Cys1 (cystin 1) - Rat Genome Database

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Gene: Cys1 (cystin 1) Rattus norvegicus
Analyze
Symbol: Cys1
Name: cystin 1
RGD ID: 1596023
Description: Predicted to enable chromatin binding activity and transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within inner ear development; kidney development; and positive regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including cytoskeleton; cytosol; and nucleus. Orthologous to human CYS1 (cystin 1); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cystin-1; LOC690489; similar to cystin 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8647,029,440 - 47,046,671 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl647,028,461 - 47,046,671 (-)EnsemblGRCr8
mRatBN7.2641,300,836 - 41,318,071 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl641,300,836 - 41,318,071 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx641,623,662 - 41,640,797 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0641,938,469 - 41,955,604 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0641,371,615 - 41,388,750 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0643,844,937 - 43,862,131 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl643,844,937 - 43,862,131 (-)Ensemblrn6Rnor6.0
Rnor_5.0660,716,420 - 60,733,664 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4642,311,213 - 42,328,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera640,588,514 - 40,604,945 (-)NCBICelera
Cytogenetic Map6q16NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axoneme  (ISO)
ciliary basal body  (ISO)
cytosol  (ISO)
membrane  (ISO)
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Identification of a prognostic 5-Gene expression signature for gastric cancer. Hou JY, etal., J Cancer Res Clin Oncol. 2017 Apr;143(4):619-629. doi: 10.1007/s00432-016-2324-z. Epub 2016 Dec 29.
2. Cystin, a novel cilia-associated protein, is disrupted in the cpk mouse model of polycystic kidney disease. Hou X, etal., J Clin Invest. 2002 Feb;109(4):533-40.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1952600   PMID:18829740   PMID:19850956   PMID:23376485   PMID:24349431  


Genomics

Comparative Map Data
Cys1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8647,029,440 - 47,046,671 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl647,028,461 - 47,046,671 (-)EnsemblGRCr8
mRatBN7.2641,300,836 - 41,318,071 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl641,300,836 - 41,318,071 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx641,623,662 - 41,640,797 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0641,938,469 - 41,955,604 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0641,371,615 - 41,388,750 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0643,844,937 - 43,862,131 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl643,844,937 - 43,862,131 (-)Ensemblrn6Rnor6.0
Rnor_5.0660,716,420 - 60,733,664 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4642,311,213 - 42,328,045 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera640,588,514 - 40,604,945 (-)NCBICelera
Cytogenetic Map6q16NCBI
CYS1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38210,056,473 - 10,080,411 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl210,056,473 - 10,080,944 (-)Ensemblhg38GRCh38
GRCh37210,196,600 - 10,220,538 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36210,116,317 - 10,137,989 (-)NCBIBuild 36Build 36hg18NCBI36
Celera210,113,148 - 10,122,388 (-)NCBICelera
Cytogenetic Map2p25.1NCBI
HuRef210,048,679 - 10,072,099 (-)NCBIHuRef
CHM1_1210,126,760 - 10,150,367 (-)NCBICHM1_1
T2T-CHM13v2.0210,085,216 - 10,109,145 (-)NCBIT2T-CHM13v2.0
Cys1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391224,715,832 - 24,731,794 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1224,715,832 - 24,731,812 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381224,665,833 - 24,681,886 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1224,665,833 - 24,681,813 (-)Ensemblmm10GRCm38
MGSCv371225,350,703 - 25,366,660 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361225,254,917 - 25,270,874 (-)NCBIMGSCv36mm8
Celera1226,126,773 - 26,142,148 (-)NCBICelera
Cytogenetic Map12A1.3NCBI
cM Map128.49NCBI
Cys1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554875,455,820 - 5,461,362 (-)NCBIChiLan1.0ChiLan1.0
CYS1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212116,436,015 - 116,462,665 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A116,443,330 - 116,466,636 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A10,053,361 - 10,078,264 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CYS1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1177,057,240 - 7,063,410 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha176,984,193 - 7,002,084 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0177,155,480 - 7,173,287 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl177,155,468 - 7,173,419 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1177,047,379 - 7,065,187 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0177,049,655 - 7,067,732 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0177,063,659 - 7,081,604 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
CYS1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3126,398,303 - 126,412,560 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.13126,398,302 - 126,411,951 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CYS1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11497,549,886 - 97,572,458 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1497,551,009 - 97,570,710 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604514,739,608 - 14,764,133 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cys1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1738,280,121 - 38,294,082 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cys1
83 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:517
Count of miRNA genes:258
Interacting mature miRNAs:320
Transcripts:ENSRNOT00000008839
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64451097489510974Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)64005241156848866Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63902865963457441Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)64095756485957564Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)64515378690153786Rat
8552910Pigfal5Plasma insulin-like growth factor 1 level QTL 54.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)62265388967653889Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)62009763565097635Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63118500276185002Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)646050607116278722Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)64604735391047353Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64451097489510974Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64451097489510974Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)63332884178328841Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62661831486868070Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)63093763275937632Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)63332884178328841Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63902865986867923Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)61608937261967788Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)62228825767288257Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)64016318385163183Rat

Markers in Region
RH128013  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2641,301,117 - 41,301,297 (+)MAPPERmRatBN7.2
Rnor_6.0643,845,219 - 43,845,398NCBIRnor6.0
Rnor_5.0660,716,702 - 60,716,881UniSTSRnor5.0
RGSC_v3.4642,311,495 - 42,311,674UniSTSRGSC3.4
Celera640,588,796 - 40,588,975UniSTS
RH 3.4 Map6236.8UniSTS
Cytogenetic Map6q16UniSTS
AV218859  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2641,300,936 - 41,301,082 (+)MAPPERmRatBN7.2
Rnor_6.0643,845,038 - 43,845,183NCBIRnor6.0
Rnor_5.0660,716,521 - 60,716,666UniSTSRnor5.0
RGSC_v3.4642,311,314 - 42,311,459UniSTSRGSC3.4
Celera640,588,615 - 40,588,760UniSTS
Cytogenetic Map6q16UniSTS


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
13 12 67 147 90 89 59 44 59 6 305 144 11 126 81 92 30 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000089859   ⟹   ENSRNOP00000071585
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl647,029,440 - 47,046,671 (-)Ensembl
mRatBN7.2 Ensembl641,300,836 - 41,318,071 (-)Ensembl
Rnor_6.0 Ensembl643,844,937 - 43,862,131 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000168145   ⟹   ENSRNOP00000103771
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl647,028,461 - 47,046,671 (-)Ensembl
RefSeq Acc Id: NM_001109597   ⟹   NP_001103067
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8647,029,440 - 47,046,671 (-)NCBI
mRatBN7.2641,300,836 - 41,318,071 (-)NCBI
Rnor_6.0643,844,937 - 43,862,131 (-)NCBI
Rnor_5.0660,716,420 - 60,733,664 (-)NCBI
RGSC_v3.4642,311,213 - 42,328,045 (-)RGD
Celera640,588,514 - 40,604,945 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103067 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03185 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000071585
  ENSRNOP00000071585.1
  ENSRNOP00000103771.1
RefSeq Acc Id: NP_001103067   ⟸   NM_001109597
- UniProtKB: D3ZCZ3 (UniProtKB/TrEMBL),   A6HAY0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071585   ⟸   ENSRNOT00000089859
Ensembl Acc Id: ENSRNOP00000103771   ⟸   ENSRNOT00000168145

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZCZ3-F1-model_v2 AlphaFold D3ZCZ3 1-145 view protein structure

Transcriptome

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

Promoters
RGD ID:13694522
Promoter ID:EPDNEW_R5045
Type:multiple initiation site
Name:Cys1_1
Description:cystin 1
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_6.0643,862,133 - 43,862,193EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596023 AgrOrtholog
BioCyc Gene G2FUF-38024 BioCyc
Ensembl Genes ENSRNOG00000058891 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089859 ENTREZGENE
  ENSRNOT00000089859.3 UniProtKB/TrEMBL
  ENSRNOT00000168145.1 UniProtKB/TrEMBL
KEGG Report rno:690489 UniProtKB/TrEMBL
NCBI Gene 690489 ENTREZGENE
PhenoGen Cys1 PhenoGen
RatGTEx ENSRNOG00000058891 RatGTEx
UniProt A0ABK0L3G2_RAT UniProtKB/TrEMBL
  A6HAY0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZCZ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-04-23 Cys1  cystin 1  LOC690489  similar to cystin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC690489  similar to cystin 1  LOC686584  similar to cystin 1  Data merged from RGD:1596319 1643240 APPROVED
2006-11-20 LOC690489  similar to cystin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC686584  similar to cystin 1      Symbol and Name status set to provisional 70820 PROVISIONAL