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IFT43 intraflagellar transport 43 [ Homo sapiens (human) ]

Gene ID: 112752, updated on 27-Nov-2024

Summary

Official Symbol
IFT43provided by HGNC
Official Full Name
intraflagellar transport 43provided by HGNC
Primary source
HGNC:HGNC:29669
See related
Ensembl:ENSG00000119650 MIM:614068; AllianceGenome:HGNC:29669
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CED3; RP81; SRTD18; C14orf179
Summary
This gene encodes a subunit of the intraflagellar transport complex A (IFT-A). IFT-A is a multiprotein complex that plays an important role in cilia assembly and maintenance by mediating retrograde ciliary transport. Mutations in this gene are a cause of cranioectodermal dysplasia-3 (CED3), also known as Sensenbrenner syndrome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in testis (RPKM 8.4), thyroid (RPKM 6.9) and 25 other tissues See more
Orthologs
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Genomic context

See IFT43 in Genome Data Viewer
Location:
14q24.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (75985763..76084073)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (70194954..70293259)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (76452106..76550416)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene tubulin tyrosine ligase like 5 Neighboring gene NANOG hESC enhancer GRCh37_chr14:76329885-76330389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5951 Neighboring gene ribosomal protein S2 pseudogene 43 Neighboring gene NANOG hESC enhancer GRCh37_chr14:76383602-76384103 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:76399606-76399787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5954 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:76451759-76452260 Neighboring gene VISTA enhancer hs2157 Neighboring gene ubiquitin conjugating enzyme E2 L3 pseudogene Neighboring gene transforming growth factor beta 3 Neighboring gene uncharacterized LOC105370573 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:76550227-76551213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76578893-76579424 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:76581183-76581684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76582665-76583491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:76597945-76598444 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76604854-76605582 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8766 Neighboring gene G-patch domain containing 2 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8767 Neighboring gene uncharacterized LOC105370575 Neighboring gene Sharpr-MPRA regulatory region 6100 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:76770917-76771070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:76776165-76776778 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76795770-76796291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:76796815-76797335 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76796292-76796814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:76800829-76801328 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:76807160-76807660 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:76807661-76808161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8768 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:76852844-76853344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5956 Neighboring gene estrogen related receptor beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:76952887-76953387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:76966323-76966862

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Cranioectodermal dysplasia 3
MedGen: C3279807 OMIM: 614099 GeneReviews: Cranioectodermal Dysplasia
Compare labs
Retinitis pigmentosa 81
MedGen: C4693443 OMIM: 617871 GeneReviews: Not available
Compare labs
Short-rib thoracic dysplasia 18 with polydactyly
MedGen: C4693420 OMIM: 617866 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study in NSAID-induced acute urticaria/angioedema in Spanish and Han Chinese populations.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TTLL5

Clone Names

  • FLJ32173, MGC16028

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cilium assembly NAS
Non-traceable Author Statement
more info
PubMed 
involved_in intraciliary retrograde transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in intraciliary retrograde transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in intraciliary retrograde transport NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in centriolar satellite IDA
Inferred from Direct Assay
more info
 
located_in centriole IEA
Inferred from Electronic Annotation
more info
 
located_in ciliary tip TAS
Traceable Author Statement
more info
 
is_active_in cilium IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cilium IDA
Inferred from Direct Assay
more info
PubMed 
located_in cilium ISS
Inferred from Sequence or Structural Similarity
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 IEA
Inferred from Electronic Annotation
more info
 
part_of intraciliary transport particle A IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of intraciliary transport particle A IDA
Inferred from Direct Assay
more info
PubMed 
part_of intraciliary transport particle A IPI
Inferred from Physical Interaction
more info
PubMed 
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
intraflagellar transport protein 43 homolog
Names
IFT complex A subunit
intraflagellar transport 43 homolog

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.

Genomic

  1. NG_031957.1 RefSeqGene

    Range
    5011..102990
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001102564.3NP_001096034.1  intraflagellar transport protein 43 homolog isoform 2

    See identical proteins and their annotated locations for NP_001096034.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon and contains two alternate exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC008015, AF107885
    Consensus CDS
    CCDS41973.1
    UniProtKB/Swiss-Prot
    B3KPT6, B4DZI9, G3V385, O95418, Q96FT9, Q9ULA9
    UniProtKB/TrEMBL
    A0A7I2V6B2
    Related
    ENSP00000324177.6, ENST00000314067.11
    Conserved Domains (1) summary
    pfam15305
    Location:67193
    IFT43; Intraflagellar transport protein 43
  2. NM_001255995.3NP_001242924.1  intraflagellar transport protein 43 homolog isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AW235031, BC042852, BU627157, DB443802
    Consensus CDS
    CCDS58330.1
    UniProtKB/Swiss-Prot
    Q96FT9
    Related
    ENSP00000451096.1, ENST00000556742.1
  3. NM_052873.3NP_443105.2  intraflagellar transport protein 43 homolog isoform 1

    See identical proteins and their annotated locations for NP_443105.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK056735, BC010436, DB443802
    Consensus CDS
    CCDS9847.1
    Related
    ENSP00000238628.6, ENST00000238628.10
    Conserved Domains (1) summary
    pfam15305
    Location:74198
    IFT43; Intraflagellar transport protein 43

RNA

  1. NR_045664.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an internal exon and uses an alternate splice site in the 3' UTR, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK302944, BI821833, DB443802
  2. NR_045665.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an internal exon, contains two alternate internal exons and uses an alternate splice site in the 3' UTR, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK302944, CB853974, DB443802

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    75985763..76084073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    70194954..70293259
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)