Cimip1 (ciliary microtubule inner protein 1) - Rat Genome Database

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Gene: Cimip1 (ciliary microtubule inner protein 1) Rattus norvegicus
Analyze
Symbol: Cimip1 (Ensembl: C3h20orf85)
Name: ciliary microtubule inner protein 1 (Ensembl:similar to human chromosome 20 open reading frame 85)
RGD ID: 1589960
Description: Predicted to be located in cilium. Orthologous to human CIMIP1 (ciliary microtubule inner protein 1); INTERACTS WITH bisphenol A; benzo[a]pyrene (ortholog); methotrexate (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: C3h20orf85; hypothetical protein LOC689618; LOC689618; similar to human chromosome 20 open reading frame 85; similar to Protein C20orf85 homolog; uncharacterized protein C20orf85 homolog; uncharacterized protein LOC689618
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83182,733,242 - 182,740,733 (+)NCBIGRCr8
mRatBN7.23162,315,542 - 162,322,456 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3162,315,622 - 162,322,455 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3166,114,698 - 166,121,529 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03174,618,539 - 174,625,370 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03172,355,492 - 172,362,323 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03171,597,319 - 171,604,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3171,597,241 - 171,604,143 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03177,658,756 - 177,665,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43164,407,395 - 164,414,314 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3161,501,291 - 161,508,086 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cilium  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Cimip1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83182,733,242 - 182,740,733 (+)NCBIGRCr8
mRatBN7.23162,315,542 - 162,322,456 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3162,315,622 - 162,322,455 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3166,114,698 - 166,121,529 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03174,618,539 - 174,625,370 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03172,355,492 - 172,362,323 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03171,597,319 - 171,604,094 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3171,597,241 - 171,604,143 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03177,658,756 - 177,665,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43164,407,395 - 164,414,314 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3161,501,291 - 161,508,086 (+)NCBICelera
Cytogenetic Map3q42NCBI
CIMIP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382058,150,902 - 58,161,150 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2058,150,902 - 58,161,150 (+)EnsemblGRCh38hg38GRCh38
GRCh372056,725,958 - 56,736,206 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362056,159,389 - 56,169,592 (+)NCBINCBI36Build 36hg18NCBI36
Build 342056,159,388 - 56,169,587NCBI
Celera2053,466,441 - 53,476,642 (+)NCBICelera
Cytogenetic Map20q13.32NCBI
HuRef2053,508,254 - 53,518,458 (+)NCBIHuRef
CHM1_12056,627,541 - 56,637,743 (+)NCBICHM1_1
T2T-CHM13v2.02059,930,302 - 59,940,549 (+)NCBIT2T-CHM13v2.0
Cimip1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392173,364,385 - 173,370,295 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2173,364,379 - 173,370,294 (+)EnsemblGRCm39 Ensembl
GRCm382173,522,592 - 173,528,502 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2173,522,586 - 173,528,501 (+)EnsemblGRCm38mm10GRCm38
MGSCv372173,348,093 - 173,354,003 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362173,165,537 - 173,171,440 (+)NCBIMGSCv36mm8
Celera2179,488,998 - 179,495,238 (+)NCBICelera
Cytogenetic Map2H4NCBI
cM Map296.88NCBI
Cimip1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554451,357,173 - 1,370,771 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554451,360,659 - 1,370,748 (-)NCBIChiLan1.0ChiLan1.0
CIMIP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22163,900,612 - 63,919,664 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12063,893,731 - 63,909,576 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02054,494,076 - 54,504,703 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12055,770,571 - 55,780,802 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2055,770,571 - 55,783,620 (+)Ensemblpanpan1.1panPan2
CIMIP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12442,960,156 - 42,968,514 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2442,960,214 - 42,969,258 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2442,207,018 - 42,228,510 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02443,825,900 - 43,847,428 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2443,825,958 - 43,838,373 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12442,928,414 - 42,936,741 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02443,049,479 - 43,071,004 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02443,707,868 - 43,729,373 (+)NCBIUU_Cfam_GSD_1.0
Cimip1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640182,541,774 - 182,548,910 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936530757,396 - 764,198 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936530757,396 - 764,198 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CIMIP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1758,373,175 - 58,383,131 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11758,373,168 - 58,383,135 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21765,584,607 - 65,594,592 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CIMIP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.125,971,913 - 5,982,108 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl25,971,474 - 5,982,161 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605054,026,368 - 54,036,563 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cimip1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474124,482,358 - 24,489,495 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474124,482,338 - 24,489,508 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cimip1
44 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:51
Count of miRNA genes:48
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000029558
Prediction methods: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
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat

Markers in Region
RH141945  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23162,322,269 - 162,322,419 (+)MAPPERmRatBN7.2
Rnor_6.03171,603,909 - 171,604,058NCBIRnor6.0
Rnor_5.03177,665,346 - 177,665,495UniSTSRnor5.0
RGSC_v3.43164,414,129 - 164,414,278UniSTSRGSC3.4
Celera3161,507,901 - 161,508,050UniSTS
RH 3.4 Map31496.9UniSTS
Cytogenetic Map3q42UniSTS


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 7
Low 1 2 2 1 7 2
Below cutoff 2 7 2 7 2 2 3 7 2 5 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029558   ⟹   ENSRNOP00000030660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3162,315,622 - 162,322,455 (+)Ensembl
Rnor_6.0 Ensembl3171,597,241 - 171,604,143 (+)Ensembl
RefSeq Acc Id: NM_001109542   ⟹   NP_001103012
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83182,733,901 - 182,740,732 (+)NCBI
mRatBN7.23162,315,622 - 162,322,455 (+)NCBI
Rnor_6.03171,597,319 - 171,604,094 (+)NCBI
Rnor_5.03177,658,756 - 177,665,531 (+)NCBI
RGSC_v3.43164,407,395 - 164,414,314 (+)RGD
Celera3161,501,291 - 161,508,086 (+)RGD
Sequence:
RefSeq Acc Id: XM_063284577   ⟹   XP_063140647
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83182,733,242 - 182,740,733 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001103012 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140647 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85112 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030660
  ENSRNOP00000030660.2
Reference Protein Sequences
RefSeq Acc Id: NP_001103012   ⟸   NM_001109542
- UniProtKB: D4A8H6 (UniProtKB/TrEMBL),   A6KL04 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030660   ⟸   ENSRNOT00000029558
RefSeq Acc Id: XP_063140647   ⟸   XM_063284577
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8H6-F1-model_v2 AlphaFold D4A8H6 1-135 view protein structure

Transcriptome

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

Promoters
RGD ID:13692714
Promoter ID:EPDNEW_R3239
Type:initiation region
Name:LOC689618_1
Description:similar to Protein C20orf85 homolog
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_6.03171,597,303 - 171,597,363EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589960 AgrOrtholog
BioCyc Gene G2FUF-46489 BioCyc
Ensembl Genes ENSRNOG00000028533 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029558 ENTREZGENE
  ENSRNOT00000029558.4 UniProtKB/TrEMBL
InterPro Uncharacterised_C20orf85 UniProtKB/TrEMBL
KEGG Report rno:689618 UniProtKB/TrEMBL
NCBI Gene 689618 ENTREZGENE
PANTHER CHROMOSOME 20 ORF85 FAMILY MEMBER UniProtKB/TrEMBL
  RCG40914 UniProtKB/TrEMBL
Pfam LLC1 UniProtKB/TrEMBL
PhenoGen Cimip1 PhenoGen
RatGTEx ENSRNOG00000028533 RatGTEx
UniProt A6KL04 ENTREZGENE, UniProtKB/TrEMBL
  D4A8H6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-05-05 Cimip1  ciliary microtubule inner protein 1  C3h20orf85  similar to human chromosome 20 open reading frame 85  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2022-08-02 C3h20orf85  similar to human chromosome 20 open reading frame 85  LOC689618  similar to Protein C20orf85 homolog  Name and Symbol changed 629549 APPROVED
2008-01-09 LOC689618  similar to Protein C20orf85 homolog  LOC679098  similar to Protein C20orf85 homolog  Data merged from RGD:1593029 1643240 APPROVED
2006-11-20 LOC689618  similar to Protein C20orf85 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC679098  similar to Protein C20orf85 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL