Ift88 (intraflagellar transport 88) - Rat Genome Database
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Gene: Ift88 (intraflagellar transport 88) Rattus norvegicus
Analyze
Symbol: Ift88
Name: intraflagellar transport 88
RGD ID: 1309717
Description: Predicted to have kinesin binding activity. Predicted to be involved in several processes, including animal organ development; regulation of organelle assembly; and spermatid development. Localizes to outer acrosomal membrane and trans-Golgi network. Orthologous to human IFT88 (intraflagellar transport 88); PARTICIPATES IN Hedgehog signaling pathway; INTERACTS WITH amphetamine; bisphenol A; furan.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: intraflagellar transport 88 homolog; intraflagellar transport 88 homolog (Chlamydomonas); intraflagellar transport protein 88 homolog; LOC305918; tetratricopeptide repeat domain 10; Ttc10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21531,573,325 - 31,666,068 (+)NCBI
Rnor_6.0 Ensembl1537,691,345 - 37,784,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01537,690,417 - 37,786,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01541,536,303 - 41,630,808 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41536,468,007 - 36,560,959 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11536,489,464 - 36,576,142 (+)NCBI
Celera1531,284,577 - 31,376,920 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (ISO)
anterior/posterior pattern specification  (ISO)
brain development  (ISO)
cardiac muscle cell differentiation  (ISO)
cardiac septum morphogenesis  (ISO)
cilium assembly  (ISO)
cilium movement  (ISO)
cochlea development  (ISO)
cytoplasmic microtubule organization  (ISO)
determination of left/right symmetry  (ISO)
dorsal/ventral pattern formation  (ISO)
embryonic digit morphogenesis  (ISO)
endothelial cell morphogenesis  (ISO)
epidermal stem cell homeostasis  (ISO)
epidermis development  (ISO)
eye development  (ISO)
forebrain development  (ISO)
forebrain morphogenesis  (ISO)
heart development  (ISO)
heart formation  (ISO)
inner ear receptor cell stereocilium organization  (IBA,ISO)
intraciliary transport  (IBA)
kidney development  (IBA,ISO)
limb development  (ISO)
liver development  (ISO)
lung development  (ISO)
lung vasculature development  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
nervous system development  (ISO)
neural precursor cell proliferation  (ISO)
non-motile cilium assembly  (IBA,ISO)
Notch signaling pathway  (ISO)
pancreas development  (ISO)
positive regulation of insulin-like growth factor receptor signaling pathway  (ISO)
primary palate development  (ISO)
protein localization  (ISO)
regulation of autophagosome assembly  (ISO)
regulation of cilium assembly  (ISO)
regulation of fat cell differentiation  (ISO)
regulation of feeding behavior  (ISO)
regulation of odontogenesis of dentin-containing tooth  (ISO)
regulation of protein processing  (ISO)
response to fluid shear stress  (ISO)
smoothened signaling pathway  (ISO)
sperm axoneme assembly  (ISO)
spermatid nucleus elongation  (ISO)
spinal cord dorsal/ventral patterning  (ISO)
telencephalon development  (ISO)

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9176412   PMID:10804177   PMID:11062270   PMID:11251073   PMID:11773599   PMID:11854326   PMID:12701101   PMID:12821668   PMID:15226261   PMID:15755804   PMID:15930098   PMID:16254602  
PMID:16775004   PMID:18066062   PMID:18285569   PMID:18297065   PMID:18590716   PMID:19036983   PMID:19208653   PMID:19253336   PMID:19384852   PMID:19596798   PMID:19654211   PMID:20159594  
PMID:20230748   PMID:20368623   PMID:21209331   PMID:21285373   PMID:21289087   PMID:21429982   PMID:21565611   PMID:21653639   PMID:21703454   PMID:21761479   PMID:21837759   PMID:22228099  
PMID:22689656   PMID:23386061   PMID:23599282   PMID:23810713   PMID:23955340   PMID:24089209   PMID:24302887   PMID:24421332   PMID:24469809   PMID:24596149   PMID:24927541   PMID:25294941  
PMID:25443296   PMID:25564561   PMID:27623382   PMID:27682589   PMID:27767179   PMID:28291836   PMID:28428259   PMID:28536011   PMID:28625565   PMID:29487109   PMID:29891944   PMID:31761534  


Genomics

Comparative Map Data
Ift88
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21531,573,325 - 31,666,068 (+)NCBI
Rnor_6.0 Ensembl1537,691,345 - 37,784,924 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01537,690,417 - 37,786,855 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01541,536,303 - 41,630,808 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41536,468,007 - 36,560,959 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11536,489,464 - 36,576,142 (+)NCBI
Celera1531,284,577 - 31,376,920 (+)NCBICelera
Cytogenetic Map15p12NCBI
IFT88
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1320,567,138 - 20,691,444 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1320,567,069 - 20,691,437 (+)EnsemblGRCh38hg38GRCh38
GRCh381320,566,446 - 20,691,444 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371321,141,296 - 21,265,583 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361320,039,208 - 20,163,576 (+)NCBINCBI36hg18NCBI36
Celera132,203,136 - 2,327,509 (+)NCBI
Cytogenetic Map13q12.11NCBI
HuRef131,944,935 - 2,068,758 (+)NCBIHuRef
CHM1_11321,109,133 - 21,233,717 (+)NCBICHM1_1
Ift88
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391457,661,519 - 57,755,393 (+)NCBIGRCm39mm39
GRCm39 Ensembl1457,661,519 - 57,755,393 (+)Ensembl
GRCm381457,424,064 - 57,517,936 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1457,424,062 - 57,517,936 (+)EnsemblGRCm38mm10GRCm38
MGSCv371458,042,908 - 58,136,773 (+)NCBIGRCm37mm9NCBIm37
MGSCv361456,378,236 - 56,472,046 (+)NCBImm8
Celera1455,219,087 - 55,313,152 (+)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1430.1NCBI
Ift88
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554971,338,904 - 1,455,122 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554971,338,959 - 1,454,788 (+)NCBIChiLan1.0ChiLan1.0
IFT88
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11320,205,881 - 20,331,204 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1320,206,471 - 20,331,204 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0131,893,102 - 2,017,771 (+)NCBIMhudiblu_PPA_v0panPan3
IFT88
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2517,414,965 - 17,551,266 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12517,414,965 - 17,551,405 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Ift88
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367201,041,216 - 1,168,725 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IFT88
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl11943,469 - 1,022,953 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.111943,444 - 1,025,617 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.211303,752 - 344,218 (-)NCBISscrofa10.2Sscrofa10.2susScr3
IFT88
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.13435,649 - 546,661 (-)NCBI
ChlSab1.1 Ensembl3436,207 - 546,583 (-)Ensembl
Ift88
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477616,954,368 - 17,086,377 (-)NCBI

Position Markers
AW546000  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0715,129,849 - 15,129,988NCBIRnor6.0
Rnor_6.01537,710,935 - 37,711,074NCBIRnor6.0
Rnor_5.01541,556,792 - 41,556,931UniSTSRnor5.0
Rnor_5.0715,288,979 - 15,289,118UniSTSRnor5.0
RGSC_v3.41536,486,687 - 36,486,826UniSTSRGSC3.4
RGSC_v3.4713,539,988 - 13,540,127UniSTSRGSC3.4
Celera1531,303,241 - 31,303,380UniSTS
Celera710,056,134 - 10,056,273UniSTS
Cytogenetic Map7q11UniSTS
Cytogenetic Map19q12UniSTS
Cytogenetic Map15p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15137708474Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15137708474Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15137708474Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15142844179Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15143521446Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15162301382Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15232787753535766Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15388113148881131Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151071919155719191Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151549236072568189Rat
9590272Scort14Serum corticosterone level QTL 142.780.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)151698090761980907Rat
8694427Bw163Body weight QTL 1634.820.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)151698090761980907Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151724964162249641Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151724964162249641Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151809320881255430Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151851391388036354Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152102134241082727Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152102134252831189Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152377896946825072Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1526381041106550657Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1526381041106550657Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1526381041106550657Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152870974173709741Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)153321910189640841Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)153321910189640841Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)153321910189640841Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)153321910189640841Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:286
Count of miRNA genes:187
Interacting mature miRNAs:213
Transcripts:ENSRNOT00000012988
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 11 4 8 4 74 21 41 10
Low 3 43 46 37 11 37 8 10 14 1 8
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012988   ⟹   ENSRNOP00000012988
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1537,691,394 - 37,784,924 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076608   ⟹   ENSRNOP00000068425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1537,691,345 - 37,784,923 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076741   ⟹   ENSRNOP00000068104
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1537,691,374 - 37,708,779 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076839   ⟹   ENSRNOP00000067945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1537,714,808 - 37,745,732 (+)Ensembl
RefSeq Acc Id: NM_001107266   ⟹   NP_001100736
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,417 - 31,666,068 (+)NCBI
Rnor_6.01537,691,394 - 37,784,924 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
RGSC_v3.41536,468,007 - 36,560,959 (+)RGD
Celera1531,284,577 - 31,376,920 (+)RGD
Sequence:
RefSeq Acc Id: XM_006252066   ⟹   XP_006252128
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,325 - 31,666,068 (+)NCBI
Rnor_6.01537,690,417 - 37,784,924 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252067   ⟹   XP_006252129
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,349 - 31,666,068 (+)NCBI
Rnor_6.01537,690,417 - 37,784,924 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252068   ⟹   XP_006252130
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01537,690,417 - 37,784,924 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252070   ⟹   XP_006252132
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,382 - 31,666,068 (+)NCBI
Rnor_6.01537,690,417 - 37,784,924 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006252071   ⟹   XP_006252133
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01537,690,417 - 37,773,754 (+)NCBI
Rnor_5.01541,536,303 - 41,630,808 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599687   ⟹   XP_017455176
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,356 - 31,666,068 (+)NCBI
Rnor_6.01537,691,471 - 37,784,924 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039093318   ⟹   XP_038949246
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,579,209 - 31,666,068 (+)NCBI
RefSeq Acc Id: XM_039093319   ⟹   XP_038949247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,591,744 - 31,666,068 (+)NCBI
RefSeq Acc Id: XR_005493725
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21531,573,382 - 31,665,147 (+)NCBI
RefSeq Acc Id: XR_596131
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01537,690,417 - 37,786,855 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001100736   ⟸   NM_001107266
- UniProtKB: D4ACI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252130   ⟸   XM_006252068
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006252129   ⟸   XM_006252067
- Peptide Label: isoform X1
- UniProtKB: A0A096MK92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252128   ⟸   XM_006252066
- Peptide Label: isoform X1
- UniProtKB: A0A096MK92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006252132   ⟸   XM_006252070
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006252133   ⟸   XM_006252071
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017455176   ⟸   XM_017599687
- Peptide Label: isoform X1
- UniProtKB: A0A096MK92 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012988   ⟸   ENSRNOT00000012988
RefSeq Acc Id: ENSRNOP00000067945   ⟸   ENSRNOT00000076839
RefSeq Acc Id: ENSRNOP00000068425   ⟸   ENSRNOT00000076608
RefSeq Acc Id: ENSRNOP00000068104   ⟸   ENSRNOT00000076741
RefSeq Acc Id: XP_038949246   ⟸   XM_039093318
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038949247   ⟸   XM_039093319
- Peptide Label: isoform X4
Protein Domains
TPR_REGION

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699720
Promoter ID:EPDNEW_R10243
Type:initiation region
Name:Ift88_1
Description:intraflagellar transport 88
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01537,691,345 - 37,691,405EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309717 AgrOrtholog
Ensembl Genes ENSRNOG00000009278 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012988 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000067945 UniProtKB/TrEMBL
  ENSRNOP00000068104 UniProtKB/TrEMBL
  ENSRNOP00000068425 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012988 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000076608 UniProtKB/TrEMBL
  ENSRNOT00000076741 UniProtKB/TrEMBL
  ENSRNOT00000076839 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
InterPro TPR-contain UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
KEGG Report rno:305918 UniProtKB/TrEMBL
NCBI Gene 305918 ENTREZGENE
Pfam TPR_6 UniProtKB/TrEMBL
  TPR_8 UniProtKB/TrEMBL
PhenoGen Ift88 PhenoGen
PROSITE TPR UniProtKB/TrEMBL
  TPR_REGION UniProtKB/TrEMBL
SMART TPR UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A096MJ06_RAT UniProtKB/TrEMBL
  A0A096MJE9_RAT UniProtKB/TrEMBL
  A0A096MK92 ENTREZGENE, UniProtKB/TrEMBL
  D4ACI9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Ift88  intraflagellar transport 88  Ift88  intraflagellar transport 88 homolog (Chlamydomonas)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ift88  intraflagellar transport 88 homolog (Chlamydomonas)   Ift88_predicted  intraflagellar transport 88 homolog (Chlamydomonas) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ift88_predicted  intraflagellar transport 88 homolog (Chlamydomonas) (predicted)  Ttc10_predicted  tetratricopeptide repeat domain 10 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Ttc10_predicted  tetratricopeptide repeat domain 10 (predicted)      Symbol and Name status set to approved 70820 APPROVED