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

IFT46 Gene

protein-coding   GIFtS: 44
GCID: GC11M118415

intraflagellar transport 46 homolog (Chlamydomonas)

(Previous name: chromosome 11 open reading frame 60 )
(Previous symbol: C11orf60)
 Explore 1 disease affiliated with
IFT46 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for IFT46    

Aliases
for IFT46 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Intraflagellar Transport 46 Homolog (Chlamydomonas)1 2     Chromosome 11 Open Reading Frame 601
C11orf21 2 3     UPF03602
C11orf601 2 3     Intraflagellar Transport Protein 46 Homolog2
FLJ218271     Intraflagellar Transport Protein IFT462

External Ids:    HGNC: 261461   Entrez Gene: 569122   Ensembl: ENSG000001180967   UniProtKB: Q9NQC83   

Export aliases for IFT46 gene to outside databases

Previous GC identifer: GC11M114351


Summaries
for IFT46 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: IFT46_HUMAN, Q9NQC8
Function: Forms part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles
required for the assembly, maintenance and functioning of primary cilia. May play a role in chondrocyte maturation and
skeletogenesis (By similarity)

Gene Wiki entry for IFT46 (C11orf60)


Genomic Views
for IFT46 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NC_018922.1  NT_033899.8  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for IFT46
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for IFT46

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat IFT46


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

Entrez Gene cytogenetic band: 11q23.3   Ensembl cytogenetic band:  11q23.3   HGNC cytogenetic band: 11q23.3

IFT46 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
IFT46 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11M118415:  view genomic region     (about GC identifiers)

Start:
 118,415,243 bp from pter      End:
 118,443,685 bp from pter
Size:
 28,443 bases      Orientation:
 minus strand

Proteins
for IFT46 gene

(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: IFT46_HUMAN, Q9NQC8 (See protein sequence)
Recommended Name: Intraflagellar transport protein 46 homolog  
Size: 304 amino acids; 34286 Da
Subunit: Part of the IFT complex B. Interacts with IFT57, IFT88 and WDR69 (By similarity)
Subcellular location: Cytoplasm, cytoskeleton, cilium basal body (By similarity). Cell projection, cilium (By
similarity). Note=Expression is concentrated at the cilium basal body but is also detected along the length of the
cilium (By similarity)
Caution: Has been termed C11orf2 (PubMed:10873569), but is not the official C11orf2 as defined by HGNC
Secondary accessions: A8K0F6 Q9H6V5
Alternative splicing: 2 isoforms:  Q9NQC8-1   Q9NQC8-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for IFT46: NX_Q9NQC8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NQC8

    • IFT46 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001162089.1  NP_064538.3  

    ENSEMBL proteins: 
     ENSP00000264021   ENSP00000264020   ENSP00000432384   ENSP00000435826   ENSP00000434175  
     ENSP00000432982   ENSP00000435278   ENSP00000435750  

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    Uscn Proteins for IFT46

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS10873569
    GO:0005737cytoplasm IDA--
    GO:0005932colocalizes with microtubule basal body ISS--
    GO:0031512motile primary cilium IEA--
    GO:0031514motile cilium ISS--


    IFT46 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for IFT46 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    IFT46 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR022088 Intraflagellar_transp_cmplxB

    Graphical View of Domain Structure for InterPro Entry Q9NQC8

    ProtoNet protein and cluster: Q9NQC8

    UniProtKB/Swiss-Prot: IFT46_HUMAN, Q9NQC8
    Similarity: Belongs to the IFT46 family


    Function
    for IFT46 gene

    (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: IFT46_HUMAN, Q9NQC8
    Function: Forms part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles
    required for the assembly, maintenance and functioning of primary cilia. May play a role in chondrocyte maturation and
    skeletogenesis (By similarity)

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate IFT46:
    hsa-miR-3200-5p
    SwitchGear 3'UTR luciferase reporter plasmid: IFT46 3' UTR sequence
    Inhib. RNA
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    OriGene shRNA RFP: IFT46
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
    GO:0008022protein C-terminus binding ISS--


    IFT46 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for IFT46:
     Increased gamma-H2AX phosphory 


    Pathways & Interactions
    for IFT46 gene

    (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 IFT46

    1 Interacting protein for IFT46 (Q9NQC83) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DTX4Q9Y2E63I2D: score=5 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--
    GO:0009296flagellum assembly ISS--
    GO:0042073intraflagellar transport ISS--
    GO:0050821protein stabilization ISS--


    IFT46 for ontologies           About GeneDecksing



    Drugs & Compounds
    for IFT46 gene

    (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 IFT46
    Search CenterWatch for drugs/clinical trials and news about IFT46 

    Transcripts
    for IFT46 gene

    (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 IFT46 gene (2 alternative transcripts): 
    NM_001168618.1  NM_020153.3  

    Unigene Cluster for IFT46:

    Intraflagellar transport 46 homolog (Chlamydomonas)
    Hs.533738  [show with all ESTs]
    Unigene Representative Sequence: NM_020153
    12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000264021(uc001ptp.2) ENST00000264020(uc001pto.2) ENST00000530872
    ENST00000531201 ENST00000525060 ENST00000531939 ENST00000534156 ENST00000534114
    ENST00000528378 ENST00000533918 ENST00000530185 ENST00000527868

    miRNA
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    1 QIAGEN miScript miRNA Assays for microRNA that regulate IFT46:
    hsa-miR-3200-5p
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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AJ249980.1 AK025480.1 AK289521.1 AL136934.1 BC011647.2 BC012802.2 BC022856.1 CR457344.1 

    12 DOTS entries:

    DT.100024274  DT.100706214  DT.100024273  DT.215628  DT.100814978  DT.100814982  DT.75106809  DT.97843693 
    DT.100814981  DT.120717141  DT.120717259  DT.75162766 

    24/188 AceView cDNA sequences (see all 188):

    BI488845 CR607003 BU627872 BM971434 BE326424 CB850922 AI377194 BQ719361 
    CA310475 BM694907 CR600708 BU169247 AA704286 CR625012 BU674449 AW027250 
    N71607 AL136934 AI961373 BF434382 AW068980 CR613135 CB854540 CN480951 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for IFT46    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9
    SP1:                    -           -                 -                     
    SP2:                    -                                                   
    SP3:                                                                        
    SP4:                                                                        


    ECgene alternative splicing isoforms for IFT46

    Expression
    for IFT46 gene

    (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

    IFT46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GAGGTTAGAT

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

    IFT46 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See IFT46 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for IFT46

    SOURCE GeneReport for Unigene cluster: Hs.533738
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    In Situ
    Assay Products:     
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    Orthologs
    for IFT46 gene

    (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 IFT46 gene from 7/26 species (see all 26)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Ift461 , 5 intraflagellar transport 46 homolog (Chlamydomonas)5
    intraflagellar transport 461    		 86.89(n)1
    95.33(a)1    		   9 (24.84 cM)5
    765681  NM_023831.31  NP_076320.21 
     447679085 
    chicken
    (Gallus gallus)    		 Aves IFT461 intraflagellar transport 46 homolog (Chlamydomonas) 73.84(n)
    79.56(a)    		   419780  XM_417918.3  XP_417918.3 
    lizard
    (Anolis carolinensis)    		 Reptilia IFT466
    		 --
    		 77(a)
    		 1 ↔ 1
    		 GL343767.1(27076-32368)
    African clawed frog
    (Xenopus laevis)    		 Amphibia Xl.99322 Xenopus laevis transcribed sequence with weak similarity more 75.22(n)    BU901760.1 
    zebrafish
    (Danio rerio)    		 Actinopterygii Dr.145522 Transcribed sequence with moderate similarity to protein more 74.62(n)    BM141236.1 
    fruit fly
    (Drosophila melanogaster)    		 Insecta CG151611 CG15161 47.86(n)
    38.46(a)    		   35114  NM_136046.2  NP_609890.2 
    worm
    (Caenorhabditis elegans)    		 Secernentea dyf-61 Protein DYF-6 53.33(n)
    47.56(a)    		   3565899  NM_001083298.1  NP_001076767.1 


    ENSEMBL Gene Tree for IFT46 (if available)
    TreeFam Gene Tree for IFT46 (if available) 

    Paralogs
    for IFT46 gene

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

    Genomic Variants
    for IFT46 gene

    (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

    10/443 NCBI SNPs in IFT46 are shown (see all 443)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 11 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1915089201,2
    		--118414744(+) GGTCTC/TGAACT 4 -- ds5001 int10--------
    rs1492887621,2
    		--118414828(+) AAACAC/TCCTTT 4 -- int1 ds50010--------
    rs1474075171,2
    		--118414957(+) ATTACC/TGCAAT 4 -- int1 ds50010--------
    rs1841269081,2
    		--118415002(+) TGGAGC/GCAGAC 4 -- ds5001 int10--------
    rs753206101,2
    		--118415106(+) ATTGGG/AGTTTC 4 -- int1 ds50011Minor allele frequency- A:0.01WA 118
    rs801304551,2
    		C,F,--118415146(+) ACTACT/GCTTCA 4 -- int1 ds50011Minor allele frequency- G:0.02WA 118
    rs1418817241,2
    		C,--118415244(+) CTGAC-/AATATA 4 -- int1 ut310--------
    rs1889204591,2
    		--118415248(+) CAATAC/TAATAG 4 -- ut31 int10--------
    rs1120519351,2
    		C,--118415360(+) CTAACC/TTCCAT 4 -- ut31 int12Minor allele frequency- T:0.03CSA WA 119
    rs1166222891,2
    		--118415370(+) TGGGAG/TCTCAG 4 -- ut31 int10--------

    HapMap Linkage Disequilibrium report for IFT46 (118415243 - 118443685 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for IFT46: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing IFT46
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    Disorders / Diseases
    for IFT46 gene

    (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
    IFT46 for disorders           About GeneDecksing

    1 disease for IFT46:    About MalaCards
    neuronitis


    Export disorders for IFT46 gene to outside databases

    Publications
    for IFT46 gene

    (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 IFT46 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with IFT46)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of five novel human genes in the 11q13-q22 region. (PubMed id 10873569)1, 2, 3 O'Brien K.P....Dumanski J.P. (2000)
    2. Characterization of mouse IFT complex B. (PubMed id 19253336)1, 3 Follit J.A....Pazour G.J. (2009)
    3. 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)
    4. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    5. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    6. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    7. Knockdown of the intraflagellar transport protein IFT46 stimulates selective gene expression in mouse chondrocytes and affects early development in zebrafish. (PubMed id 17720815)1 Gouttenoire J....Mallein-Gerin F. (2007)
    8. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (2006)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (2006)

    External Searches for IFT46 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing IFT46 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56912 HGNC: 26146 AceView: FLJ21827 Ensembl:ENSG00000118096 euGenes: HUgn56912
    ECgene: IFT46 H-InvDB: IFT46

    Other Databases showing IFT46 gene

    (According to HUGE)
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    Specialized Databases showing IFT46 gene

    (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 IFT46 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
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    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    		Patent Information for IFT46 gene:
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