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IFT46 intraflagellar transport 46 [ Homo sapiens (human) ]

Gene ID: 56912, updated on 27-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
  • 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)

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 protein binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
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

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