Human Gene IFT80 (uc021xgq.1) Description and Page Index
  Description: Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas) (IFT80), transcript variant 1, mRNA.
RefSeq Summary (NM_020800): The protein encoded by this gene is part of the intraflagellar transport complex B and is necessary for the function of motile and sensory cilia. Defects in this gene are a cause of asphyxiating thoracic dystrophy 2 (ATD2). Three transcript variants encoding two different isoforms have been found for this gene.[provided by RefSeq, Jun 2010].
Transcript (Including UTRs)
   Position: hg19 chr3:159,974,774-160,117,320 Size: 142,547 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr3:159,976,313-160,102,388 Size: 126,076 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:159,974,774-160,117,320)mRNA (may differ from genome)Protein (777 aa)
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: IFT80_HUMAN
DESCRIPTION: RecName: Full=Intraflagellar transport protein 80 homolog; AltName: Full=WD repeat-containing protein 56;
FUNCTION: Component of the intraflagellar transport (IFT) complex B, which is essential for the development and maintenance of motile and sensory cilia.
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, cytoskeleton, cilium basal body (By similarity). Cytoplasm, cytoskeleton, cilium axoneme (By similarity). Note=Basal body and ciliary axoneme (By similarity).
DISEASE: Defects in IFT80 are the cause of asphyxiating thoracic dystrophy type 2 (ATD2) [MIM:611263]. An autosomal recessive chondrodysplasia characterized by a severely constricted thoracic cage, short-limbed short stature, and polydactyly. It often leads to death in infancy because of respiratory insufficiency. Retinal degeneration, cystic renal disease and hepatic disease can be present in affected individuals who survive early childhood.
SIMILARITY: Contains 7 WD repeats.

-  MalaCards Disease Associations
  MalaCards Gene Search: IFT80
Diseases sorted by gene-association score: short-rib thoracic dysplasia 2 with or without polydactyly* (1331), asphyxiating thoracic dystrophy* (178), short-rib thoracic dysplasia 3 with or without polydactyly* (164), aspiration pneumonitis (11), ellis-van creveld syndrome (9), cranioectodermal dysplasia 1 (7), short-rib thoracic dysplasia 6 with or without polydactyly (6), cleft lip/palate (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.98 RPKM in Pituitary
Total median expression: 106.23 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -147.90433-0.342 Picture PostScript Text
3' UTR -334.721539-0.217 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Prolyl oligopeptidase, N-terminal domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - Dipeptidyl peptidase IV/CD26, N-terminal domain

ModBase Predicted Comparative 3D Structure on Q9P2H3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0035735 intraciliary transport involved in cilium assembly
GO:0060271 cilium assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0030992 intraciliary transport particle B
GO:0042995 cell projection
GO:0097542 ciliary tip


-  Descriptions from all associated GenBank mRNAs
  BC033011 - Homo sapiens cDNA clone IMAGE:4823529, **** WARNING: chimeric clone ****.
BC068444 - Homo sapiens cDNA clone IMAGE:4822540, **** WARNING: chimeric clone ****.
AB037795 - Homo sapiens KIAA1374 mRNA for KIAA1374 protein.
BC042027 - Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas), mRNA (cDNA clone IMAGE:5312709), partial cds.
BC030774 - Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas), mRNA (cDNA clone IMAGE:4824388), with apparent retained intron.
AK303410 - Homo sapiens cDNA FLJ52072 complete cds, highly similar to Intraflagellar transport 80 homolog.
AK055904 - Homo sapiens cDNA FLJ31342 fis, clone MESAN1000079.
BC101494 - Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas), mRNA (cDNA clone MGC:126543 IMAGE:8069000), complete cds.
BC113669 - Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas), mRNA (cDNA clone MGC:142229 IMAGE:8322721), complete cds.
KJ904401 - Synthetic construct Homo sapiens clone ccsbBroadEn_13795 hypothetical protein, encodes complete protein.
HQ258513 - Synthetic construct Homo sapiens clone IMAGE:100072942 intraflagellar transport 80 homolog (Chlamydomonas) (IFT80) gene, encodes complete protein.
KJ894437 - Synthetic construct Homo sapiens clone ccsbBroadEn_03831 IFT80 gene, encodes complete protein.
KR711605 - Synthetic construct Homo sapiens clone CCSBHm_00027670 IFT80 (IFT80) mRNA, encodes complete protein.
KR711606 - Synthetic construct Homo sapiens clone CCSBHm_00027671 IFT80 (IFT80) mRNA, encodes complete protein.
AK125342 - Homo sapiens cDNA FLJ43352 fis, clone NT2RP7009147, weakly similar to CHE-2 protein.
AL133045 - Homo sapiens mRNA; cDNA DKFZp434A2115 (from clone DKFZp434A2115).
JD239315 - Sequence 220339 from Patent EP1572962.
JD286405 - Sequence 267429 from Patent EP1572962.
JD311333 - Sequence 292357 from Patent EP1572962.
JD254339 - Sequence 235363 from Patent EP1572962.
JD207010 - Sequence 188034 from Patent EP1572962.
JD535858 - Sequence 516882 from Patent EP1572962.
JD321574 - Sequence 302598 from Patent EP1572962.
JD317656 - Sequence 298680 from Patent EP1572962.
JD280491 - Sequence 261515 from Patent EP1572962.
JD552502 - Sequence 533526 from Patent EP1572962.
JD496328 - Sequence 477352 from Patent EP1572962.
AK025109 - Homo sapiens cDNA: FLJ21456 fis, clone COL04704.
JD503291 - Sequence 484315 from Patent EP1572962.
BC036596 - Homo sapiens intraflagellar transport 80 homolog (Chlamydomonas), mRNA (cDNA clone IMAGE:5273080), with apparent retained intron.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9P2H3 (Reactome details) participates in the following event(s):

R-HSA-5617820 Assembly of IFT B complex
R-HSA-5624949 Assembly of the anterograde IFT train
R-HSA-5625424 The retrograde IFT train dissociates
R-HSA-5624952 Assembly of the retrograde IFT train
R-HSA-5625421 The anterograde IFT train dissociates
R-HSA-5620924 Intraflagellar transport
R-HSA-5617833 Cilium Assembly
R-HSA-1852241 Organelle biogenesis and maintenance

-  Other Names for This Gene
  Alternate Gene Symbols: B4E0K1, IFT80_HUMAN, KIAA1374, NM_020800, NP_001177171, Q3MJC4, Q86YF4, Q9P2H3, Q9UIX1, WDR56
UCSC ID: uc021xgq.1
RefSeq Accession: NM_020800
Protein: Q9P2H3 (aka IFT80_HUMAN)
CCDS: CCDS3188.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene IFT80:
hepatic-fibrosis (Congenital Hepatic Fibrosis Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020800.2
exon count: 20CDS single in 3' UTR: no RNA size: 4322
ORF size: 2328CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4677.00frame shift in genome: no % Coverage: 99.49
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 1481# strange splices: 1
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.