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Protein

Intraflagellar transport protein 88 homolog

Gene

IFT88

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Involved in primary cilium biogenesis. Also involved in autophagy since it is required for trafficking of ATG16L and the expansion of the autophagic compartment (By similarity).By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cilium biogenesis/degradation

Enzyme and pathway databases

ReactomeiREACT_268024. Intraflagellar transport.
REACT_268323. Hedgehog 'off' state.

Names & Taxonomyi

Protein namesi
Recommended name:
Intraflagellar transport protein 88 homolog
Alternative name(s):
Recessive polycystic kidney disease protein Tg737 homolog
Tetratricopeptide repeat protein 10
Short name:
TPR repeat protein 10
Gene namesi
Name:IFT88
Synonyms:TG737, TTC10
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:20606. IFT88.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell projection, Cilium, Cytoplasm, Cytoskeleton

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134991804.

Polymorphism and mutation databases

BioMutaiIFT88.
DMDMi206729873.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 833833Intraflagellar transport protein 88 homologPRO_0000106391Add
BLAST

Proteomic databases

MaxQBiQ13099.
PaxDbiQ13099.
PRIDEiQ13099.

PTM databases

PhosphoSiteiQ13099.

Expressioni

Tissue specificityi

Expressed in the heart, brain, liver, lung, kidney, skeletal muscle and pancreas.1 Publication

Gene expression databases

BgeeiQ13099.
CleanExiHS_IFT88.
ExpressionAtlasiQ13099. baseline and differential.
GenevisibleiQ13099. HS.

Organism-specific databases

HPAiHPA040731.

Interactioni

Subunit structurei

Component of the IFT complex B, at least composed of IFT20, IFT22, HSPB11/IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88. Interacts with IFT20, IFT22, HSPB11, IFT27, IFT46, IFT52, TRAF3IP1, IFT57, IFT74, IFT80, IFT81, IFT88 AND IFT172. Interacts with C2CD3 (By similarity).By similarity

Protein-protein interaction databases

BioGridi113771. 5 interactions.
IntActiQ13099. 3 interactions.
STRINGi9606.ENSP00000323580.

Structurei

3D structure databases

ProteinModelPortaliQ13099.
SMRiQ13099. Positions 210-341, 429-695.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati206 – 23934TPR 1Add
BLAST
Repeati242 – 27534TPR 2Add
BLAST
Repeati281 – 31434TPR 3Add
BLAST
Repeati316 – 34732TPR 4Add
BLAST
Repeati424 – 45734TPR 5Add
BLAST
Repeati459 – 49234TPR 6Add
BLAST
Repeati493 – 52634TPR 7Add
BLAST
Repeati527 – 56034TPR 8Add
BLAST
Repeati561 – 59434TPR 9Add
BLAST
Repeati595 – 62834TPR 10Add
BLAST
Repeati629 – 66234TPR 11Add
BLAST
Repeati663 – 69634TPR 12Add
BLAST

Sequence similaritiesi

Contains 12 TPR repeats.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, TPR repeat

Phylogenomic databases

eggNOGiCOG0457.
GeneTreeiENSGT00390000015473.
HOGENOMiHOG000258203.
HOVERGENiHBG059328.
InParanoidiQ13099.
KOiK16474.
OMAiCTDLGLK.
OrthoDBiEOG7N37D5.
PhylomeDBiQ13099.
TreeFamiTF313218.

Family and domain databases

Gene3Di1.25.40.10. 2 hits.
InterProiIPR006597. Sel1-like.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR001440. TPR_1.
IPR013105. TPR_2.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF00515. TPR_1. 4 hits.
PF07719. TPR_2. 1 hit.
PF13174. TPR_6. 1 hit.
PF13181. TPR_8. 1 hit.
[Graphical view]
SMARTiSM00671. SEL1. 4 hits.
SM00028. TPR. 7 hits.
[Graphical view]
PROSITEiPS50005. TPR. 9 hits.
PS50293. TPR_REGION. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q13099-1) [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
MKFTNTKVQM MQNVHLAPET DEDDLYSGYN DYNPIYDIEE LENDAAFQQA
60 70 80 90 100
VRTSHGRRPP ITAKISSTAV TRPIATGYGS KTSLASSIGR PMTGAIQDGV
110 120 130 140 150
TRPMTAVRAA GFTKAALRGS AFDPLSQSRG PASPLEAKKK DSPEEKIKQL
160 170 180 190 200
EKEVNELVEE SCIANSCGDL KLALEKAKDA GRKERVLVRQ REQVTTPENI
210 220 230 240 250
NLDLTYSVLF NLASQYSVNE MYAEALNTYQ VIVKNKMFSN AGILKMNMGN
260 270 280 290 300
IYLKQRNYSK AIKFYRMALD QVPSVNKQMR IKIMQNIGVT FIQAGQYSDA
310 320 330 340 350
INSYEHIMSM APNLKAGYNL TICYFAIGDR EKMKKAFQKL ITVPLEIDED
360 370 380 390 400
KYISPSDDPH TNLVTEAIKN DHLRQMERER KAMAEKYIMT SAKLIAPVIE
410 420 430 440 450
TSFAAGYDWC VEVVKASQYV ELANDLEINK AVTYLRQKDY NQAVEILKVL
460 470 480 490 500
EKKDSRVKSA AATNLSALYY MGKDFAQASS YADIAVNSDR YNPAALTNKG
510 520 530 540 550
NTVFANGDYE KAAEFYKEAL RNDSSCTEAL YNIGLTYEKL NRLDEALDCF
560 570 580 590 600
LKLHAILRNS AEVLYQIANI YELMENPSQA IEWLMQVVSV IPTDPQVLSK
610 620 630 640 650
LGELYDREGD KSQAFQYYYE SYRYFPCNIE VIEWLGAYYI DTQFWEKAIQ
660 670 680 690 700
YFERASLIQP TQVKWQLMVA SCFRRSGNYQ KALDTYKDTH RKFPENVECL
710 720 730 740 750
RFLVRLCTDL GLKDAQEYAR KLKRLEKMKE IREQRIKSGR DGSGGSRGKR
760 770 780 790 800
EGSASGDSGQ NYSASSKGER LSARLRALPG TNEPYESSSN KEIDASYVDP
810 820 830
LGPQIERPKT AAKKRIDEDD FADEELGDDL LPE
Length:833
Mass (Da):94,270
Last modified:September 23, 2008 - v2
Checksum:i383887C9D79AF0DA
GO
Isoform 2 (identifier: Q13099-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-9: Missing.

Show »
Length:824
Mass (Da):93,192
Checksum:i12E30169CFC5476B
GO
Isoform 3 (identifier: Q13099-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     61-79: Missing.

Note: No experimental confirmation available.
Show »
Length:814
Mass (Da):92,381
Checksum:iB5364A6022DC66F3
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti210 – 2101F → S in AAA86720 (PubMed:7633404).Curated
Sequence conflicti335 – 3351K → E in AAH30776 (PubMed:15489334).Curated
Sequence conflicti388 – 3881I → V in AAH30776 (PubMed:15489334).Curated
Sequence conflicti389 – 3891M → T in AAA86720 (PubMed:7633404).Curated
Sequence conflicti407 – 4071Y → C in AAA86720 (PubMed:7633404).Curated
Sequence conflicti608 – 6081E → G in AAH30776 (PubMed:15489334).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti383 – 3831M → I.1 Publication
Corresponds to variant rs2442455 [ dbSNP | Ensembl ].
VAR_046464
Natural varianti455 – 4551S → N.1 Publication
Corresponds to variant rs9509307 [ dbSNP | Ensembl ].
VAR_046465
Natural varianti671 – 6711S → G.
Corresponds to variant rs9552254 [ dbSNP | Ensembl ].
VAR_046466

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 99Missing in isoform 2. 1 PublicationVSP_035429
Alternative sequencei61 – 7919Missing in isoform 3. 1 PublicationVSP_040620Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20362 mRNA. Translation: AAA86720.1.
AK300769 mRNA. Translation: BAG62434.1.
AL161772, AL590096 Genomic DNA. Translation: CAM13405.1.
AL590096, AL161772 Genomic DNA. Translation: CAM20430.1.
AL161772, AL590096 Genomic DNA. Translation: CAH70874.2.
AL590096, AL161772 Genomic DNA. Translation: CAI14390.2.
CH471075 Genomic DNA. Translation: EAX08272.1.
BC030776 mRNA. Translation: AAH30776.2.
CCDSiCCDS31944.1. [Q13099-1]
CCDS31945.1. [Q13099-2]
RefSeqiNP_006522.2. NM_006531.3. [Q13099-2]
NP_783195.2. NM_175605.3. [Q13099-1]
XP_005266610.1. XM_005266553.2. [Q13099-1]
XP_006719933.1. XM_006719870.2. [Q13099-2]
XP_011533543.1. XM_011535241.1. [Q13099-1]
XP_011533544.1. XM_011535242.1. [Q13099-2]
XP_011533545.1. XM_011535243.1. [Q13099-2]
XP_011533546.1. XM_011535244.1. [Q13099-2]
UniGeneiHs.187376.

Genome annotation databases

EnsembliENST00000319980; ENSP00000323580; ENSG00000032742.
ENST00000351808; ENSP00000261632; ENSG00000032742. [Q13099-2]
GeneIDi8100.
KEGGihsa:8100.
UCSCiuc001unh.3. human. [Q13099-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U20362 mRNA. Translation: AAA86720.1.
AK300769 mRNA. Translation: BAG62434.1.
AL161772, AL590096 Genomic DNA. Translation: CAM13405.1.
AL590096, AL161772 Genomic DNA. Translation: CAM20430.1.
AL161772, AL590096 Genomic DNA. Translation: CAH70874.2.
AL590096, AL161772 Genomic DNA. Translation: CAI14390.2.
CH471075 Genomic DNA. Translation: EAX08272.1.
BC030776 mRNA. Translation: AAH30776.2.
CCDSiCCDS31944.1. [Q13099-1]
CCDS31945.1. [Q13099-2]
RefSeqiNP_006522.2. NM_006531.3. [Q13099-2]
NP_783195.2. NM_175605.3. [Q13099-1]
XP_005266610.1. XM_005266553.2. [Q13099-1]
XP_006719933.1. XM_006719870.2. [Q13099-2]
XP_011533543.1. XM_011535241.1. [Q13099-1]
XP_011533544.1. XM_011535242.1. [Q13099-2]
XP_011533545.1. XM_011535243.1. [Q13099-2]
XP_011533546.1. XM_011535244.1. [Q13099-2]
UniGeneiHs.187376.

3D structure databases

ProteinModelPortaliQ13099.
SMRiQ13099. Positions 210-341, 429-695.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113771. 5 interactions.
IntActiQ13099. 3 interactions.
STRINGi9606.ENSP00000323580.

PTM databases

PhosphoSiteiQ13099.

Polymorphism and mutation databases

BioMutaiIFT88.
DMDMi206729873.

Proteomic databases

MaxQBiQ13099.
PaxDbiQ13099.
PRIDEiQ13099.

Protocols and materials databases

DNASUi8100.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000319980; ENSP00000323580; ENSG00000032742.
ENST00000351808; ENSP00000261632; ENSG00000032742. [Q13099-2]
GeneIDi8100.
KEGGihsa:8100.
UCSCiuc001unh.3. human. [Q13099-1]

Organism-specific databases

CTDi8100.
GeneCardsiGC13P021141.
HGNCiHGNC:20606. IFT88.
HPAiHPA040731.
MIMi600595. gene.
neXtProtiNX_Q13099.
PharmGKBiPA134991804.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0457.
GeneTreeiENSGT00390000015473.
HOGENOMiHOG000258203.
HOVERGENiHBG059328.
InParanoidiQ13099.
KOiK16474.
OMAiCTDLGLK.
OrthoDBiEOG7N37D5.
PhylomeDBiQ13099.
TreeFamiTF313218.

Enzyme and pathway databases

ReactomeiREACT_268024. Intraflagellar transport.
REACT_268323. Hedgehog 'off' state.

Miscellaneous databases

ChiTaRSiIFT88. human.
GeneWikiiIFT88.
GenomeRNAii8100.
NextBioi30744.
PROiQ13099.
SOURCEiSearch...

Gene expression databases

BgeeiQ13099.
CleanExiHS_IFT88.
ExpressionAtlasiQ13099. baseline and differential.
GenevisibleiQ13099. HS.

Family and domain databases

Gene3Di1.25.40.10. 2 hits.
InterProiIPR006597. Sel1-like.
IPR013026. TPR-contain_dom.
IPR011990. TPR-like_helical_dom.
IPR001440. TPR_1.
IPR013105. TPR_2.
IPR019734. TPR_repeat.
[Graphical view]
PfamiPF00515. TPR_1. 4 hits.
PF07719. TPR_2. 1 hit.
PF13174. TPR_6. 1 hit.
PF13181. TPR_8. 1 hit.
[Graphical view]
SMARTiSM00671. SEL1. 4 hits.
SM00028. TPR. 7 hits.
[Graphical view]
PROSITEiPS50005. TPR. 9 hits.
PS50293. TPR_REGION. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the human homologue of the mouse Tg737 candidate polycystic kidney disease gene."
    Schrick J.J., Onuchic L.F., Reeders S.T., Korenberg J., Chen X.-N., Moyer J.H., Wilkinson J.E., Woychik R.P.
    Hum. Mol. Genet. 4:559-567(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY, VARIANT ASN-455.
    Tissue: Liver.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Tissue: Neuroepithelioma.
  3. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. 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] (ISOFORM 1), VARIANT ILE-383.
    Tissue: Testis.

Entry informationi

Entry nameiIFT88_HUMAN
AccessioniPrimary (citable) accession number: Q13099
Secondary accession number(s): A2A491
, B4DUS2, Q5SZJ6, Q8N719
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: September 23, 2008
Last modified: July 22, 2015
This is version 138 of the entry and version 2 of the sequence. [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

Documents

  1. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.