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

    Gene ID: 100362124, updated on 9-Dec-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, Dec 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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