Ift57 (intraflagellar transport 57) - Rat Genome Database

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Gene: Ift57 (intraflagellar transport 57) Rattus norvegicus
Analyze
Symbol: Ift57
Name: intraflagellar transport 57
RGD ID: 1305947
Description: Predicted to be involved in intraciliary transport and non-motile cilium assembly. Predicted to act upstream of or within several processes, including epithelial tube morphogenesis; motile cilium assembly; and negative regulation of keratinocyte proliferation. Predicted to be located in several cellular components, including ciliary base; cytoskeleton; and photoreceptor connecting cilium. Predicted to be part of intraciliary transport particle B. Predicted to be active in Golgi apparatus; cilium; and microtubule organizing center. Human ortholog(s) of this gene implicated in orofaciodigital syndrome XVIII. Orthologous to human IFT57 (intraflagellar transport 57); PARTICIPATES IN Huntington's disease pathway; INTERACTS WITH 17alpha-ethynylestradiol; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Esrrbl1; estrogen-related receptor beta like 1; intraflagellar transport 57 homolog; intraflagellar transport 57 homolog (Chlamydomonas); intraflagellar transport protein 57 homolog; LOC303968
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81164,528,349 - 64,593,545 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1164,528,349 - 64,593,545 (-)EnsemblGRCr8
mRatBN7.21151,051,520 - 51,124,909 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1151,059,611 - 51,124,812 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1159,828,491 - 59,893,684 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01152,490,246 - 52,555,439 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01151,617,600 - 51,682,895 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01153,664,638 - 53,731,779 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1153,664,638 - 53,731,779 (-)Ensemblrn6Rnor6.0
Rnor_5.01156,827,640 - 56,856,819 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01156,880,772 - 56,895,355 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41152,251,655 - 52,321,489 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1150,700,486 - 50,764,317 (-)NCBICelera
RGSC_v3.11152,310,266 - 52,379,067 (-)NCBI
Cytogenetic Map11q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. A novel function of Huntingtin in the cilium and retinal ciliopathy in Huntington's disease mice. Karam A, etal., Neurobiol Dis. 2015 Aug;80:15-28. doi: 10.1016/j.nbd.2015.05.008. Epub 2015 May 16.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11788820   PMID:12821668   PMID:17027958   PMID:17931679   PMID:19253336   PMID:20368623   PMID:21209331   PMID:21703454   PMID:23810713   PMID:23955340   PMID:24596149   PMID:25443296  


Genomics

Comparative Map Data
Ift57
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81164,528,349 - 64,593,545 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1164,528,349 - 64,593,545 (-)EnsemblGRCr8
mRatBN7.21151,051,520 - 51,124,909 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1151,059,611 - 51,124,812 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1159,828,491 - 59,893,684 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01152,490,246 - 52,555,439 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01151,617,600 - 51,682,895 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01153,664,638 - 53,731,779 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1153,664,638 - 53,731,779 (-)Ensemblrn6Rnor6.0
Rnor_5.01156,827,640 - 56,856,819 (-)NCBIRnor_5.0Rnor_5.0rn5
Rnor_5.01156,880,772 - 56,895,355 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41152,251,655 - 52,321,489 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1150,700,486 - 50,764,317 (-)NCBICelera
RGSC_v3.11152,310,266 - 52,379,067 (-)NCBI
Cytogenetic Map11q21NCBI
IFT57
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383108,160,812 - 108,222,424 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3108,160,812 - 108,222,553 (-)Ensemblhg38GRCh38
GRCh373107,879,659 - 107,941,271 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363109,362,349 - 109,423,938 (-)NCBIBuild 36Build 36hg18NCBI36
Build 343109,362,349 - 109,423,938NCBI
Celera3106,276,278 - 106,338,042 (-)NCBICelera
Cytogenetic Map3q13.12-q13.13NCBI
HuRef3105,252,904 - 105,314,664 (-)NCBIHuRef
CHM1_13107,843,767 - 107,905,541 (-)NCBICHM1_1
T2T-CHM13v2.03110,880,592 - 110,942,211 (-)NCBIT2T-CHM13v2.0
Ift57
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391649,519,657 - 49,585,489 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1649,519,596 - 49,585,489 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381649,699,294 - 49,765,126 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1649,699,233 - 49,765,126 (+)Ensemblmm10GRCm38
MGSCv371649,699,407 - 49,765,239 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361649,618,920 - 49,684,752 (+)NCBIMGSCv36mm8
Celera1650,040,931 - 50,108,491 (+)NCBICelera
Cytogenetic Map16B5NCBI
cM Map1631.08NCBI
Ift57
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554278,814,298 - 8,871,720 (-)Ensembl
ChiLan1.0NW_0049554278,814,298 - 8,871,671 (-)NCBIChiLan1.0ChiLan1.0
IFT57
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22106,139,368 - 106,199,646 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13106,144,147 - 106,204,316 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03105,287,086 - 105,348,872 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13112,220,461 - 112,282,317 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3112,222,128 - 112,282,069 (-)EnsemblpanPan2panpan1.1
IFT57
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13313,432,902 - 13,486,692 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3313,410,544 - 13,486,612 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3313,538,630 - 13,592,513 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03313,598,605 - 13,652,479 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3313,597,771 - 13,652,518 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13313,468,264 - 13,522,112 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03313,533,830 - 13,587,699 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03313,946,751 - 14,000,605 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ift57
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602141,321,427 - 141,374,229 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366451,468,375 - 1,524,238 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366451,471,393 - 1,524,193 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IFT57
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13151,298,554 - 151,357,155 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113151,298,552 - 151,356,715 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213160,336,854 - 160,394,816 (+)NCBISscrofa10.2Sscrofa10.2susScr3
IFT57
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12272,560,168 - 72,629,066 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2272,560,221 - 72,632,158 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604193,860,406 - 93,929,212 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ift57
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473141,322,033 - 41,388,570 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473141,321,574 - 41,390,133 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ift57
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1434,112,317 - 34,168,202 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ift57
681 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:166
Count of miRNA genes:129
Interacting mature miRNAs:156
Transcripts:ENSRNOT00000002684
Prediction methods:Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)113330600878306008Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113330600878306008Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113191546976915469Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)113642841681428416Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)113461876079618760Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)113674945981749459Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)113674945981749459Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)113674945981749459Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat
631510Spl2Serum phospholipid level QTL 24.1blood phospholipid amount (VT:0006084)serum phospholipid level (CMO:0001171)112755668572556685Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000002684   ⟹   ENSRNOP00000002684
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1164,528,349 - 64,593,545 (-)Ensembl
mRatBN7.2 Ensembl1151,059,611 - 51,124,812 (-)Ensembl
Rnor_6.0 Ensembl1153,664,638 - 53,731,779 (-)Ensembl
RefSeq Acc Id: NM_001107093   ⟹   NP_001100563
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81164,528,349 - 64,593,545 (-)NCBI
mRatBN7.21151,059,611 - 51,124,812 (-)NCBI
Rnor_6.01153,664,638 - 53,731,779 (-)NCBI
Rnor_5.01156,827,640 - 56,856,819 (-)NCBI
Rnor_5.01156,880,772 - 56,895,355 (-)NCBI
RGSC_v3.41152,251,655 - 52,321,489 (-)RGD
Celera1150,700,486 - 50,764,317 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100563 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11101 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002684
  ENSRNOP00000002684.4
RefSeq Acc Id: NP_001100563   ⟸   NM_001107093
- UniProtKB: D4A1V1 (UniProtKB/TrEMBL),   A6IQU7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000002684   ⟸   ENSRNOT00000002684

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A1V1-F1-model_v2 AlphaFold D4A1V1 1-429 view protein structure

Transcriptome

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

Promoters
RGD ID:13698122
Promoter ID:EPDNEW_R8647
Type:initiation region
Name:Ift57_1
Description:intraflagellar transport 57
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_6.01153,731,829 - 53,731,889EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305947 AgrOrtholog
BioCyc Gene G2FUF-21431 BioCyc
Ensembl Genes ENSRNOG00000001958 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002684 ENTREZGENE
  ENSRNOT00000002684.7 UniProtKB/TrEMBL
InterPro Intra-flagellar_transport_57 UniProtKB/TrEMBL
KEGG Report rno:303968 UniProtKB/TrEMBL
NCBI Gene 303968 ENTREZGENE
PANTHER Intra-flagellar_transport_57 UniProtKB/TrEMBL
  INTRAFLAGELLAR TRANSPORT PROTEIN 57 HOMOLOG UniProtKB/TrEMBL
Pfam IFT57 UniProtKB/TrEMBL
PhenoGen Ift57 PhenoGen
RatGTEx ENSRNOG00000001958 RatGTEx
UniProt A6IQU7 ENTREZGENE, UniProtKB/TrEMBL
  D4A1V1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Ift57  intraflagellar transport 57  Ift57  intraflagellar transport 57 homolog (Chlamydomonas)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ift57  intraflagellar transport 57 homolog (Chlamydomonas)   Ift57_predicted  intraflagellar transport 57 homolog (Chlamydomonas) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ift57_predicted  intraflagellar transport 57 homolog (Chlamydomonas) (predicted)  Esrrbl1_predicted  estrogen-related receptor beta like 1 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-12 Esrrbl1_predicted  estrogen-related receptor beta like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED