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Q96RY7 (IF140_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Intraflagellar transport protein 140 homolog
Alternative name(s):
WD and tetratricopeptide repeats protein 2
Gene names
Name:IFT140
Synonyms:KIAA0590, WDTC2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1462 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.9

Subunit structure

Component of the IFT complex A (IFT-A). Ref.8

Subcellular location

Cytoplasmcytoskeletoncilium basal body. Cytoplasmcytoskeletonmicrotubule organizing centercentrosome Ref.9 Ref.10.

Involvement in disease

Short-rib thoracic dysplasia 9 with or without polydactyly (SRTD9) [MIM:266920]: A 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.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.9 Ref.10

Sequence similarities

Contains 9 TPR repeats.

Contains 5 WD repeats.

Sequence caution

The sequence BAA25516.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 14621462Intraflagellar transport protein 140 homolog
PRO_0000051046

Regions

Repeat13 – 5745WD 1
Repeat59 – 9840WD 2
Repeat101 – 14040WD 3
Repeat263 – 31351WD 4
Repeat322 – 36140WD 5
Repeat772 – 80736TPR 1
Repeat869 – 90436TPR 2
Repeat906 – 93429TPR 3
Repeat955 – 98834TPR 4
Repeat1010 – 104334TPR 5
Repeat1078 – 111134TPR 6
Repeat1123 – 115634TPR 7
Repeat1189 – 122234TPR 8
Repeat1376 – 140934TPR 9

Amino acid modifications

Modified residue14431Phosphoserine Ref.7

Natural variations

Natural variant1101R → H. Ref.10
Corresponds to variant rs371077545 [ dbSNP | Ensembl ].
VAR_070999
Natural variant1521L → F in SRTD9. Ref.10
VAR_071000
Natural variant1611P → T. Ref.10
VAR_071001
Natural variant1651D → A.
Corresponds to variant rs35588860 [ dbSNP | Ensembl ].
VAR_053396
Natural variant2121G → R in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. Ref.9
VAR_068523
Natural variant2331I → M in SRTD9. Ref.9
VAR_068524
Natural variant2431E → G. Ref.10
VAR_071002
Natural variant2671E → G in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. Ref.10
VAR_071003
Natural variant2791R → P.
Corresponds to variant rs4786350 [ dbSNP | Ensembl ].
VAR_053397
Natural variant2801R → Q.
Corresponds to variant rs35404373 [ dbSNP | Ensembl ].
VAR_053398
Natural variant2921V → M in SRTD9; impairs centrosomal localization. Ref.9 Ref.10
VAR_068525
Natural variant3111Y → C in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. Ref.9
VAR_068526
Natural variant3981V → I.
Corresponds to variant rs34762152 [ dbSNP | Ensembl ].
VAR_053399
Natural variant4511A → V.
Corresponds to variant rs8060532 [ dbSNP | Ensembl ].
VAR_053400
Natural variant4591W → S. Ref.10
VAR_071004
Natural variant5141L → H. Ref.10
Corresponds to variant rs150903791 [ dbSNP | Ensembl ].
VAR_071005
Natural variant5221G → E in SRTD9. Ref.9 Ref.10
VAR_068527
Natural variant5611S → N.
Corresponds to variant rs8050974 [ dbSNP | Ensembl ].
VAR_062098
Natural variant5761R → Q in SRTD9. Ref.9
VAR_068528
Natural variant6211R → Q.
Corresponds to variant rs11648609 [ dbSNP | Ensembl ].
VAR_053401
Natural variant6641E → K in SRTD9; partial to complete loss of basal body localization and increase of cytoplasmic localization. Ref.9
VAR_068529
Natural variant6701P → S.
Corresponds to variant rs34900355 [ dbSNP | Ensembl ].
VAR_053402
Natural variant7871D → G. Ref.10
Corresponds to variant rs144938800 [ dbSNP | Ensembl ].
VAR_071006
Natural variant10701A → V. Ref.1
Corresponds to variant rs2235638 [ dbSNP | Ensembl ].
VAR_053403
Natural variant13531P → R. Ref.10
VAR_071007
Natural variant13601C → R in SRTD9; disease phenotype consistent with Mainzer-Saldino syndrome. Ref.10
VAR_071008

Experimental info

Sequence conflict5421H → L in BAA25516. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q96RY7 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: 2F3CCBD998F80E3B

FASTA1,462165,193
        10         20         30         40         50         60 
MALYYDHQIE APDAAGSPSF ISWHPVHPFL AVAYISTTST GSVDIYLEQG ECVPDTHVER 

        70         80         90        100        110        120 
PFRVASLCWH PTRLVLAVGW ETGEVTVFNK QDKEQHTMPL THTADITVLR WSPSGNCLLS 

       130        140        150        160        170        180 
GDRLGVLLLW RLDQRGRVQG TPLLKHEYGK HLTHCIFRLP PPGEDLVQLA KAAVSGDEKA 

       190        200        210        220        230        240 
LDMFNWKKSS SGSLLKMGSH EGLLFFVSLM DGTVHYVDEK GKTTQVVSAD STIQMLFYME 

       250        260        270        280        290        300 
KREALVVVTE NLRLSLYTVP PEGKAEEVMK VKLSGKTGRR ADIALIEGSL LVMAVGEAAL 

       310        320        330        340        350        360 
RFWDIERGEN YILSPDEKFG FEKGENMNCV CYCKVKGLLA AGTDRGRVAM WRKVPDFLGS 

       370        380        390        400        410        420 
PGAEGKDRWA LQTPTELQGN ITQIQWGSRK NLLAVNSVIS VAILSERAMS SHFHQQVAAM 

       430        440        450        460        470        480 
QVSPSLLNVC FLSTGVAHSL RTDMHISGVF ATKDAVAVWN GRQVAIFELS GAAIRSAGTF 

       490        500        510        520        530        540 
LCETPVLAMH EENVYTVESN RVQVRTWQGT VKQLLLFSET EGNPCFLDIC GNFLVVGTDL 

       550        560        570        580        590        600 
AHFKSFDLSR REAKAHCSCR SLAELVPGVG GIASLRCSSS GSTISILPSK ADNSPDSKIC 

       610        620        630        640        650        660 
FYDVEMDTVT VFDFKTGQID RRETLSFNEQ ETNKSHLFVD EGLKNYVPVN HFWDQSEPRL 

       670        680        690        700        710        720 
FVCEAVQETP RSQPQSANGQ PQDGRAGPAA DVLILSFFIS EEHGFLLHES FPRPATSHSL 

       730        740        750        760        770        780 
LGMEVPYYYF TRKPEEADRE DEVEPGCHHI PQMVSRRPLR DFVGLEDCDK ATRDAMLHFS 

       790        800        810        820        830        840 
FFVTIGDMDE AFKSIKLIKS EAVWENMARM CVKTQRLDVA KVCLGNMGHA RGARALREAE 

       850        860        870        880        890        900 
QEPELEARVA VLATQLGMLE DAEQLYRKCK RHDLLNKFYQ AAGRWQEALQ VAEHHDRVHL 

       910        920        930        940        950        960 
RSTYHRYAGH LEASADCSRA LSYYEKSDTH RFEVPRMLSE DLPSLELYVN KMKDKTLWRW 

       970        980        990       1000       1010       1020 
WAQYLESQGE MDAALHYYEL ARDHFSLVRI HCFQGNVQKA AQIANETGNL AASYHLARQY 

      1030       1040       1050       1060       1070       1080 
ESQEEVGQAV HFYTRAQAFK NAIRLCKENG LDDQLMNLAL LSSPEDMIEA ARYYEEKGVQ 

      1090       1100       1110       1120       1130       1140 
MDRAVMLYHK AGHFSKALEL AFATQQFVAL QLIAEDLDET SDPALLARCS DFFIEHSQYE 

      1150       1160       1170       1180       1190       1200 
RAVELLLAAR KYQEALQLCL GQNMSITEEM AEKMTVAKDS SDLPEESRRE LLEQIADCCM 

      1210       1220       1230       1240       1250       1260 
RQGSYHLATK KYTQAGNKLK AMRALLKSGD TEKITFFASV SRQKEIYIMA ANYLQSLDWR 

      1270       1280       1290       1300       1310       1320 
KEPEIMKNII GFYTKGRALD LLAGFYDACA QVEIDEYQNY DKAHGALTEA YKCLAKAKAK 

      1330       1340       1350       1360       1370       1380 
SPLDQETRLA QLQSRMALVK RFIQARRTYT EDPKESIKQC ELLLEEPDLD STIRIGDVYG 

      1390       1400       1410       1420       1430       1440 
FLVEHYVRKE EYQTAYRFLE EMRRRLPLAN MSYYVSPQAV DAVHRGLGLP LPRTVPEQVR 

      1450       1460 
HNSMEDAREL DEEVVEEADD DP 

« Hide

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."
Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 5:31-39(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT VAL-1070.
Tissue: Brain.
[2]"Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16."
Daniels R.J., Peden J.F., Lloyd C., Horsley S.W., Clark K., Tufarelli C., Kearney L., Buckle V.J., Doggett N.A., Flint J., Higgs D.R.
Hum. Mol. Genet. 10:339-352(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The sequence and analysis of duplication-rich human chromosome 16."
Martin J., Han C., Gordon L.A., Terry A., Prabhakar S., She X., Xie G., Hellsten U., Chan Y.M., Altherr M., Couronne O., Aerts A., Bajorek E., Black S., Blumer H., Branscomb E., Brown N.C., Bruno W.J. expand/collapse author list , Buckingham J.M., Callen D.F., Campbell C.S., Campbell M.L., Campbell E.W., Caoile C., Challacombe J.F., Chasteen L.A., Chertkov O., Chi H.C., Christensen M., Clark L.M., Cohn J.D., Denys M., Detter J.C., Dickson M., Dimitrijevic-Bussod M., Escobar J., Fawcett J.J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Goodwin L.A., Grady D.L., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Hildebrand C.E., Huang W., Israni S., Jett J., Jewett P.B., Kadner K., Kimball H., Kobayashi A., Krawczyk M.-C., Leyba T., Longmire J.L., Lopez F., Lou Y., Lowry S., Ludeman T., Manohar C.F., Mark G.A., McMurray K.L., Meincke L.J., Morgan J., Moyzis R.K., Mundt M.O., Munk A.C., Nandkeshwar R.D., Pitluck S., Pollard M., Predki P., Parson-Quintana B., Ramirez L., Rash S., Retterer J., Ricke D.O., Robinson D.L., Rodriguez A., Salamov A., Saunders E.H., Scott D., Shough T., Stallings R.L., Stalvey M., Sutherland R.D., Tapia R., Tesmer J.G., Thayer N., Thompson L.S., Tice H., Torney D.C., Tran-Gyamfi M., Tsai M., Ulanovsky L.E., Ustaszewska A., Vo N., White P.S., Williams A.L., Wills P.L., Wu J.-R., Wu K., Yang J., DeJong P., Bruce D., Doggett N.A., Deaven L., Schmutz J., Grimwood J., Richardson P., Rokhsar D.S., Eichler E.E., Gilna P., Lucas S.M., Myers R.M., Rubin E.M., Pennacchio L.A.
Nature 432:988-994(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Lymph.
[6]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[7]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1443, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[8]"TULP3 bridges the IFT-A complex and membrane phosphoinositides to promote trafficking of G protein-coupled receptors into primary cilia."
Mukhopadhyay S., Wen X., Chih B., Nelson C.D., Lane W.S., Scales S.J., Jackson P.K.
Genes Dev. 24:2180-2193(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE IFT-A COMPLEX.
[9]"Mainzer-Saldino syndrome is a ciliopathy caused by IFT140 mutations."
Perrault I., Saunier S., Hanein S., Filhol E., Bizet A.A., Collins F., Salih M.A., Gerber S., Delphin N., Bigot K., Orssaud C., Silva E., Baudouin V., Oud M.M., Shannon N., Le Merrer M., Roche O., Pietrement C. expand/collapse author list , Goumid J., Baumann C., Bole-Feysot C., Nitschke P., Zahrate M., Beales P., Arts H.H., Munnich A., Kaplan J., Antignac C., Cormier-Daire V., Rozet J.M.
Am. J. Hum. Genet. 90:864-870(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, VARIANTS SRTD9 ARG-212; MET-233; MET-292; CYS-311; GLU-522; GLN-576 AND LYS-664, CHARACTERIZATION OF VARIANTS SRTD9 ARG-212; CYS-311 AND LYS-664.
[10]"Combined NGS approaches identify mutations in the intraflagellar transport gene IFT140 in skeletal ciliopathies with early progressive kidney Disease."
Schmidts M., Frank V., Eisenberger T., Al Turki S., Bizet A.A., Antony D., Rix S., Decker C., Bachmann N., Bald M., Vinke T., Toenshoff B., Di Donato N., Neuhann T., Hartley J.L., Maher E.R., Bogdanovic R., Peco-Antic A. expand/collapse author list , Mache C., Hurles M.E., Joksic I., Guc-Scekic M., Dobricic J., Brankovic-Magic M., Bolz H.J., Pazour G.J., Beales P.L., Scambler P.J., Saunier S., Mitchison H.M., Bergmann C.
Hum. Mutat. 34:714-724(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, VARIANTS HIS-110; THR-161; GLY-243; SER-459; HIS-514; GLY-787 AND ARG-1353, VARIANTS SRTD9 PHE-152; GLY-267; MET-292; GLU-522 AND ARG-1360, CHARACTERIZATION OF VARIANT SRTD9 MET-292.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB011162 mRNA. Translation: BAA25516.2. Different initiation.
AE006467 Genomic DNA. Translation: AAK61285.1.
AL031705 expand/collapse EMBL AC list , AL031719, AL133297, Z97633, Z97652 Genomic DNA. Translation: CAM26342.1.
Z97633 expand/collapse EMBL AC list , AL031705, AL031719, AL133297, Z97652 Genomic DNA. Translation: CAM26352.1.
AL031719 expand/collapse EMBL AC list , AL031705, AL133297, Z97633, Z97652 Genomic DNA. Translation: CAM26410.1.
Z97652 expand/collapse EMBL AC list , AL031705, AL031719, AL133297, Z97633 Genomic DNA. Translation: CAM26430.1.
AL133297 expand/collapse EMBL AC list , AL031705, AL031719, Z97633, Z97652 Genomic DNA. Translation: CAM26447.1.
CH471112 Genomic DNA. Translation: EAW85642.1.
CH471112 Genomic DNA. Translation: EAW85644.1.
BC035577 mRNA. Translation: AAH35577.1.
CCDSCCDS10439.1.
PIRT00345.
RefSeqNP_055529.2. NM_014714.3.
XP_006721052.1. XM_006720989.1.
XP_006721053.1. XM_006720990.1.
XP_006721054.1. XM_006720991.1.
UniGeneHs.389438.

3D structure databases

ProteinModelPortalQ96RY7.
SMRQ96RY7. Positions 65-132, 195-220, 902-927, 955-1004.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115090. 4 interactions.
IntActQ96RY7. 4 interactions.
MINTMINT-8247576.
STRING9606.ENSP00000354895.

PTM databases

PhosphoSiteQ96RY7.

Polymorphism databases

DMDM74761083.

Proteomic databases

MaxQBQ96RY7.
PaxDbQ96RY7.
PRIDEQ96RY7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000426508; ENSP00000406012; ENSG00000187535.
GeneID9742.
KEGGhsa:9742.
UCSCuc002clz.3. human.

Organism-specific databases

CTD9742.
GeneCardsGC16M001560.
HGNCHGNC:29077. IFT140.
HPAHPA042197.
MIM266920. phenotype.
614620. gene.
neXtProtNX_Q96RY7.
Orphanet474. Jeune syndrome.
140969. Saldino-Mainzer syndrome.
PharmGKBPA142671665.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG301450.
HOGENOMHOG000230867.
HOVERGENHBG055589.
InParanoidQ96RY7.
OMAKGRVAMW.
PhylomeDBQ96RY7.
TreeFamTF105851.

Enzyme and pathway databases

SignaLinkQ96RY7.

Gene expression databases

ArrayExpressQ96RY7.
BgeeQ96RY7.
CleanExHS_IFT140.
GenevestigatorQ96RY7.

Family and domain databases

Gene3D2.130.10.10. 2 hits.
InterProIPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamPF00400. WD40. 1 hit.
[Graphical view]
SMARTSM00320. WD40. 3 hits.
[Graphical view]
SUPFAMSSF50978. SSF50978. 4 hits.
PROSITEPS50082. WD_REPEATS_2. 1 hit.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSIFT140. human.
GenomeRNAi9742.
NextBio36659.
PROQ96RY7.
SOURCESearch...

Entry information

Entry nameIF140_HUMAN
AccessionPrimary (citable) accession number: Q96RY7
Secondary accession number(s): A2A2A8, D3DU75, O60332
Entry history
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: December 1, 2001
Last modified: July 9, 2014
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 16

Human chromosome 16: entries, gene names and cross-references to MIM