about RTTN 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RTTN gene: 
    NM_173630.3  

    Unigene Cluster for RTTN:

    Rotatin
    Hs.654809  [show with all ESTs]
    Unigene Representative Sequence: NM_173630
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255674(uc002lkn.2 uc010dqp.2 uc002lko.2 uc002lkp.2 uc010xfb.1)
    ENST00000578780 ENST00000583043 ENST00000581161 ENST00000580034 ENST00000579986
    ENST00000579021 ENST00000583765 ENST00000581709 ENST00000584659 ENST00000581583(uc002lkq.1)
    ENST00000437017 ENST00000454359

    miRNA
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    Inhib. RNA
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    Browse OriGene siRNA
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RTTN
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RTTN

    Additional cDNA sequence: 

    AK096404.1 AK126538.1 AK128137.1 AK129866.1 AL117635.1 BC007359.2 BC013774.1 BC026879.1 
    BC046222.2 BC046931.1 BC047602.1 BC143723.1 CR749799.1 

    11 DOTS entries:

    DT.444094  DT.438604  DT.99997560  DT.100784064  DT.91942438  DT.415482  DT.100784063  DT.95189045 
    DT.121103742  DT.92002339  DT.99946562 

    24/80 AceView cDNA sequences (see all 80):

    BU616804 T35272 AI470445 AI262864 AL117635 BC046931 AW269969 AA779492 
    CF527857 CK299447 BC047602 AI767701 AA381572 BI766357 D29317 AK129866 
    BM470706 NM_173630 CD515831 CA433110 BG283349 BC026879 BC013774 AA535713 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for RTTN    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
    SP1:                                                                                      -                                                                     
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43a · 43b ^ 44 ^ 45a · 45b ^ 46 ^ 47a · 47b ^
    SP1:                                                                                                                                -           -               
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                -                           
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                            -               

    ExUns: 48 ^ 49 ^ 50a · 50b · 50c
    SP1:                              
    SP2:                              
    SP3:                              
    SP4:              -               
    SP5:                              


    ECgene alternative splicing isoforms for RTTN

    (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

    RTTN expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See RTTN Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RTTN

    SOURCE GeneReport for Unigene cluster: Hs.654809
        SABiosciences Custom PCR Arrays for RTTN
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTTN

    (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 animals.

    Orthologs for RTTN gene from 5/16 species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rttn1 , 5 rotatin1, 5 83.9(n)1
    82.41(a)1
      18 (58.93 cM)5
    2461021  NM_175542.31  NP_780751.21 
     889717905 
    chicken
    (Gallus gallus)
    Aves RTTN1 rotatin 69.33(n)
    64.91(a)
      421023  XM_001235278.2  XP_001235279.2 
    lizard
    (Anolis carolinensis)
    Reptilia RTTN6
    --
    64(a)
    1 ↔ 1
    4(46997164-47085562)
    zebrafish
    (Danio rerio)
    Actinopterygii rttn1 rotatin 55.11(n)
    50.5(a)
      100151439  XM_001920408.2  XP_001920443.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta ana36
    anastral spindle 3
    17(a)
    1 ↔ 1
    2R(8232591-8238583)


    ENSEMBL Gene Tree for RTTN (if available)
    TreeFam Gene Tree for RTTN (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, UniProtKB, 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

    10/3473 NCBI SNPs in RTTN are shown (see all 3473    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 18 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs755005001,2
    C,F,--67670618(+) TGTTTT/GGNNNN 1 -- int11Minor allele frequency- G:0.06NA 120
    rs1160465461,2
    C,F,--67670745(+) AGGAAA/G/TAAGAT 1 -- int11WA 118
    rs739708061,2
    C,--67670760(+) TCACTA/GAAACT 1 -- int12Minor allele frequency- G:0.08WA 120
    rs739708071,2
    C,--67670768(+) ACTTGC/GCTAAG 1 -- int12Minor allele frequency- G:0.04WA 120
    rs1487970881,2
    --67670796(+) ATGTAC/GATTTA 1 -- int10--------
    rs1449311301,2
    --67670865(+) GTGGAC/TGCTCT 1 -- int10--------
    rs1477612771,2
    --67670975(+) TCTTAC/TTTCAA 1 -- int10--------
    rs79981,2
    C,F,O,A,H,--67671294(-) AAGACG/ATGCTA 1 -- ut31 ese320Minor allele frequency- A:0.06MN NA NS EA 2168
    rs355584291,2
    C,--67671432(+) TTCAAA/GTAATA 2 Y syn12Minor allele frequency- G:0.02NA WA 196
    rs1127689601,2
    C,--67671532(+) ACTTAG/AGAGGC 1 -- int12Minor allele frequency- A:0.04CSA WA 119

    HapMap Linkage Disequilibrium report for RTTN (67671029 - 67873181 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for RTTN
         2 CNVs: 5061 7188
    Human Gene Mutation Database (HGMD): RTTN

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RTTN
    DNA2.0 Custom Variant and Variant Library Synthesis for RTTN

    (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.)
    About This Section

    RTTN for disorders           About GeneDecksing

    OMIM gene information: 610436    OMIM disorders: --

    UniProtKB/Swiss-Prot: RTTN_HUMAN, Q86VV8
  • Defects in RTTN are the cause of polymicrogyria with seizures (PMGYS) [MIM:614833]. A disease characterized by
  • many irregular small gyri in the brain surface and fusion of the molecular layer over multiple small gyri, which gives
    a festooned appearance to the cortical surface, without abnormal neuronal migration. Polymicrogyria is a heterogeneous
    disorder, considered

    2 diseases for RTTN:    About MalaCards
    fanconi's anemia    anemia


    Export disorders for RTTN 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 RTTN gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with RTTN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. RTTN mutations link primary cilia function to organization of the human cerebral cortex. (PubMed id 22939636)1, 2 Kheradmand Kia S....Mancini G.M. (2012)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Rotatin is a novel gene required for axial rotation and left-right specification in mouse embryos. (PubMed id 11900971)1, 3 Faisst A.M....Gruss P. (2002)
    4. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    5. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    6. TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. (PubMed id 19850743)1 Vanderwerf S.M....Bagby G.C. (2009)
    7. Lysine acetylation targets protein complexes and co-regulates major cellular functions. (PubMed id 19608861)2 Choudhary C.... Mann M. (2009)
    8. Ana3 is a conserved protein required for the structura l integrity of centrioles and basal bodies. (PubMed id 19948479)1 Stevens N.R....Raff J.W. (2009)
    9. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    10. DNA sequence and analysis of human chromosome 18. (PubMed id 16177791)2 Nusbaum C.... Lander E.S. (2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 25914 HGNC: 18654 AceView: RTTN Ensembl:ENSG00000176225 euGenes: HUgn25914
    ECgene: RTTN H-InvDB: RTTN

    (According to HUGE)
    About This Section
      --

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

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

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



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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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