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    IFT46 intraflagellar transport 46 [ Homo sapiens (human) ]

    Gene ID: 56912, updated on 2-Nov-2024

    Summary

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    Official Symbol
    IFT46provided by HGNC
    Official Full Name
    intraflagellar transport 46provided by HGNC
    Primary source
    HGNC:HGNC:26146
    See related
    Ensembl:ENSG00000118096 MIM:620506; AllianceGenome:HGNC:26146
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FAP32; CFAP32; C11orf2; C11orf60
    Summary
    Predicted to be involved in cilium assembly; intraciliary transport; and protein stabilization. Predicted to act upstream of or within smoothened signaling pathway. Located in cytoplasm. Part of intraciliary transport particle B. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 6.3), thyroid (RPKM 5.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IFT46 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118544543..118576898, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118563838..118596187, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118415258..118436646, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:118306179-118307176 and GRCh37_chr11:118307177-118308175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118308176-118309173 Neighboring gene Sharpr-MPRA regulatory region 11577 Neighboring gene lysine methyltransferase 2A Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118358704-118358932 Neighboring gene TTC36 and KMT2A antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 12917 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3947 Neighboring gene tetratricopeptide repeat domain 36 Neighboring gene transmembrane protein 25 Neighboring gene uncharacterized LOC124902764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5595 Neighboring gene ribosomal protein L5 pseudogene 30 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:118461541-118461751 Neighboring gene archain 1 Neighboring gene RNA, U6 small nuclear 1157, pseudogene Neighboring gene uncharacterized LOC124902765 Neighboring gene CRISPRi-validated cis-regulatory element chr11.5498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3949 Neighboring gene Sharpr-MPRA regulatory region 10010 Neighboring gene pleckstrin homology like domain family B member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SARS-CoV-2 ORF10 impairs cilia by enhancing CUL2ZYG11B activity. Wang L, et al. J Cell Biol, 2022 Jul 4. PMID 35674692, Free PMC Article
    2. Knockdown of the intraflagellar transport protein IFT46 stimulates selective gene expression in mouse chondrocytes and affects early development in zebrafish. Gouttenoire J, et al. J Biol Chem, 2007 Oct 19. PMID 17720815
    3. Characterization of five novel human genes in the 11q13-q22 region. O'Brien KP, et al. Biochem Biophys Res Commun, 2000 Jun 24. PMID 10873569
    4. Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex. Katoh Y, et al. J Biol Chem, 2016 May 20. PMID 26980730, Free PMC Article
    5. Characterization of mouse IFT complex B. Follit JA, et al. Cell Motil Cytoskeleton, 2009 Aug. PMID 19253336, Free PMC Article

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the ciliary protein IFT46 has a specific function in chondrocytes and is also essential for normal development of vertebrates.
      Title: Knockdown of the intraflagellar transport protein IFT46 stimulates selective gene expression in mouse chondrocytes and affects early development in zebrafish.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21827

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    enables protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in cilium assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intraciliary anterograde transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in intraciliary transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intraciliary transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein stabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    colocalizes_with ciliary basal body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in ciliary tip TAS
    Traceable Author Statement
    more info
    		  
    located_in cilium NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in cilium TAS
    Traceable Author Statement
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    part_of intraciliary transport particle B IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of intraciliary transport particle B IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of intraciliary transport particle B ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in motile cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in motile cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    intraflagellar transport protein 46 homolog
    Names
    UPF0360
    cilia and flagella associated protein 32
    intraflagellar transport 46 homolog
    intraflagellar transport protein IFT46

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001168618.2 → NP_001162089.1  intraflagellar transport protein 46 homolog isoform 2

      See identical proteins and their annotated locations for NP_001162089.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AK289521, BC022856
      Consensus CDS
      CCDS53718.1
      UniProtKB/Swiss-Prot
      A8K0F6, Q9H6V5, Q9NQC8
      UniProtKB/TrEMBL
      A0A5F9ZH13
      Related
      ENSP00000264021.3, ENST00000264021.8
      Conserved Domains (1) summary
      pfam12317
      Location:65 → 267
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    2. NM_020153.4 → NP_064538.3  intraflagellar transport protein 46 homolog isoform 1

      See identical proteins and their annotated locations for NP_064538.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK025480, AP000941, BC022856
      Consensus CDS
      CCDS8399.1
      UniProtKB/TrEMBL
      E9PR06
      Related
      ENSP00000264020.2, ENST00000264020.6
      Conserved Domains (1) summary
      pfam12317
      Location:116 → 318
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      118544543..118576898 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011542906.4 → XP_011541208.1  intraflagellar transport protein 46 homolog isoform X2

      See identical proteins and their annotated locations for XP_011541208.1

      UniProtKB/Swiss-Prot
      A8K0F6, Q9H6V5, Q9NQC8
      UniProtKB/TrEMBL
      A0A5F9ZH13
      Conserved Domains (1) summary
      pfam12317
      Location:65 → 267
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    2. XM_011542905.4 → XP_011541207.1  intraflagellar transport protein 46 homolog isoform X1

      See identical proteins and their annotated locations for XP_011541207.1

      UniProtKB/TrEMBL
      E9PR06
      Conserved Domains (1) summary
      pfam12317
      Location:116 → 318
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    3. XM_017018018.3 → XP_016873507.1  intraflagellar transport protein 46 homolog isoform X2

      UniProtKB/Swiss-Prot
      A8K0F6, Q9H6V5, Q9NQC8
      UniProtKB/TrEMBL
      A0A5F9ZH13
      Conserved Domains (1) summary
      pfam12317
      Location:65 → 267
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    4. XM_017018017.2 → XP_016873506.1  intraflagellar transport protein 46 homolog isoform X1

      UniProtKB/TrEMBL
      E9PR06
      Conserved Domains (1) summary
      pfam12317
      Location:116 → 318
      IFT46_B_C; Intraflagellar transport complex B protein 46 C terminal

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      118563838..118596187 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369380.1 → XP_054225355.1  intraflagellar transport protein 46 homolog isoform X2

      UniProtKB/Swiss-Prot
      A8K0F6, Q9H6V5, Q9NQC8

    2. XM_054369378.1 → XP_054225353.1  intraflagellar transport protein 46 homolog isoform X1

    3. XM_054369381.1 → XP_054225356.1  intraflagellar transport protein 46 homolog isoform X2

      UniProtKB/Swiss-Prot
      A8K0F6, Q9H6V5, Q9NQC8

    4. XM_054369379.1 → XP_054225354.1  intraflagellar transport protein 46 homolog isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQC8.1 GenPept UniProtKB/Swiss-Prot:Q9NQC8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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