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IFT88 intraflagellar transport 88 [ Homo sapiens (human) ]

Gene ID: 8100, updated on 17-Jun-2019

Summary

Official Symbol
IFT88provided by HGNC
Official Full Name
intraflagellar transport 88provided by HGNC
Primary source
HGNC:HGNC:20606
See related
Ensembl:ENSG00000032742 MIM:600595
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
Also known as
DAF19; TG737; TTC10; hTg737; D13S1056E
Summary
This gene encodes a member of the tetratrico peptide repeat (TPR) family. The encoded protein is involved in cilium biogenesis. Mutations of a similar gene in mouse can cause polycystic kidney disease. Several transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2017]
Expression
Broad expression in testis (RPKM 23.5), thyroid (RPKM 6.6) and 19 other tissues See more
Orthologs

Genomic context

See IFT88 in Genome Data Viewer
Location:
13q12.11
Exon count:
34
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 13 NC_000013.11 (20566446..20691444)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (21140585..21265576)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene crystallin lambda 1 Neighboring gene microRNA 4499 Neighboring gene Sharpr-MPRA regulatory region 6807 Neighboring gene uncharacterized LOC105370103 Neighboring gene solute carrier family 35 member E1 pseudogene 1 Neighboring gene RNA, U2 small nuclear 7, pseudogene Neighboring gene interleukin 17D Neighboring gene EEF1A lysine methyltransferase 1 Neighboring gene RAN pseudogene 8

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
Cross-disorder genomewide analysis of schizophrenia, bipolar disorder, and depression.
NHGRI GWA Catalog
Genetics of coronary artery calcification among African Americans, a meta-analysis.
NHGRI GWA Catalog
GWAS of dental caries patterns in the permanent dentition.
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...
  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Hedgehog 'off' state, organism-specific biosystem (from REACTOME)
    Hedgehog 'off' state, organism-specific biosystemHedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh ...
  • Hedgehog signaling events mediated by Gli proteins, organism-specific biosystem (from Pathway Interaction Database)
    Hedgehog signaling events mediated by Gli proteins, organism-specific biosystem
    Hedgehog signaling events mediated by Gli proteins
  • 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...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC26259

Gene Ontology Provided by GOA

Function Evidence Code Pubs
kinesin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
inner ear receptor cell stereocilium organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
non-motile cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of autophagosome assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
centriole IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
centriole IDA
Inferred from Direct Assay
more info
PubMed 
centriole ISS
Inferred from Sequence or Structural Similarity
more info
 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary basal body IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body ISS
Inferred from Sequence or Structural Similarity
more info
 
ciliary base IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ciliary tip TAS
Traceable Author Statement
more info
 
cilium IDA
Inferred from Direct Assay
more info
PubMed 
cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
cilium TAS
Traceable Author Statement
more info
 
intraciliary transport particle B ISS
Inferred from Sequence or Structural Similarity
more info
 
motile cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
non-motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sperm flagellum ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
intraflagellar transport protein 88 homolog
Names
TPR repeat protein 10
intraflagellar transport 88 homolog
polaris homolog
probe hTg737 (polycystic kidney disease, autosomal recessive)
recessive polycystic kidney disease protein Tg737 homolog
testicular tissue protein Li 93
tetratricopeptide repeat domain 10
tetratricopeptide repeat protein 10

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_001318491.2NP_001305420.1  intraflagellar transport protein 88 homolog isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple alternate exons in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (3) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK300769, AL161772, BC030776, BG182322
    UniProtKB/Swiss-Prot
    Q13099
    UniProtKB/TrEMBL
    B3KX42
    Conserved Domains (6) summary
    sd00006
    Location:465493
    TPR; TPR repeat [structural motif]
    cd15832
    Location:210241
    SNAP; TPR repeat [structural motif]
    pfam00515
    Location:500524
    TPR_1; Tetratricopeptide repeat
    pfam13414
    Location:464528
    TPR_11; TPR repeat
    pfam13424
    Location:216285
    TPR_12; Tetratricopeptide repeat
    cl24038
    Location:210311
    SNAP; Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family
  2. NM_001318493.2NP_001305422.1  intraflagellar transport protein 88 homolog isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an additional segment in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1 and 4 encode the same isoform (1).
    Source sequence(s)
    AK126668, AK308281, AL161772, BC059357, BG182322
    Consensus CDS
    CCDS31944.1
    UniProtKB/Swiss-Prot
    Q13099
    UniProtKB/TrEMBL
    B3KX42
    Conserved Domains (2) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    cl26002
    Location:222730
    TPR_11; TPR repeat
  3. NM_001353565.2NP_001340494.1  intraflagellar transport protein 88 homolog isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variants 1, 4, 7, and 8, encodes isoform 1.
    Source sequence(s)
    AL161772, AL590096
    Consensus CDS
    CCDS31944.1
    Conserved Domains (2) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    cl26002
    Location:222730
    TPR_11; TPR repeat
  4. NM_001353566.2NP_001340495.1  intraflagellar transport protein 88 homolog isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7), as well as variants 1, 4, 6, and 8, encodes isoform 1.
    Source sequence(s)
    AL161772, AL590096
    Consensus CDS
    CCDS31944.1
    Conserved Domains (2) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    cl26002
    Location:222730
    TPR_11; TPR repeat
  5. NM_001353567.2NP_001340496.1  intraflagellar transport protein 88 homolog isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8), as well as variants 1, 4, 6, and 7, encodes isoform 1.
    Source sequence(s)
    AL161772, AL590096
    Consensus CDS
    CCDS31944.1
    Conserved Domains (2) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    cl26002
    Location:222730
    TPR_11; TPR repeat
  6. NM_001353568.2NP_001340497.1  intraflagellar transport protein 88 homolog isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9), as well as variant 2, encodes isoform 2.
    Source sequence(s)
    AL161772, AL590096
    Consensus CDS
    CCDS31945.1
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat
  7. NM_001353569.2NP_001340498.1  intraflagellar transport protein 88 homolog isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10), as well as variant 11, encodes isoform 5.
    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  8. NM_001353570.2NP_001340499.1  intraflagellar transport protein 88 homolog isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11), as well as variant 10, encodes isoform 5.
    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  9. NM_001353571.2NP_001340500.1  intraflagellar transport protein 88 homolog isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    smart00028
    Location:238265
    TPR; Tetratricopeptide repeats
    sd00006
    Location:450478
    TPR; TPR repeat [structural motif]
    cl26002
    Location:388657
    TPR_11; TPR repeat
  10. NM_001353572.2NP_001340501.1  intraflagellar transport protein 88 homolog isoform 7

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat
  11. NM_001353573.2NP_001340502.1  intraflagellar transport protein 88 homolog isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (2) summary
    sd00006
    Location:436464
    TPR; TPR repeat [structural motif]
    cl26002
    Location:184664
    TPR_11; TPR repeat
  12. NM_001353574.2NP_001340503.1  intraflagellar transport protein 88 homolog isoform 9

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    smart00028
    Location:219246
    TPR; Tetratricopeptide repeats
    sd00006
    Location:431459
    TPR; TPR repeat [structural motif]
    cl26002
    Location:369638
    TPR_11; TPR repeat
  13. NM_001353575.2NP_001340504.1  intraflagellar transport protein 88 homolog isoform 10

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (2) summary
    sd00006
    Location:465493
    TPR; TPR repeat [structural motif]
    cl26002
    Location:194674
    TPR_11; TPR repeat
  14. NM_001353576.2NP_001340505.1  intraflagellar transport protein 88 homolog isoform 11

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17), as well as variantm18, encodes isoform 11.
    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  15. NM_001353577.2NP_001340506.1  intraflagellar transport protein 88 homolog isoform 11

    Status: REVIEWED

    Description
    Transcript Variant: This variant (18), as well as variant 17, encodes isoform 11.
    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  16. NM_001353578.2NP_001340507.1  intraflagellar transport protein 88 homolog isoform 12

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (3) summary
    smart00028
    Location:238265
    TPR; Tetratricopeptide repeats
    sd00006
    Location:450478
    TPR; TPR repeat [structural motif]
    cl26002
    Location:388657
    TPR_11; TPR repeat
  17. NM_001353579.2NP_001340508.1  intraflagellar transport protein 88 homolog isoform 13

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
    Conserved Domains (2) summary
    sd00006
    Location:273301
    TPR; TPR repeat [structural motif]
    cl26002
    Location:2510
    TPR_11; TPR repeat
  18. NM_006531.5NP_006522.2  intraflagellar transport protein 88 homolog isoform 2

    See identical proteins and their annotated locations for NP_006522.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks multiple alternate exons in the 5' UTR and lacks a portion of the 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Variants 2 and 9 both encode the same isoform (2).
    Source sequence(s)
    AK126668, AK308281, AK310223, AL161772, BC059357, BG182322
    Consensus CDS
    CCDS31945.1
    UniProtKB/TrEMBL
    A0A140VJL7, B3KX42
    Related
    ENSP00000261632.5, ENST00000351808.9
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat
  19. NM_175605.5NP_783195.2  intraflagellar transport protein 88 homolog isoform 1

    See identical proteins and their annotated locations for NP_783195.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 4, 6, 7, and 8 all encode the same isoform (1).
    Source sequence(s)
    AK126668, AL161772, BC030776, BG182322
    Consensus CDS
    CCDS31944.1
    UniProtKB/Swiss-Prot
    Q13099
    UniProtKB/TrEMBL
    B3KX42
    Related
    ENSP00000323580.6, ENST00000319980.10
    Conserved Domains (2) summary
    sd00006
    Location:493521
    TPR; TPR repeat [structural motif]
    cl26002
    Location:222730
    TPR_11; TPR repeat

RNA

  1. NR_134653.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs at both the 5' and 3' ends, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK126668, AK310223, BC059357, BG182322
  2. NR_148462.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
  3. NR_148463.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
  4. NR_148464.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096
  5. NR_148465.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL161772, AL590096

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_000013.11 Reference GRCh38.p13 Primary Assembly

    Range
    20566446..20691444
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020773.1XP_016876262.1  intraflagellar transport protein 88 homolog isoform X11

  2. XM_017020757.1XP_016876246.1  intraflagellar transport protein 88 homolog isoform X1

    UniProtKB/TrEMBL
    A0A140VJL7
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat
  3. XM_011535243.1XP_011533545.1  intraflagellar transport protein 88 homolog isoform X1

    See identical proteins and their annotated locations for XP_011533545.1

    UniProtKB/TrEMBL
    A0A140VJL7
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat
  4. XM_017020763.1XP_016876252.1  intraflagellar transport protein 88 homolog isoform X6

  5. XM_017020762.1XP_016876251.1  intraflagellar transport protein 88 homolog isoform X5

  6. XM_017020759.1XP_016876248.1  intraflagellar transport protein 88 homolog isoform X3

  7. XM_024449411.1XP_024305179.1  intraflagellar transport protein 88 homolog isoform X4

    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  8. XM_024449414.1XP_024305182.1  intraflagellar transport protein 88 homolog isoform X10

    Conserved Domains (3) summary
    COG0457
    Location:235509
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:459487
    TPR; TPR repeat [structural motif]
    cl26002
    Location:397666
    TPR_11; TPR repeat
  9. XM_017020768.1XP_016876257.1  intraflagellar transport protein 88 homolog isoform X9

  10. XM_017020758.1XP_016876247.1  intraflagellar transport protein 88 homolog isoform X2

    UniProtKB/Swiss-Prot
    Q13099
  11. XM_024449412.1XP_024305180.1  intraflagellar transport protein 88 homolog isoform X7

    Conserved Domains (2) summary
    sd00006
    Location:445473
    TPR; TPR repeat [structural motif]
    cl26002
    Location:193673
    TPR_11; TPR repeat
  12. XM_024449413.1XP_024305181.1  intraflagellar transport protein 88 homolog isoform X8

    Conserved Domains (3) summary
    smart00028
    Location:228255
    TPR; Tetratricopeptide repeats
    sd00006
    Location:440468
    TPR; TPR repeat [structural motif]
    cl26002
    Location:378647
    TPR_11; TPR repeat
  13. XM_017020775.1XP_016876264.1  intraflagellar transport protein 88 homolog isoform X12

  14. XM_017020776.1XP_016876265.1  intraflagellar transport protein 88 homolog isoform X14

  15. XM_024449415.1XP_024305183.1  intraflagellar transport protein 88 homolog isoform X13

    Conserved Domains (2) summary
    COG0457
    Location:199352
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    sd00006
    Location:247270
    TPR; TPR repeat [structural motif]
  16. XM_006719870.3XP_006719933.1  intraflagellar transport protein 88 homolog isoform X1

    See identical proteins and their annotated locations for XP_006719933.1

    UniProtKB/TrEMBL
    A0A140VJL7
    Conserved Domains (2) summary
    sd00006
    Location:484512
    TPR; TPR repeat [structural motif]
    cl26002
    Location:213721
    TPR_11; TPR repeat

RNA

  1. XR_001749683.1 RNA Sequence

  2. XR_002957474.1 RNA Sequence

  3. XR_001749682.1 RNA Sequence

  4. XR_001749686.1 RNA Sequence

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