Cct2 (chaperonin containing TCP1 subunit 2) - Rat Genome Database

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Gene: Cct2 (chaperonin containing TCP1 subunit 2) Rattus norvegicus
Analyze
Symbol: Cct2
Name: chaperonin containing TCP1 subunit 2
RGD ID: 1359143
Description: Predicted to have protein folding chaperone; ubiquitin protein ligase binding activity; and unfolded protein binding activity. Predicted to be involved in several processes, including binding activity of sperm to zona pellucida; positive regulation of DNA biosynthetic process; and positive regulation of cellular protein localization. Predicted to localize to several cellular components, including chaperonin-containing T-complex; microtubule; and zona pellucida receptor complex. Orthologous to human CCT2 (chaperonin containing TCP1 subunit 2); INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CCT-beta; chaperonin containing TCP1, subunit 2 (beta); MGC94480; T-complex protein 1 subunit beta; TCP-1-beta
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Cct2-ps1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2752,692,725 - 52,705,478 (-)NCBI
Rnor_6.0 Ensembl760,109,974 - 60,122,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0760,106,532 - 60,122,779 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0760,106,598 - 60,122,867 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4756,391,341 - 56,404,084 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1756,412,071 - 56,424,814 (-)NCBI
Celera749,468,323 - 49,481,066 (-)NCBICelera
Cytogenetic Map7q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
osteoporosis  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
1H-pyrazole  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3-chloropropane-1,2-diol  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
amphetamine  (ISO)
arsenous acid  (ISO)
artesunate  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
ceruletide  (EXP)
chloropicrin  (ISO)
chromium(6+)  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diazinon  (EXP)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
finasteride  (EXP)
flutamide  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
hyaluronic acid  (EXP)
hydralazine  (ISO)
hydrogen peroxide  (EXP,ISO)
lead(II) chloride  (ISO)
menadione  (ISO)
methamphetamine  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosomorpholine  (EXP)
naphthalene  (ISO)
nefazodone  (EXP)
nickel dichloride  (EXP)
nimesulide  (EXP)
oxaliplatin  (EXP)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
PhIP  (EXP)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
silicon dioxide  (ISO)
sodium dichromate  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
topotecan  (EXP)
trimellitic anhydride  (ISO)
triptonide  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)

References

Additional References at PubMed
PMID:7828721   PMID:7953530   PMID:15489334   PMID:17634366   PMID:19056867   PMID:20080638   PMID:20193073   PMID:20458337   PMID:21525035   PMID:21753002   PMID:21880732   PMID:23011926  
PMID:23376485   PMID:23533145   PMID:23716698   PMID:23979707   PMID:24625528   PMID:25467444   PMID:29476059   PMID:31904090  


Genomics

Comparative Map Data
Cct2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2752,692,725 - 52,705,478 (-)NCBI
Rnor_6.0 Ensembl760,109,974 - 60,122,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0760,106,532 - 60,122,779 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0760,106,598 - 60,122,867 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4756,391,341 - 56,404,084 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1756,412,071 - 56,424,814 (-)NCBI
Celera749,468,323 - 49,481,066 (-)NCBICelera
Cytogenetic Map7q22NCBI
CCT2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1269,585,426 - 69,601,570 (+)EnsemblGRCh38hg38GRCh38
GRCh381269,585,459 - 69,601,570 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371269,979,239 - 69,995,350 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361268,265,475 - 68,281,624 (+)NCBINCBI36hg18NCBI36
Build 341268,265,474 - 68,281,624NCBI
Celera1269,642,857 - 69,659,010 (+)NCBI
Cytogenetic Map12q15NCBI
HuRef1267,028,675 - 67,044,820 (+)NCBIHuRef
CHM1_11269,947,631 - 69,963,780 (+)NCBICHM1_1
Cct2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910116,886,902 - 116,899,757 (-)NCBIGRCm39mm39
GRCm39 Ensembl10116,886,906 - 116,899,719 (-)Ensembl
GRCm3810117,050,997 - 117,063,852 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10117,051,001 - 117,063,814 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710116,488,054 - 116,500,870 (-)NCBIGRCm37mm9NCBIm37
MGSCv3610116,455,109 - 116,467,875 (-)NCBImm8
Celera10118,994,151 - 119,006,966 (-)NCBICelera
Cytogenetic Map10D2NCBI
Cct2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554059,892,116 - 9,904,407 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554059,892,089 - 9,904,407 (+)NCBIChiLan1.0ChiLan1.0
CCT2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11269,883,710 - 69,898,671 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1269,883,710 - 69,898,671 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01267,113,221 - 67,128,159 (+)NCBIMhudiblu_PPA_v0panPan3
CCT2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11011,560,287 - 11,586,559 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1011,560,396 - 11,578,433 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1011,492,095 - 11,518,353 (+)NCBI
ROS_Cfam_1.01011,683,661 - 11,709,923 (+)NCBI
UMICH_Zoey_3.11011,550,671 - 11,576,938 (+)NCBI
UNSW_CanFamBas_1.01011,797,739 - 11,824,127 (+)NCBI
UU_Cfam_GSD_1.01011,920,916 - 11,939,358 (+)NCBI
Cct2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494546,673,102 - 46,693,918 (-)NCBI
SpeTri2.0NW_0049365457,416,257 - 7,436,024 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCT2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl533,858,572 - 34,033,939 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1533,858,514 - 33,873,596 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2536,457,610 - 36,471,587 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCT2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11165,213,992 - 65,230,318 (+)NCBI
ChlSab1.1 Ensembl1165,214,060 - 65,230,379 (+)Ensembl
Cct2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475028,202,524 - 28,217,223 (-)NCBI

Position Markers
WI-19751  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0760,104,727 - 60,104,979NCBIRnor6.0
Rnor_6.0760,110,004 - 60,110,257NCBIRnor6.0
Rnor_5.0760,110,093 - 60,110,346UniSTSRnor5.0
Rnor_5.0760,104,791 - 60,105,043UniSTSRnor5.0
RGSC_v3.4756,391,359 - 56,391,612UniSTSRGSC3.4
Celera749,468,341 - 49,468,594UniSTS
Cytogenetic Map7q22UniSTS
RH143421  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0760,115,813 - 60,116,577NCBIRnor6.0
Rnor_5.0760,115,902 - 60,116,666UniSTSRnor5.0
RGSC_v3.4756,397,168 - 56,397,932UniSTSRGSC3.4
Celera749,474,150 - 49,474,914UniSTS
RH 3.4 Map7483.0UniSTS
Cytogenetic Map7q22UniSTS
MARC_36444-36445:1067884409:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0760,113,639 - 60,114,496NCBIRnor6.0
Rnor_5.0760,113,728 - 60,114,585UniSTSRnor5.0
RGSC_v3.4756,394,994 - 56,395,851UniSTSRGSC3.4
Celera749,471,976 - 49,472,833UniSTS
Cytogenetic Map7q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)71232846767193263Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)712328467106995532Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)71268785067801690Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)72216841267168412Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)72473146569731465Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)72536563360317612Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)72536563393155402Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72820465373204653Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)73138152976381529Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)73203505377035053Rat
61439Cia8Collagen induced arthritis QTL 85.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)73257294277572942Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)73304444971352127Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)73586772961047824Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)73586772980867729Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)73586772993155402Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73854770683547706Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)74087268285872682Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)74087268285872682Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74530157390301573Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74789509963372754Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)75025210395252103Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)75079381895793818Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)751252005111589099Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)75320034498200344Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)75425951299259512Rat
10059605Kidm47Kidney mass QTL 472.910.05kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)75453499673293934Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)75507286269399731Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)755495689100495689Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)755495689100495689Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)755495689100495689Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)755495689100495689Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)755495689100495689Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)755495689100495689Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)755495689100495689Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:25
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000037946
Prediction methods:Miranda, Rnahybrid
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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000037946   ⟹   ENSRNOP00000029234
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl760,109,974 - 60,122,805 (-)Ensembl
RefSeq Acc Id: NM_001005905   ⟹   NP_001005905
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,692,733 - 52,705,478 (-)NCBI
Rnor_6.0760,109,986 - 60,122,729 (-)NCBI
Rnor_5.0760,106,598 - 60,122,867 (-)NCBI
RGSC_v3.4756,391,341 - 56,404,084 (-)RGD
Celera749,468,323 - 49,481,066 (-)RGD
Sequence:
RefSeq Acc Id: XM_006241371   ⟹   XP_006241433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0760,106,532 - 60,122,779 (-)NCBI
Rnor_5.0760,106,598 - 60,122,867 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078736   ⟹   XP_038934664
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2752,692,725 - 52,705,441 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001005905 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934664 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH83650 (Get FASTA)   NCBI Sequence Viewer  
  EDM16634 (Get FASTA)   NCBI Sequence Viewer  
  Q5XIM9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001005905   ⟸   NM_001005905
- UniProtKB: Q5XIM9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241433   ⟸   XM_006241371
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000029234   ⟸   ENSRNOT00000037946
RefSeq Acc Id: XP_038934664   ⟸   XM_039078736
- Peptide Label: isoform X1

Transcriptome

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

Promoters
RGD ID:13695207
Promoter ID:EPDNEW_R5732
Type:multiple initiation site
Name:Cct2_1
Description:chaperonin containing TCP1 subunit 2
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_6.0760,122,757 - 60,122,817EPDNEW

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)
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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
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)
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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
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
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 60113331 60113332 C T snv F344/NCrl (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359143 AgrOrtholog
Ensembl Genes ENSRNOG00000021317 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000029234 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000037946 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.560.10 UniProtKB/Swiss-Prot
  3.30.260.10 UniProtKB/Swiss-Prot
  3.50.7.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135109 IMAGE-MGC_LOAD
InterPro Chap_CCT_beta UniProtKB/Swiss-Prot
  Chaperone_TCP-1 UniProtKB/Swiss-Prot
  Chaperonin_TCP-1_CS UniProtKB/Swiss-Prot
  Cpn60/TCP-1 UniProtKB/Swiss-Prot
  GroEL-like_apical_dom_sf UniProtKB/Swiss-Prot
  GROEL-like_equatorial_sf UniProtKB/Swiss-Prot
  TCP-1-like_intermed_sf UniProtKB/Swiss-Prot
KEGG Report rno:299809 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94480 IMAGE-MGC_LOAD
NCBI Gene 299809 ENTREZGENE
PANTHER PTHR11353:SF23 UniProtKB/Swiss-Prot
Pfam Cpn60_TCP1 UniProtKB/Swiss-Prot
PhenoGen Cct2 PhenoGen
PRINTS TCOMPLEXTCP1 UniProtKB/Swiss-Prot
PROSITE TCP1_1 UniProtKB/Swiss-Prot
  TCP1_2 UniProtKB/Swiss-Prot
  TCP1_3 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48592 UniProtKB/Swiss-Prot
  SSF52029 UniProtKB/Swiss-Prot
  SSF54849 UniProtKB/Swiss-Prot
TIGRFAMs chap_CCT_beta UniProtKB/Swiss-Prot
UniProt Q5XIM9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Cct2  chaperonin containing TCP1 subunit 2  Cct2  chaperonin containing TCP1, subunit 2 (beta)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Cct2  chaperonin containing TCP1, subunit 2 (beta)      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Cct2  chaperonin containing TCP1, subunit 2 (beta)      Symbol and Name status set to provisional 70820 PROVISIONAL