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Ift140 intraflagellar transport 140 [ Rattus norvegicus (Norway rat) ]

Gene ID: 100362124, updated on 27-Nov-2024

Summary

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Official Symbol
Ift140provided by RGD
Official Full Name
intraflagellar transport 140provided by RGD
Primary source
RGD:2318759
See related
EnsemblRapid:ENSRNOG00000016545 AllianceGenome:RGD:2318759
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to be involved in intraciliary retrograde transport and regulation of cilium assembly. Predicted to act upstream of or within several processes, including cilium organization; embryonic organ development; and regionalization. Predicted to be located in microtubule organizing center and photoreceptor cell cilium. Predicted to be part of intraciliary transport particle A. Predicted to be active in axoneme and ciliary basal body. Human ortholog(s) of this gene implicated in retinitis pigmentosa and short-rib thoracic dysplasia 9 with or without polydactyly. Orthologous to human IFT140 (intraflagellar transport 140). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Adrenal (RPKM 122.0), Testes (RPKM 104.7) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Ift140 in Genome Data Viewer
Location:
10q12
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (14537134..14624926)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (14032665..14121682)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (14373668..14461509)

Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134480762 Neighboring gene Jupiter microtubule associated homolog 2 Neighboring gene cramped chromatin regulator homolog 1 Neighboring gene uncharacterized LOC134480761 Neighboring gene transmembrane protein 204 Neighboring gene telomere maintenance 2 Neighboring gene pentraxin 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Mainzer-Saldino syndrome is a ciliopathy caused by IFT140 mutations. Perrault I, et al. Am J Hum Genet, 2012 May 4. PMID 22503633, Free PMC Article
  2. Partial uniparental isodisomy of chromosome 16 unmasks a deleterious biallelic mutation in IFT140 that causes Mainzer-Saldino syndrome. Helm BM, et al. Hum Genomics, 2017 Jul 19. PMID 28724397, Free PMC Article
  3. Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease. Schmidts M, et al. Hum Mutat, 2013 May. PMID 23418020, Free PMC Article
  4. Distinct functions for IFT140 and IFT20 in opsin transport. Crouse JA, et al. Cytoskeleton (Hoboken), 2014 May. PMID 24619649, Free PMC Article
  5. Disruption of IFT complex A causes cystic kidneys without mitotic spindle misorientation. Jonassen JA, et al. J Am Soc Nephrol, 2012 Apr. PMID 22282595, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
acts_upstream_of_or_within cilium assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in cilium assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within determination of left/right symmetry ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within embryonic brain development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within embryonic camera-type eye development ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within embryonic digit morphogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within heart development ISO
Inferred from Sequence Orthology
more info
  
involved_in intraciliary retrograde transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within intraciliary retrograde transport ISO
Inferred from Sequence Orthology
more info
  
involved_in intraciliary retrograde transport ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within intraciliary transport ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within limb morphogenesis ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within neural tube patterning ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within non-motile cilium assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within photoreceptor cell outer segment organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within protein localization to cilium ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to cilium ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of cilium assembly ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of smoothened signaling pathway ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in axoneme IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in axoneme ISO
Inferred from Sequence Orthology
more info
  
located_in centriole ISO
Inferred from Sequence Orthology
more info
  
located_in centrosome ISO
Inferred from Sequence Orthology
more info
  
is_active_in ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in ciliary basal body ISO
Inferred from Sequence Orthology
more info
  
located_in cilium ISO
Inferred from Sequence Orthology
more info
  
located_in cone photoreceptor outer segment ISO
Inferred from Sequence Orthology
more info
  
part_of intraciliary transport particle A IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of intraciliary transport particle A ISO
Inferred from Sequence Orthology
more info
  
located_in non-motile cilium ISO
Inferred from Sequence Orthology
more info
  
located_in photoreceptor connecting cilium ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
intraflagellar transport protein 140 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.

mRNA and Protein(s)

  1. NM_001427126.1 → NP_001414055.1  intraflagellar transport protein 140 homolog

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000010
    UniProtKB/TrEMBL
    F1LY69
    Related
    ENSRNOP00000022063.5, ENSRNOT00000022063.8

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086028.1 Reference GRCr8

    Range
    14537134..14624926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039087092.2 → XP_038943020.1  intraflagellar transport protein 140 homolog isoform X1

    Conserved Domains (3) summary
    COG2319
    Location:86 → 437
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:19 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:15 → 139
    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_039087097.2 → XP_038943025.1  intraflagellar transport protein 140 homolog isoform X5

    Conserved Domains (3) summary
    COG2319
    Location:86 → 437
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:19 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:15 → 139
    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 ...

  3. XM_039087093.2 → XP_038943021.1  intraflagellar transport protein 140 homolog isoform X2

    Conserved Domains (3) summary
    COG2319
    Location:86 → 437
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:19 → 57
    7WD40; WD40 repeat [structural motif]
    cl29593
    Location:15 → 139
    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 ...

  4. XM_063268240.1 → XP_063124310.1  intraflagellar transport protein 140 homolog isoform X3

    Related
    ENSRNOP00000100739.1, ENSRNOT00000146112.1

  5. XM_039087096.2 → XP_038943024.1  intraflagellar transport protein 140 homolog isoform X4

Nucleotide Protein Strain
Heading Accession and Version

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