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IFT46 Gene

protein-coding   GIFtS: 47
GCID: GC11M118415

Intraflagellar Transport 46 Homolog (Chlamydomonas)

(Previous name: chromosome 11 open reading frame 60)
(Previous symbol: C11orf60)
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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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Aliases
Intraflagellar Transport 46 Homolog (Chlamydomonas)1 2     UPF03602
C11orf601 2 3     Intraflagellar Transport Protein 46 Homolog2
C11orf22 3     Intraflagellar Transport Protein IFT462
Chromosome 11 Open Reading Frame 601     

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

Export aliases for IFT46 gene to outside databases

Previous GC identifer: GC11M114351


(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 IFT46 Gene:
IFT46 (intraflagellar transport 46 homolog (Chlamydomonas)) is a protein-coding gene. GO annotations related to this gene include protein C-terminus binding.

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) 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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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NT_033899.9  NC_018922.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for IFT46
         Other transcription factors

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

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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

(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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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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 DAW1 (By similarity). Interacts with ARL13B
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

Explore proteomics data for IFT46 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See IFT46 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000264021   ENSP00000264020   ENSP00000432384   ENSP00000435826   ENSP00000434175  
     ENSP00000432982   ENSP00000435278   ENSP00000435750  

    IFT46 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for IFT46

     
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    antibodies-online proteins for IFT46 (5 products) 

     
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    antibodies-online kits for IFT46 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    IFT: Intraflagellar transport homologs

    1 InterPro protein domain:
     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


    Find genes that share domains with IFT46           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: 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 Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
    GO:0005515protein binding ----
    GO:0008022protein C-terminus binding ISS--
         
    Find genes that share ontologies with IFT46           About GenesLikeMe


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

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for IFT46

    miRNA
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    miRTarBase miRNAs that target IFT46:
    hsa-mir-375 (MIRT019794)

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    1 qRT-PCR Assays for microRNA that regulate IFT46:
    hsa-miR-3200-5p
    SwitchGear 3'UTR luciferase reporter plasmidIFT46 3' UTR sequence
    Inhib. RNA
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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
    IFT46_HUMAN, Q9NQC8: 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)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytoskeleton2
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus NAS10873569
    GO:0005737cytoplasm IDA--
    GO:0031512motile primary cilium IEA--
    GO:0031514motile cilium ISS--
    GO:0036064colocalizes with ciliary basal body ISS--

    Find genes that share ontologies with IFT46           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 IFT46
    Interactions:

        Search GeneGlobe Interaction Network for IFT46

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

    2 Interacting proteins for IFT46 (Q9NQC83 ENSP000002640204) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    DTX4Q9Y2E63I2D: score=5 
    SH3D19ENSP000003029134STRING: ENSP00000302913
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--
    GO:0042073intraciliary transport ISS--
    GO:0042384cilium assembly ISS--
    GO:0050821protein stabilization ISS--

    Find genes that share ontologies with IFT46           About GenesLikeMe



    (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
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for IFT46



    (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 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 qRT-PCR Assays for microRNA that regulate IFT46:
    hsa-miR-3200-5p
    SwitchGear 3'UTR luciferase reporter plasmidIFT46 3' UTR sequence
    Inhib. RNA
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    Additional mRNA 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 

    Selected AceView cDNA sequences (see all 188):

    CR610960 BM694907 BE326424 BC012802 BF434382 CR625012 CK725207 AI961373 
    BE207853 CA310475 CR617874 CR617203 CR613135 BQ719361 CR605306 BU169247 
    CF272485 CB069813 BM982050 BQ026923 BQ019051 BF725042 CR600708 AW338473 

    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

    (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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    IFT46 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGGTTAGAT
    IFT46 Expression
    About this image

    IFT46 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    IFT46 Protein Expression

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

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IFT46

    (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 animals.

    Orthologs for IFT46 gene from Selected species (see all 17)    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
    84.87(n)1
    90.78(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) 75.37(n)
    81.53(a)
      419780  XM_417918.4  XP_417918.4 
    lizard
    (Anolis carolinensis)
    Reptilia IFT466
    intraflagellar transport 46 homolog (Chlamydomonas...
    65(a)
    1 ↔ 1
    GL343767.1(26187-33718)
    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 CG151616
    --
    21(a)
    1 ↔ 1
    2L(18614339-18616067)
    worm
    (Caenorhabditis elegans)
    Secernentea dyf-61 dyf-6 53.86(n)
    47.29(a)
      3565899  NM_001083301.2  NP_001076770.1 


    ENSEMBL Gene Tree for IFT46 (if available)
    TreeFam Gene Tree for IFT46 (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 IFT46 (see all 482)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs775307681,2
    C,F--118418038(+) AGGGCG/AGGGAA 2 -- int11Minor allele frequency- A:0.03WA 118
    rs1412055141,2
    --118418157(+) GAGACA/GGAGTC 2 -- int10--------
    rs1469834901,2
    C--118418255(+) CAGCCC/TCCTGA 2 -- int10--------
    rs1506899861,2
    C--118418326(+) AGACA-/GGGGTC 2 -- int10--------
    rs2007332751,2
    --118418457(+) TTCTT-/TTCTTTTT 2 -- int10--------
    rs1838104131,2
    --118418891(+) CCGTGC/TCTGGC 2 -- int10--------
    rs1884487481,2
    --118418941(+) TTGGAC/TGGTAA 2 -- int10--------
    rs1920876861,2
    --118419014(+) GTTTAC/TGGTGT 2 -- int10--------
    rs46271201,2
    C,F,H--118419033(+) ATGTAG/AAACCT 2 -- int16Minor allele frequency- A:0.00NS EA NA 604
    rs1381543811,2
    --118419256(+) TGTATC/TTTTAG 2 -- int10--------

    HapMap Linkage Disequilibrium report for IFT46 (118415243 - 118443685 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for IFT46:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2666357CNV Deletion23128226
    dgv1319n71CNV Loss21882294
    nsv7224OTHER Inversion18451855

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing IFT46
    DNA2.0 Custom Variant and Variant Library Synthesis for IFT46

    (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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    (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 IFT46 gene, integrated from 10 sources (see all 16):
    (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. (Biochem. Biophys. Res. Commun. 2000)
    2. Characterization of mouse IFT complex B. (PubMed id 19253336)1, 3 Follit J.A....Pazour G.J. (Cell Motil. Cytoskeleton 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. (Genome Res. 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. (Genome Res. 2001)
    5. Active transport and diffusion barriers restrict Joubert Syndrome-associated ARL13B/ARL-13 to an Inv-like ciliary membrane subdomain. (PubMed id 24339792)2 Cevik S....Blacque O.E. (PLoS Genet. 2013)
    6. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    7. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    8. 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. (J. Biol. Chem. 2007)
    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. (Genome Res. 2006)
    10. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PubMed id 16554811)2 Taylor T.D....Sakaki Y. (Nature 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

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

    (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 IFT46 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for IFT46 gene:
    Search GeneIP for patents involving IFT46

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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