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IFT140 intraflagellar transport 140 [ Homo sapiens (human) ]

Gene ID: 9742, updated on 8-Oct-2018

Summary

Official Symbol
IFT140provided by HGNC
Official Full Name
intraflagellar transport 140provided by HGNC
Primary source
HGNC:HGNC:29077
See related
Ensembl:ENSG00000187535 MIM:614620; Vega:OTTHUMG00000128585
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
RP80; MZSDS; SRTD9; WDTC2; gs114; c305C8.4; c380F5.1
Summary
This gene encodes one of the subunits of the intraflagellar transport (IFT) complex A. Intraflagellar transport is involved in the genesis, resorption and signaling of primary cilia. The primary cilium is a microtubule-based sensory organelle at the surface of most quiescent mammalian cells, that receives signals from its environment, such as the flow of fluid, light or odors, and transduces those signals to the nucleus. Loss of the corresponding protein in mouse results in renal cystic disease. [provided by RefSeq, Jun 2012]
Expression
Broad expression in testis (RPKM 6.4), thyroid (RPKM 4.0) and 24 other tissues See more
Orthologs

Genomic context

See IFT140 in Genome Data Viewer
Location:
16p13.3
Exon count:
40
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (1510427..1612108, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (1560428..1662109, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S3A pseudogene 2 Neighboring gene pentraxin 4 Neighboring gene telomere maintenance 2 Neighboring gene transmembrane protein 204 Neighboring gene uncharacterized LOC105371046 Neighboring gene cramped chromatin regulator homolog 1 Neighboring gene Jupiter microtubule associated homolog 2

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • Hedgehog 'off' state, organism-specific biosystem (from REACTOME)
    Hedgehog 'off' state, organism-specific biosystemHedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh ...
  • Intraflagellar transport, organism-specific biosystem (from REACTOME)
    Intraflagellar transport, organism-specific biosystemIntraflagellar transport (IFT) is a motor-based process that controls the anterograde and retrograde transport of large protein complexes, ciliary cargo and structural components along the ciliary ax...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10306, FLJ30571, KIAA0590, DKFZp564L232

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
determination of left/right symmetry IEA
Inferred from Electronic Annotation
more info
 
embryonic brain development IEA
Inferred from Electronic Annotation
more info
 
embryonic camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic digit morphogenesis IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
intraciliary retrograde transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport involved in cilium assembly TAS
Traceable Author Statement
more info
 
neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
non-motile cilium assembly IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell outer segment organization IEA
Inferred from Electronic Annotation
more info
 
protein localization to cilium IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
renal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
axoneme IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axoneme ISS
Inferred from Sequence or Structural Similarity
more info
 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
ciliary tip TAS
Traceable Author Statement
more info
 
cilium TAS
Traceable Author Statement
more info
 
intraciliary transport particle A IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport particle A IDA
Inferred from Direct Assay
more info
PubMed 
photoreceptor connecting cilium IEA
Inferred from Electronic Annotation
more info
 
photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
intraflagellar transport protein 140 homolog
Names
WD and tetratricopeptide repeats protein 2
intraflagellar transport 140 homolog

NCBI Reference Sequences (RefSeq)

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_032783.1 RefSeqGene

    Range
    5001..106682
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014714.3NP_055529.2  intraflagellar transport protein 140 homolog

    See identical proteins and their annotated locations for NP_055529.2

    Status: REVIEWED

    Source sequence(s)
    AW245075, BC035577, DC401677
    Consensus CDS
    CCDS10439.1
    UniProtKB/Swiss-Prot
    Q96RY7
    Related
    ENSP00000406012.2, OTTHUMP00000158737, ENST00000426508.6, OTTHUMT00000250438
    Conserved Domains (5) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:957983
    TPR; TPR repeat [structural motif]
    sd00039
    Location:1959
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:19121
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl26002
    Location:9511233
    TPR_11; TPR repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

    Range
    1510427..1612108 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011522766.3XP_011521068.1  intraflagellar transport protein 140 homolog isoform X2

    Conserved Domains (4) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:721755
    TPR; TPR repeat [structural motif]
    sd00039
    Location:1959
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. XM_006720990.3XP_006721053.1  intraflagellar transport protein 140 homolog isoform X1

    See identical proteins and their annotated locations for XP_006721053.1

    UniProtKB/Swiss-Prot
    Q96RY7
    Conserved Domains (5) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:957983
    TPR; TPR repeat [structural motif]
    sd00039
    Location:1959
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:19121
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl26002
    Location:9511233
    TPR_11; TPR repeat
  3. XM_006720991.3XP_006721054.1  intraflagellar transport protein 140 homolog isoform X1

    See identical proteins and their annotated locations for XP_006721054.1

    UniProtKB/Swiss-Prot
    Q96RY7
    Conserved Domains (5) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:957983
    TPR; TPR repeat [structural motif]
    sd00039
    Location:1959
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:19121
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl26002
    Location:9511233
    TPR_11; TPR repeat
  4. XM_017023910.1XP_016879399.1  intraflagellar transport protein 140 homolog isoform X1

    UniProtKB/Swiss-Prot
    Q96RY7
    Conserved Domains (5) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00006
    Location:957983
    TPR; TPR repeat [structural motif]
    sd00039
    Location:1959
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:19121
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    cl26002
    Location:9511233
    TPR_11; TPR repeat
  5. XM_017023911.1XP_016879400.1  intraflagellar transport protein 140 homolog isoform X4

  6. XM_011522767.2XP_011521069.1  intraflagellar transport protein 140 homolog isoform X3

    Conserved Domains (2) summary
    TIGR02917
    Location:626908
    PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein
    sd00006
    Location:478512
    TPR; TPR repeat [structural motif]
  7. XM_006720992.3XP_006721055.1  intraflagellar transport protein 140 homolog isoform X10

    Related
    ENSP00000354895.5, OTTHUMP00000254622, ENST00000361339.9, OTTHUMT00000432772
  8. XM_011522771.3XP_011521073.1  intraflagellar transport protein 140 homolog isoform X7

    Conserved Domains (3) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2155
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  9. XM_011522772.3XP_011521074.1  intraflagellar transport protein 140 homolog isoform X8

    Conserved Domains (3) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2155
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  10. XM_005255725.5XP_005255782.1  intraflagellar transport protein 140 homolog isoform X6

    Conserved Domains (3) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2155
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  11. XM_005255726.4XP_005255783.1  intraflagellar transport protein 140 homolog isoform X9

    Conserved Domains (3) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2155
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  12. XM_011522769.3XP_011521071.1  intraflagellar transport protein 140 homolog isoform X5

    Conserved Domains (3) summary
    COG2319
    Location:102434
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:2155
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:15229
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
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