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IFT20 intraflagellar transport 20 [ Homo sapiens (human) ]

Gene ID: 90410, updated on 17-Jun-2019

Summary

Official Symbol
IFT20provided by HGNC
Official Full Name
intraflagellar transport 20provided by HGNC
Primary source
HGNC:HGNC:30989
See related
Ensembl:ENSG00000109083 MIM:614394
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
Summary
This gene encodes a intraflagellar transport protein important for intracellular transport. The encoded protein forms part of a complex involved in trafficking of proteins from the Golgi body, including recycling of immune signalling components (Finetti et al., PubMed: 19855387). This gene is part of a complex set of sense-antisense loci that may be co-regulated. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A pseudogene of this gene is located on the long arm of chromosome 14.[provided by RefSeq, Jun 2012]
Expression
Broad expression in testis (RPKM 51.9), liver (RPKM 45.8) and 25 other tissues See more
Orthologs

Genomic context

See IFT20 in Genome Data Viewer
Location:
17q11.2
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (28328325..28335489, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26655351..26662515, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene leucine-rich repeat-containing protein 37A3 Neighboring gene keratin 18 pseudogene 55 Neighboring gene transmembrane protein 97 Neighboring gene TNF alpha induced protein 1 Neighboring gene DNA polymerase delta interacting protein 2 Neighboring gene transmembrane protein 199 Neighboring gene microRNA 4723

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?

Phenotypes

NHGRI GWAS Catalog

Description
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels.
NHGRI GWA Catalog

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

  • FLJ53813, FLJ99273

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
opsin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
centrosome localization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
cochlea development IEA
Inferred from Electronic Annotation
more info
 
establishment of planar polarity IEA
Inferred from Electronic Annotation
more info
 
inner ear receptor cell stereocilium organization IEA
Inferred from Electronic Annotation
more info
 
intraciliary transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport involved in cilium assembly TAS
Traceable Author Statement
more info
 
kidney development IEA
Inferred from Electronic Annotation
more info
 
neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
opsin transport IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell outer segment organization IEA
Inferred from Electronic Annotation
more info
 
protein localization to Golgi apparatus IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein localization to plasma membrane IEA
Inferred from Electronic Annotation
more info
 
regulation of autophagosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of canonical Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
 
regulation of cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of platelet-derived growth factor receptor-alpha signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
visual learning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
Golgi membrane TAS
Traceable Author Statement
more info
 
centriole IEA
Inferred from Electronic Annotation
more info
 
centrosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary base IEA
Inferred from Electronic Annotation
more info
 
ciliary tip TAS
Traceable Author Statement
more info
 
cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
cilium TAS
Traceable Author Statement
more info
 
cis-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
dendrite terminus 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
 
kinociliary basal body IEA
Inferred from Electronic Annotation
more info
 
microvillus IEA
Inferred from Electronic Annotation
more info
 
motile cilium IEA
Inferred from Electronic Annotation
more info
 
photoreceptor connecting cilium IEA
Inferred from Electronic Annotation
more info
 
photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
 
stereocilium IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
intraflagellar transport protein 20 homolog
Names
intraflagellar transport 20 homolog
intraflagellar transport protein IFT20

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.

mRNA and Protein(s)

  1. NM_001267774.2NP_001254703.1  intraflagellar transport protein 20 homolog isoform 1

    See identical proteins and their annotated locations for NP_001254703.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI768816, AL713094, AY224601, BC002640
    Consensus CDS
    CCDS58535.1
    UniProtKB/Swiss-Prot
    Q8IY31
    Related
    ENSP00000464443.1, ENST00000585089.5
    Conserved Domains (1) summary
    pfam14931
    Location:36154
    IFT20; Intraflagellar transport complex B, subunit 20
  2. NM_001267775.2NP_001254704.1  intraflagellar transport protein 20 homolog isoform 3

    See identical proteins and their annotated locations for NP_001254704.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI768816, AL713094, BC002640, BE619475
    Consensus CDS
    CCDS58534.1
    UniProtKB/Swiss-Prot
    Q8IY31
    UniProtKB/TrEMBL
    A0A024QZ08
    Related
    ENSP00000463138.1, ENST00000585313.5
    Conserved Domains (1) summary
    pfam14931
    Location:10128
    IFT20; Intraflagellar transport complex B, subunit 20
  3. NM_001267776.2NP_001254705.1  intraflagellar transport protein 20 homolog isoform 3

    See identical proteins and their annotated locations for NP_001254705.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AI768816, AL713094, BC002640, BC038094
    Consensus CDS
    CCDS58534.1
    UniProtKB/Swiss-Prot
    Q8IY31
    UniProtKB/TrEMBL
    A0A024QZ08
    Related
    ENSP00000378809.3, ENST00000395418.7
    Conserved Domains (1) summary
    pfam14931
    Location:10128
    IFT20; Intraflagellar transport complex B, subunit 20
  4. NM_001267777.2NP_001254706.1  intraflagellar transport protein 20 homolog isoform 4

    See identical proteins and their annotated locations for NP_001254706.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR, cause translation initiation at a downstream start codon, and result in a frameshift compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AI768816, AL713094, BC002640, BQ639919
    Consensus CDS
    CCDS58533.1
    UniProtKB/Swiss-Prot
    Q8IY31
    Related
    ENSP00000463322.1, ENST00000579419.5
    Conserved Domains (1) summary
    pfam14931
    Location:10106
    IFT20; Intraflagellar transport complex B, subunit 20
  5. NM_001267778.1NP_001254707.1  intraflagellar transport protein 20 homolog isoform 5

    See identical proteins and their annotated locations for NP_001254707.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR, cause translation initiation at a downstream start codon, and result in a frameshift compared to variant 1. The encoded isoform (5) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AA490722, AC002094, AI768816, AL713094, BC002640
    Consensus CDS
    CCDS74017.1
    UniProtKB/Swiss-Prot
    Q8IY31
    UniProtKB/TrEMBL
    A0A087X2B4
    Related
    ENSP00000484842.1, ENST00000588477.5
    Conserved Domains (1) summary
    cl20817
    Location:1074
    GBP_C; Guanylate-binding protein, C-terminal domain
  6. NM_174887.4NP_777547.1  intraflagellar transport protein 20 homolog isoform 2

    See identical proteins and their annotated locations for NP_777547.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR, cause translation initiation at a downstream start codon, and result in a frameshift compared to variant 1. The encoded protein (isoform 2) is shorter than isoform 1 and has a distinct C-terminus.
    Source sequence(s)
    AI768816, AL713094, BC002640
    Consensus CDS
    CCDS32593.1
    UniProtKB/Swiss-Prot
    Q8IY31
    Related
    ENSP00000350570.3, ENST00000357896.7
    Conserved Domains (1) summary
    pfam14931
    Location:1080
    IFT20; Intraflagellar transport complex B, subunit 20

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_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    28328325..28335489 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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