IFT20 intraflagellar transport 20 [Homo sapiens (human)] - Gene

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; AllianceGenome:HGNC:30989
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: mouse all
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Genomic context

Location:: 17q11.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (28328326..28335472, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (29270174..29277320, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (26655352..26662498, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associations of IFT20 and GM130 protein expressions with clinicopathological features and survival of patients with lung adenocarcinoma.
Title: Associations of IFT20 and GM130 protein expressions with clinicopathological features and survival of patients with lung adenocarcinoma.
The intraflagellar transport protein IFT20 controls lysosome biogenesis by regulating the post-Golgi transport of acid hydrolases.
Title: The intraflagellar transport protein IFT20 controls lysosome biogenesis by regulating the post-Golgi transport of acid hydrolases.
These results indicate that IFT20 plays an important role in collective invasion of CRC cells by regulating organization of Golgi-associated, stabilized microtubules and Golgi polarity in leader cells.
Title: Intraflagellar transport 20 promotes collective cancer cell invasion by regulating polarized organization of Golgi-associated microtubules.
Authors showed that in chondrocytes from human (ACH, TD) and mouse Fgfr3Y367C/+ cartilage, the constitutively active FGFR3 perturbed PC length and the sorting and trafficking of intraflagellar transport (IFT) 20 to the PC.
Title: Constitutively-active FGFR3 disrupts primary cilium length and IFT20 trafficking in various chondrocyte models of achondroplasia.
intraflagellar transport protein 20 (IFT20) interacts with E3 ubiquitin ligases c-Cbl and Cbl-b and is required for Cbl-mediated ubiquitination and internalization of PDGFRalpha for feedback inhibition of receptor signaling.
Title: IFT20 modulates ciliary PDGFRα signaling by regulating the stability of Cbl E3 ubiquitin ligases.
the traffic-related role of an IFT20 complex that includes components of the intracellular trafficking machinery in immune synapse assembly, is reported.
Title: The T cell IFT20 interactome reveals new players in immune synapse assembly.
IFT20 is required for the delivery of the intracellular pool of LAT to the immune synapse in naive primary T lymphocytes.
Title: IFT20 controls LAT recruitment to the immune synapse and T-cell activation in vivo.
This work suggests that IFT20 functions in the delivery of ciliary membrane proteins from the Golgi complex to the cilium.
Title: The intraflagellar transport protein IFT20 is associated with the Golgi complex and is required for cilia assembly.
Data report the molecular cloning and characterization of a novel human cDNA encoding a putative protein of 158 amino acid residues which shares high homology to Mus musculus intraflagellar transport protein mIFT20.
Title: Cloning and characterization of the human IFT20 gene.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D20S1105 (e-PCR)
- UniSTS:31004

RH17628 (e-PCR)
- UniSTS:85029

SHGC-11786 (e-PCR)
- UniSTS:80181

D17S1824 (e-PCR), detects polymorphism
- UniSTS:10314

NoName (e-PCR)
- UniSTS:21338

D1S1423 (e-PCR)
- UniSTS:149619

SHGC-132058 (e-PCR)
- UniSTS:170621

RH24980 (e-PCR)
- UniSTS:87995

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables opsin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cardiac muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in cochlea development	IEA Inferred from Electronic Annotation more info
involved_in establishment of epithelial cell apical/basal polarity	IEA Inferred from Electronic Annotation more info
involved_in establishment of planar polarity	IEA Inferred from Electronic Annotation more info
involved_in inner ear receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
involved_in intraciliary anterograde transport	NAS Non-traceable Author Statement more info	PubMed
involved_in kidney development	IEA Inferred from Electronic Annotation more info
involved_in neural precursor cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in opsin transport	IEA Inferred from Electronic Annotation more info
involved_in photoreceptor cell outer segment organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to Golgi apparatus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to cilium	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in protein transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of autophagosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in regulation of cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of platelet-derived growth factor receptor-alpha signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in smoothened signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in visual learning	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in acrosomal vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in centriole	IEA Inferred from Electronic Annotation more info
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in ciliary basal body	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
is_active_in ciliary base	IBA Inferred from Biological aspect of Ancestor more info
located_in ciliary base	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary tip	TAS Traceable Author Statement more info
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
located_in cilium	NAS Non-traceable Author Statement more info	PubMed
located_in cilium	TAS Traceable Author Statement more info
located_in cis-Golgi network	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in dendrite terminus	IEA Inferred from Electronic Annotation more info
part_of intraciliary transport particle	IBA Inferred from Biological aspect of Ancestor more info
part_of intraciliary transport particle B	IPI Inferred from Physical Interaction more info	PubMed
part_of intraciliary transport particle B	ISS Inferred from Sequence or Structural Similarity more info
located_in kinociliary basal body	IEA Inferred from Electronic Annotation more info
located_in manchette	ISS Inferred from Sequence or Structural Similarity more info
located_in microvillus	IEA Inferred from Electronic Annotation more info
located_in motile cilium	IEA Inferred from Electronic Annotation more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in non-motile cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
located_in stereocilium	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intraflagellar transport protein 20 homolog

Names: intraflagellar transport 20 homolog; intraflagellar transport protein IFT20

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)

NM_001267774.2 → NP_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/TrEMBL

J3QR43

Related

ENSP00000464443.1, ENST00000585089.5

Conserved Domains (1) summary

pfam14931
Location:37 → 145

IFT20; Intraflagellar transport complex B, subunit 20
NM_001267775.2 → NP_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

J3QL09, Q5GLZ2, Q8IY31, Q9BUG5

UniProtKB/TrEMBL

J3QR43

Related

ENSP00000463138.1, ENST00000585313.5

Conserved Domains (1) summary

pfam14931
Location:11 → 119

IFT20; Intraflagellar transport complex B, subunit 20
NM_001267776.2 → NP_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

J3QL09, Q5GLZ2, Q8IY31, Q9BUG5

UniProtKB/TrEMBL

J3QR43

Related

ENSP00000378809.3, ENST00000395418.8

Conserved Domains (1) summary

pfam14931
Location:11 → 119

IFT20; Intraflagellar transport complex B, subunit 20
NM_001267777.2 → NP_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/TrEMBL

J3QRC6

Related

ENSP00000463322.1, ENST00000579419.5

Conserved Domains (1) summary

pfam14931
Location:10 → 106

IFT20; Intraflagellar transport complex B, subunit 20
NM_001267778.2 → NP_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/TrEMBL

A0A087X2B4, J3QRH2

Related

ENSP00000484842.1, ENST00000588477.5

Conserved Domains (1) summary

cl20817
Location:11 → 71

GBP_C; Guanylate-binding protein, C-terminal domain
NM_174887.4 → NP_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:10 → 80

IFT20; Intraflagellar transport complex B, subunit 20