Ift140 (intraflagellar transport 140) - Rat Genome Database

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Gene: Ift140 (intraflagellar transport 140) Rattus norvegicus
Analyze
Symbol: Ift140
Name: intraflagellar transport 140
RGD ID: 2318759
Description: Predicted to be involved in intraciliary retrograde transport and regulation of cilium assembly. Predicted to act upstream of or within several processes, including cilium organization; embryonic organ development; and regionalization. Predicted to be located in microtubule organizing center and photoreceptor cell cilium. Predicted to be part of intraciliary transport particle A. Predicted to be active in axoneme and ciliary basal body. Human ortholog(s) of this gene implicated in retinitis pigmentosa and short-rib thoracic dysplasia 9 with or without polydactyly. Orthologous to human IFT140 (intraflagellar transport 140); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; endosulfan.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: intraflagellar transport protein 140 homolog; LOC100362124
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Ift140em1Kyo  
Genetic Models: W-Ift140em1Kyo
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,537,134 - 14,624,926 (+)NCBIGRCr8
mRatBN7.21014,032,665 - 14,121,682 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,032,648 - 14,120,433 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01014,373,668 - 14,461,509 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,373,679 - 14,461,160 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01014,189,328 - 14,276,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41014,258,556 - 14,348,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1013,711,169 - 13,793,096 (+)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:20368623   PMID:20889716   PMID:21209331   PMID:22282595   PMID:22503633   PMID:23418020   PMID:23469164   PMID:23955340   PMID:24009529   PMID:24619649   PMID:25807483   PMID:27932497  
PMID:28724397   PMID:29487109  


Genomics

Comparative Map Data
Ift140
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81014,537,134 - 14,624,926 (+)NCBIGRCr8
mRatBN7.21014,032,665 - 14,121,682 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,032,648 - 14,120,433 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01014,373,668 - 14,461,509 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1014,373,679 - 14,461,160 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01014,189,328 - 14,276,940 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41014,258,556 - 14,348,468 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1013,711,169 - 13,793,096 (+)NCBICelera
Cytogenetic Map10q12NCBI
IFT140
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38161,510,427 - 1,612,072 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl161,510,427 - 1,612,072 (-)EnsemblGRCh38hg38GRCh38
GRCh37161,560,428 - 1,662,073 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36161,500,431 - 1,597,299 (-)NCBINCBI36Build 36hg18NCBI36
Celera161,772,703 - 1,874,383 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef161,486,013 - 1,587,550 (-)NCBIHuRef
CHM1_1161,560,388 - 1,662,050 (-)NCBICHM1_1
T2T-CHM13v2.0161,525,455 - 1,627,919 (-)NCBIT2T-CHM13v2.0
Ift140
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391725,235,056 - 25,318,461 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1725,235,059 - 25,318,469 (+)EnsemblGRCm39 Ensembl
GRCm381725,016,083 - 25,099,499 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,016,085 - 25,099,495 (+)EnsemblGRCm38mm10GRCm38
MGSCv371725,153,031 - 25,236,444 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361724,744,323 - 24,827,086 (+)NCBIMGSCv36mm8
Celera1725,543,013 - 25,624,378 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.53NCBI
Ift140
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544215,630,501 - 15,718,484 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544215,625,429 - 15,719,006 (+)NCBIChiLan1.0ChiLan1.0
IFT140
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2181,772,348 - 1,877,046 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1165,560,156 - 5,659,086 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v016130,150 - 232,369 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1161,566,309 - 1,662,833 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl161,566,824 - 1,658,884 (-)Ensemblpanpan1.1panPan2
IFT140
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,262,887 - 39,308,912 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,295,045 - 39,308,758 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha640,497,349 - 40,577,227 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0639,574,931 - 39,655,255 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl639,577,733 - 39,655,241 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1639,252,090 - 39,332,397 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,224,274 - 39,304,564 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0639,702,970 - 39,783,289 (+)NCBIUU_Cfam_GSD_1.0
Ift140
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344104,290,046 - 104,364,999 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366942,344,283 - 2,423,520 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366942,344,448 - 2,419,396 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IFT140
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl340,309,635 - 40,372,135 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1340,309,298 - 40,372,139 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,776,363 - 41,835,312 (+)NCBISscrofa10.2Sscrofa10.2susScr3
IFT140
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.151,419,432 - 1,523,342 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl51,415,664 - 1,521,843 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606829,562,562 - 29,667,409 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ift140
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624913621,203 - 711,493 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624913616,283 - 712,040 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ift140
282 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:107
Count of miRNA genes:94
Interacting mature miRNAs:99
Transcripts:ENSRNOT00000022063
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat

Markers in Region
RH127790  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,076,808 - 14,077,001 (+)MAPPERmRatBN7.2
Rnor_6.01014,417,899 - 14,418,091NCBIRnor6.0
Rnor_5.01014,233,321 - 14,233,513UniSTSRnor5.0
RGSC_v3.41014,304,856 - 14,305,048UniSTSRGSC3.4
Celera1013,749,486 - 13,749,678UniSTS
Cytogenetic Map10q12UniSTS
RH133574  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,056,395 - 14,056,595 (+)MAPPERmRatBN7.2
Rnor_6.01014,397,500 - 14,397,699NCBIRnor6.0
Rnor_5.01014,213,142 - 14,213,341UniSTSRnor5.0
RGSC_v3.41014,284,461 - 14,284,660UniSTSRGSC3.4
Celera1013,729,059 - 13,729,258UniSTS
RH 3.4 Map10168.8UniSTS


Genetic Models
This gene Ift140 is modified in the following models/strains:
W-Ift140em1Kyo    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000022063   ⟹   ENSRNOP00000022063
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1014,032,648 - 14,120,433 (+)Ensembl
Rnor_6.0 Ensembl1014,373,679 - 14,461,160 (+)Ensembl
RefSeq Acc Id: NM_001427126   ⟹   NP_001414055
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,537,466 - 14,624,926 (+)NCBI
RefSeq Acc Id: XM_039087092   ⟹   XP_038943020
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,537,134 - 14,624,926 (+)NCBI
mRatBN7.21014,032,668 - 14,121,682 (+)NCBI
RefSeq Acc Id: XM_039087093   ⟹   XP_038943021
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,537,165 - 14,624,926 (+)NCBI
mRatBN7.21014,032,668 - 14,121,682 (+)NCBI
RefSeq Acc Id: XM_039087096   ⟹   XP_038943024
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,571,927 - 14,624,926 (+)NCBI
mRatBN7.21014,067,416 - 14,121,682 (+)NCBI
RefSeq Acc Id: XM_039087097   ⟹   XP_038943025
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,537,134 - 14,606,569 (+)NCBI
mRatBN7.21014,032,665 - 14,092,962 (+)NCBI
RefSeq Acc Id: XM_063268240   ⟹   XP_063124310
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81014,537,165 - 14,624,926 (+)NCBI
Ensembl Acc Id: ENSRNOP00000022063   ⟸   ENSRNOT00000022063
RefSeq Acc Id: XP_038943025   ⟸   XM_039087097
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038943020   ⟸   XM_039087092
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943021   ⟸   XM_039087093
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038943024   ⟸   XM_039087096
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063124310   ⟸   XM_063268240
- Peptide Label: isoform X3
RefSeq Acc Id: NP_001414055   ⟸   NM_001427126
- UniProtKB: F1LY69 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LY69-F1-model_v2 AlphaFold F1LY69 1-1463 view protein structure

Transcriptome

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

Promoters
RGD ID:13697040
Promoter ID:EPDNEW_R7563
Type:single initiation site
Name:Ift140_1
Description:intraflagellar transport 140
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7564  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01014,373,691 - 14,373,751EPDNEW
RGD ID:13697044
Promoter ID:EPDNEW_R7564
Type:initiation region
Name:Ift140_2
Description:intraflagellar transport 140
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R7563  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01014,373,994 - 14,374,054EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2318759 AgrOrtholog
BioCyc Gene G2FUF-25809 BioCyc
Ensembl Genes ENSRNOG00000016545 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022063.7 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.470 UniProtKB/TrEMBL
  2.130.10.10 UniProtKB/TrEMBL
InterPro TPR-like_helical_dom UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
  WD40_repeat UniProtKB/TrEMBL
  WD40_repeat_dom_sf UniProtKB/TrEMBL
NCBI Gene 100362124 ENTREZGENE
PANTHER IFT140/172-RELATED UniProtKB/TrEMBL
  INTRAFLAGELLAR TRANSPORT PROTEIN 140 HOMOLOG UniProtKB/TrEMBL
PhenoGen Ift140 PhenoGen
RatGTEx ENSRNOG00000016545 RatGTEx
SMART WD40 UniProtKB/TrEMBL
Superfamily-SCOP NHL repeat UniProtKB/TrEMBL
  SSF48452 UniProtKB/TrEMBL
  WD40_like UniProtKB/TrEMBL
UniProt F1LY69 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-27 Ift140  intraflagellar transport 140  LOC100362124  intraflagellar transport 140  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100362124  intraflagellar transport 140      Symbol and Name status set to provisional 70820 PROVISIONAL