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Protein

Intraflagellar transport protein 140 homolog

Gene

IFT140

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport. Plays a pivotal role in proper development and function of ciliated cells. Involved in ciliogenesis and cilia maintenance (PubMed:22503633). May play a role in ciliary assembly. Required for the development and maintenance of the outer segments of rod and cone photoreceptor cells. Plays a role in maintenance and the delivery of opsin to the outer segment of photoreceptor cells (By similarity).By similarity1 Publication

GO - Biological processi

  • determination of left/right symmetry Source: Ensembl
  • embryonic brain development Source: Ensembl
  • embryonic camera-type eye development Source: Ensembl
  • embryonic cranial skeleton morphogenesis Source: Ensembl
  • embryonic digit morphogenesis Source: Ensembl
  • heart development Source: Ensembl
  • intraciliary retrograde transport Source: GO_Central
  • intraciliary transport involved in cilium assembly Source: Reactome
  • neural tube patterning Source: Ensembl
  • non-motile cilium assembly Source: Ensembl
  • photoreceptor cell outer segment organization Source: Ensembl
  • protein localization to cilium Source: UniProtKB
  • regulation of cilium assembly Source: UniProtKB
  • regulation of smoothened signaling pathway Source: Ensembl
  • renal system development Source: UniProtKB
  • retina development in camera-type eye Source: UniProtKB
  • skeletal system morphogenesis Source: UniProtKB

Keywordsi

Biological processCilium biogenesis/degradation

Enzyme and pathway databases

ReactomeiR-HSA-5610787 Hedgehog 'off' state
R-HSA-5620924 Intraflagellar transport
SignaLinkiQ96RY7

Names & Taxonomyi

Protein namesi
Recommended name:
Intraflagellar transport protein 140 homolog
Alternative name(s):
WD and tetratricopeptide repeats protein 2
Gene namesi
Name:IFT140
Synonyms:KIAA0590, WDTC2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

EuPathDBiHostDB:ENSG00000187535.13
HGNCiHGNC:29077 IFT140
MIMi614620 gene
neXtProtiNX_Q96RY7

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cell projection, Cilium, Cytoplasm, Cytoskeleton

Pathology & Biotechi

Involvement in diseasei

Short-rib thoracic dysplasia 9 with or without polydactyly (SRTD9)3 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. SRTD9 is characterized by phalangeal cone-shaped epiphyses, chronic renal disease, nearly constant retinal dystrophy, and mild radiographic abnormality of the proximal femur. Occasional features include short stature, cerebellar ataxia, and hepatic fibrosis.
See also OMIM:266920
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_071000152L → F in SRTD9. 1 Publication1
Natural variantiVAR_068523212G → R in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs201188361Ensembl.1
Natural variantiVAR_068524233I → M in SRTD9. 1 Publication1
Natural variantiVAR_071003267E → G in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. 1 Publication1
Natural variantiVAR_078817280R → W in SRTD9. 1 PublicationCorresponds to variant dbSNP:rs8058674Ensembl.1
Natural variantiVAR_068525292V → M in SRTD9; impairs centrosomal localization. 2 PublicationsCorresponds to variant dbSNP:rs431905521Ensembl.1
Natural variantiVAR_068526311Y → C in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs387907193Ensembl.1
Natural variantiVAR_068527522G → E in SRTD9. 2 PublicationsCorresponds to variant dbSNP:rs199826737Ensembl.1
Natural variantiVAR_068528576R → Q in SRTD9. 1 PublicationCorresponds to variant dbSNP:rs373111085Ensembl.1
Natural variantiVAR_068529664E → K in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs387907192Ensembl.1
Natural variantiVAR_0710081360C → R in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. 1 PublicationCorresponds to variant dbSNP:rs431905520Ensembl.1

Keywords - Diseasei

Ciliopathy, Disease mutation

Organism-specific databases

DisGeNETi9742
MalaCardsiIFT140
MIMi266920 phenotype
OpenTargetsiENSG00000187535
Orphaneti474 Jeune syndrome
140969 Saldino-Mainzer syndrome
PharmGKBiPA142671665

Polymorphism and mutation databases

BioMutaiIFT140
DMDMi74761083

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000510461 – 1462Intraflagellar transport protein 140 homologAdd BLAST1462

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei360PhosphoserineCombined sources1
Modified residuei1443PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96RY7
MaxQBiQ96RY7
PaxDbiQ96RY7
PeptideAtlasiQ96RY7
PRIDEiQ96RY7

PTM databases

iPTMnetiQ96RY7
PhosphoSitePlusiQ96RY7

Expressioni

Gene expression databases

BgeeiENSG00000187535
CleanExiHS_IFT140
ExpressionAtlasiQ96RY7 baseline and differential
GenevisibleiQ96RY7 HS

Organism-specific databases

HPAiHPA042197

Interactioni

Subunit structurei

Component of the IFT complex A (IFT-A) (PubMed:20889716). Interacts with TTC25 (PubMed:25860617).2 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi115090, 20 interactors
CORUMiQ96RY7
IntActiQ96RY7, 16 interactors
MINTiQ96RY7
STRINGi9606.ENSP00000406012

Structurei

3D structure databases

ProteinModelPortaliQ96RY7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati4 – 48WD 1Add BLAST45
Repeati51 – 90WD 2Add BLAST40
Repeati93 – 132WD 3Add BLAST40
Repeati139 – 188WD 4Add BLAST50
Repeati221 – 259WD 5Add BLAST39
Repeati266 – 305WD 6Add BLAST40
Repeati322 – 361WD 7Add BLAST40
Repeati772 – 807TPR 1Add BLAST36
Repeati869 – 904TPR 2Add BLAST36
Repeati906 – 934TPR 3Add BLAST29
Repeati955 – 988TPR 4Add BLAST34
Repeati1010 – 1043TPR 5Add BLAST34
Repeati1078 – 1111TPR 6Add BLAST34
Repeati1123 – 1156TPR 7Add BLAST34
Repeati1189 – 1222TPR 8Add BLAST34
Repeati1376 – 1409TPR 9Add BLAST34

Keywords - Domaini

Repeat, TPR repeat, WD repeat

Phylogenomic databases

eggNOGiKOG3617 Eukaryota
ENOG410XSS4 LUCA
GeneTreeiENSGT00390000007515
HOGENOMiHOG000230867
HOVERGENiHBG055589
InParanoidiQ96RY7
KOiK19672
OMAiHFWDQSE
OrthoDBiEOG091G00FU
PhylomeDBiQ96RY7
TreeFamiTF105851

Family and domain databases

Gene3Di1.25.40.10, 1 hit
2.130.10.10, 2 hits
InterProiView protein in InterPro
IPR011990 TPR-like_helical_dom_sf
IPR015943 WD40/YVTN_repeat-like_dom_sf
IPR001680 WD40_repeat
IPR017986 WD40_repeat_dom
IPR036322 WD40_repeat_dom_sf
SMARTiView protein in SMART
SM00320 WD40, 3 hits
SUPFAMiSSF50978 SSF50978, 4 hits
PROSITEiView protein in PROSITE
PS50082 WD_REPEATS_2, 1 hit
PS50294 WD_REPEATS_REGION, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96RY7-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MALYYDHQIE APDAAGSPSF ISWHPVHPFL AVAYISTTST GSVDIYLEQG
60 70 80 90 100
ECVPDTHVER PFRVASLCWH PTRLVLAVGW ETGEVTVFNK QDKEQHTMPL
110 120 130 140 150
THTADITVLR WSPSGNCLLS GDRLGVLLLW RLDQRGRVQG TPLLKHEYGK
160 170 180 190 200
HLTHCIFRLP PPGEDLVQLA KAAVSGDEKA LDMFNWKKSS SGSLLKMGSH
210 220 230 240 250
EGLLFFVSLM DGTVHYVDEK GKTTQVVSAD STIQMLFYME KREALVVVTE
260 270 280 290 300
NLRLSLYTVP PEGKAEEVMK VKLSGKTGRR ADIALIEGSL LVMAVGEAAL
310 320 330 340 350
RFWDIERGEN YILSPDEKFG FEKGENMNCV CYCKVKGLLA AGTDRGRVAM
360 370 380 390 400
WRKVPDFLGS PGAEGKDRWA LQTPTELQGN ITQIQWGSRK NLLAVNSVIS
410 420 430 440 450
VAILSERAMS SHFHQQVAAM QVSPSLLNVC FLSTGVAHSL RTDMHISGVF
460 470 480 490 500
ATKDAVAVWN GRQVAIFELS GAAIRSAGTF LCETPVLAMH EENVYTVESN
510 520 530 540 550
RVQVRTWQGT VKQLLLFSET EGNPCFLDIC GNFLVVGTDL AHFKSFDLSR
560 570 580 590 600
REAKAHCSCR SLAELVPGVG GIASLRCSSS GSTISILPSK ADNSPDSKIC
610 620 630 640 650
FYDVEMDTVT VFDFKTGQID RRETLSFNEQ ETNKSHLFVD EGLKNYVPVN
660 670 680 690 700
HFWDQSEPRL FVCEAVQETP RSQPQSANGQ PQDGRAGPAA DVLILSFFIS
710 720 730 740 750
EEHGFLLHES FPRPATSHSL LGMEVPYYYF TRKPEEADRE DEVEPGCHHI
760 770 780 790 800
PQMVSRRPLR DFVGLEDCDK ATRDAMLHFS FFVTIGDMDE AFKSIKLIKS
810 820 830 840 850
EAVWENMARM CVKTQRLDVA KVCLGNMGHA RGARALREAE QEPELEARVA
860 870 880 890 900
VLATQLGMLE DAEQLYRKCK RHDLLNKFYQ AAGRWQEALQ VAEHHDRVHL
910 920 930 940 950
RSTYHRYAGH LEASADCSRA LSYYEKSDTH RFEVPRMLSE DLPSLELYVN
960 970 980 990 1000
KMKDKTLWRW WAQYLESQGE MDAALHYYEL ARDHFSLVRI HCFQGNVQKA
1010 1020 1030 1040 1050
AQIANETGNL AASYHLARQY ESQEEVGQAV HFYTRAQAFK NAIRLCKENG
1060 1070 1080 1090 1100
LDDQLMNLAL LSSPEDMIEA ARYYEEKGVQ MDRAVMLYHK AGHFSKALEL
1110 1120 1130 1140 1150
AFATQQFVAL QLIAEDLDET SDPALLARCS DFFIEHSQYE RAVELLLAAR
1160 1170 1180 1190 1200
KYQEALQLCL GQNMSITEEM AEKMTVAKDS SDLPEESRRE LLEQIADCCM
1210 1220 1230 1240 1250
RQGSYHLATK KYTQAGNKLK AMRALLKSGD TEKITFFASV SRQKEIYIMA
1260 1270 1280 1290 1300
ANYLQSLDWR KEPEIMKNII GFYTKGRALD LLAGFYDACA QVEIDEYQNY
1310 1320 1330 1340 1350
DKAHGALTEA YKCLAKAKAK SPLDQETRLA QLQSRMALVK RFIQARRTYT
1360 1370 1380 1390 1400
EDPKESIKQC ELLLEEPDLD STIRIGDVYG FLVEHYVRKE EYQTAYRFLE
1410 1420 1430 1440 1450
EMRRRLPLAN MSYYVSPQAV DAVHRGLGLP LPRTVPEQVR HNSMEDAREL
1460
DEEVVEEADD DP
Length:1,462
Mass (Da):165,193
Last modified:December 1, 2001 - v1
Checksum:i2F3CCBD998F80E3B
GO
Isoform 2 (identifier: Q96RY7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-806: Missing.

Note: No experimental confirmation available.
Show »
Length:656
Mass (Da):75,572
Checksum:iA5D5629CAA150DC0
GO

Sequence cautioni

The sequence BAA25516 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti542H → L in BAA25516 (PubMed:9628581).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_070999110R → H1 PublicationCorresponds to variant dbSNP:rs371077545Ensembl.1
Natural variantiVAR_071000152L → F in SRTD9. 1 Publication1
Natural variantiVAR_071001161P → T1 PublicationCorresponds to variant dbSNP:rs148462329Ensembl.1
Natural variantiVAR_053396165D → A. Corresponds to variant dbSNP:rs35588860Ensembl.1
Natural variantiVAR_068523212G → R in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs201188361Ensembl.1
Natural variantiVAR_068524233I → M in SRTD9. 1 Publication1
Natural variantiVAR_071002243E → G1 PublicationCorresponds to variant dbSNP:rs539181813Ensembl.1
Natural variantiVAR_071003267E → G in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. 1 Publication1
Natural variantiVAR_053397279R → P. Corresponds to variant dbSNP:rs4786350Ensembl.1
Natural variantiVAR_053398280R → Q. Corresponds to variant dbSNP:rs35404373Ensembl.1
Natural variantiVAR_078817280R → W in SRTD9. 1 PublicationCorresponds to variant dbSNP:rs8058674Ensembl.1
Natural variantiVAR_068525292V → M in SRTD9; impairs centrosomal localization. 2 PublicationsCorresponds to variant dbSNP:rs431905521Ensembl.1
Natural variantiVAR_068526311Y → C in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs387907193Ensembl.1
Natural variantiVAR_053399398V → I. Corresponds to variant dbSNP:rs34762152Ensembl.1
Natural variantiVAR_053400451A → V. Corresponds to variant dbSNP:rs8060532Ensembl.1
Natural variantiVAR_071004459W → S1 PublicationCorresponds to variant dbSNP:rs778311141Ensembl.1
Natural variantiVAR_071005514L → H1 PublicationCorresponds to variant dbSNP:rs150903791Ensembl.1
Natural variantiVAR_068527522G → E in SRTD9. 2 PublicationsCorresponds to variant dbSNP:rs199826737Ensembl.1
Natural variantiVAR_062098561S → N. Corresponds to variant dbSNP:rs8050974Ensembl.1
Natural variantiVAR_068528576R → Q in SRTD9. 1 PublicationCorresponds to variant dbSNP:rs373111085Ensembl.1
Natural variantiVAR_053401621R → Q. Corresponds to variant dbSNP:rs11648609Ensembl.1
Natural variantiVAR_068529664E → K in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. 1 PublicationCorresponds to variant dbSNP:rs387907192Ensembl.1
Natural variantiVAR_053402670P → S. Corresponds to variant dbSNP:rs34900355Ensembl.1
Natural variantiVAR_071006787D → G1 PublicationCorresponds to variant dbSNP:rs144938800Ensembl.1
Natural variantiVAR_0534031070A → V1 PublicationCorresponds to variant dbSNP:rs2235638Ensembl.1
Natural variantiVAR_0710071353P → R1 PublicationCorresponds to variant dbSNP:rs146666187Ensembl.1
Natural variantiVAR_0710081360C → R in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. 1 PublicationCorresponds to variant dbSNP:rs431905520Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0563921 – 806Missing in isoform 2. 1 PublicationAdd BLAST806

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011162 mRNA Translation: BAA25516.2 Different initiation.
AE006467 Genomic DNA Translation: AAK61285.1
AL080069 mRNA Translation: CAB45696.1
AL031705 Genomic DNA No translation available.
Z97633 Genomic DNA No translation available.
AL031719 Genomic DNA No translation available.
Z97652 Genomic DNA No translation available.
AL133297 Genomic DNA No translation available.
CH471112 Genomic DNA Translation: EAW85642.1
CH471112 Genomic DNA Translation: EAW85644.1
BC035577 mRNA Translation: AAH35577.1
CCDSiCCDS10439.1 [Q96RY7-1]
PIRiT00345
RefSeqiNP_055529.2, NM_014714.3 [Q96RY7-1]
XP_006721053.1, XM_006720990.3 [Q96RY7-1]
XP_006721054.1, XM_006720991.3 [Q96RY7-1]
XP_016879399.1, XM_017023910.1 [Q96RY7-1]
UniGeneiHs.389438

Genome annotation databases

EnsembliENST00000361339; ENSP00000354895; ENSG00000187535 [Q96RY7-2]
ENST00000426508; ENSP00000406012; ENSG00000187535 [Q96RY7-1]
GeneIDi9742
KEGGihsa:9742
UCSCiuc002cmb.4 human [Q96RY7-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiIF140_HUMAN
AccessioniPrimary (citable) accession number: Q96RY7
Secondary accession number(s): A2A2A8
, D3DU75, O60332, Q9UG52
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 1, 2001
Last modified: March 28, 2018
This is version 147 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health