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IFT80 intraflagellar transport 80 [ Homo sapiens (human) ]

Gene ID: 57560, updated on 17-Jun-2019

Summary

Official Symbol
IFT80provided by HGNC
Official Full Name
intraflagellar transport 80provided by HGNC
Primary source
HGNC:HGNC:29262
See related
Ensembl:ENSG00000068885 MIM:611177
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
ATD2; SRTD2; WDR56
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 12.7), brain (RPKM 10.4) and 25 other tissues See more
Orthologs

Genomic context

See IFT80 in Genome Data Viewer
Location:
3q25.33
Exon count:
21
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (160256986..160399225, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (159974774..160118028, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene IL12A antisense RNA 1 Neighboring gene uncharacterized LOC107986149 Neighboring gene TRIM59-IFT80 protein Neighboring gene chromosome 3 open reading frame 80 Neighboring gene ribosomal protein L35a pseudogene 10 Neighboring gene microRNA 16-2 Neighboring gene microRNA 15b Neighboring gene structural maintenance of chromosomes 4

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

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...
  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1374, MGC126543

Gene Ontology Provided by GOA

Process Evidence Code Pubs
bone morphogenesis IEA
Inferred from Electronic Annotation
more info
 
chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport involved in cilium assembly TAS
Traceable Author Statement
more info
 
negative regulation of epithelial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of non-canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
non-motile cilium assembly IEA
Inferred from Electronic Annotation
more info
 
osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
centrosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary tip TAS
Traceable Author Statement
more info
 
cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium TAS
Traceable Author Statement
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
intraciliary transport particle B IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport particle B ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
intraflagellar transport protein 80 homolog
Names
WD repeat domain 56
WD repeat-containing protein 56
intraflagellar transport 80 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_022932.1 RefSeqGene

    Range
    5001..147547
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001190241.2NP_001177170.1  intraflagellar transport protein 80 homolog isoform b

    See identical proteins and their annotated locations for NP_001177170.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform.
    Source sequence(s)
    AB037795, AK125342, BC030774, CA421514
    Consensus CDS
    CCDS54668.1
    UniProtKB/Swiss-Prot
    Q9P2H3
    Related
    ENSP00000420646.1, ENST00000496589.5
    Conserved Domains (3) summary
    COG2319
    Location:3423
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:1349
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:12176
    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. NM_001190242.1NP_001177171.1  intraflagellar transport protein 80 homolog isoform b

    See identical proteins and their annotated locations for NP_001177171.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform.
    Source sequence(s)
    AB037795, CA421514, DR000297
    Consensus CDS
    CCDS54668.1
    UniProtKB/Swiss-Prot
    Q9P2H3
    Related
    ENSP00000418196.1, ENST00000483465.5
    Conserved Domains (3) summary
    COG2319
    Location:3423
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:1349
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:12176
    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. NM_020800.3NP_065851.1  intraflagellar transport protein 80 homolog isoform a

    See identical proteins and their annotated locations for NP_065851.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AB037795, AK125342, CA421514
    Consensus CDS
    CCDS3188.1
    UniProtKB/Swiss-Prot
    Q9P2H3
    Related
    ENSP00000312778.7, ENST00000326448.12
    Conserved Domains (2) summary
    sd00039
    Location:110145
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:17254
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    160256986..160399225 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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