Cct6a (chaperonin containing TCP1 subunit 6A) - Rat Genome Database
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Gene: Cct6a (chaperonin containing TCP1 subunit 6A) Rattus norvegicus
Analyze
Symbol: Cct6a
Name: chaperonin containing TCP1 subunit 6A
RGD ID: 1304763
Description: Predicted to have WD40-repeat domain 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 cellular protein localization; and positive regulation of telomerase RNA localization to Cajal body. Predicted to localize to several cellular components, including acrosomal vesicle; chaperonin-containing T-complex; and zona pellucida receptor complex. Orthologous to human CCT6A (chaperonin containing TCP1 subunit 6A); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,4,6-trinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: chaperonin containing Tcp1, subunit 6A (zeta 1); chaperonin subunit 6a (zeta); LOC288620; MGC125121; T-complex protein 1 subunit zeta
Orthologs:
Homo sapiens (human) : CCT6A (chaperonin containing TCP1 subunit 6A)  HGNC  Alliance
Mus musculus (house mouse) : Cct6a (chaperonin containing Tcp1, subunit 6a (zeta))  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Cct6a (chaperonin containing TCP1 subunit 6A)
Pan paniscus (bonobo/pygmy chimpanzee) : CCT6A (chaperonin containing TCP1 subunit 6A)
Canis lupus familiaris (dog) : CCT6A (chaperonin containing TCP1 subunit 6A)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Cct6a (chaperonin containing TCP1 subunit 6A)
Sus scrofa (pig) : CCT6A (chaperonin containing TCP1 subunit 6A)
Chlorocebus sabaeus (African green monkey) : CCT6A (chaperonin containing TCP1 subunit 6A)
Heterocephalus glaber (naked mole-rat) : Cct6a (chaperonin containing TCP1 subunit 6A)
more info ...
Related Pseudogenes: Cct6a-ps1   Cct6a-ps10   Cct6a-ps11   Cct6a-ps12   Cct6a-ps14   Cct6a-ps15   Cct6a-ps2   Cct6a-ps3   Cct6a-ps4   Cct6a-ps5   Cct6a-ps6   Cct6a-ps7   Cct6a-ps8   Cct6a-ps9  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01230,491,584 - 30,501,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1230,491,416 - 30,501,860 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01232,433,505 - 32,443,734 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41227,992,348 - 28,002,578 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11227,855,700 - 27,866,156 (+)NCBI
Celera1228,578,429 - 28,588,659 (-)NCBICelera
Cytogenetic Map12q13NCBI
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
References

Additional References at PubMed
PMID:7828721   PMID:7953530   PMID:9013858   PMID:12477932   PMID:19056867   PMID:20193073   PMID:20458337   PMID:21525035   PMID:21880732   PMID:22658674   PMID:23011926   PMID:23106098  
PMID:23376485   PMID:23533145   PMID:23716698   PMID:23979707   PMID:25467444  


Genomics

Comparative Map Data
Cct6a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01230,491,584 - 30,501,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1230,491,416 - 30,501,860 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01232,433,505 - 32,443,734 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41227,992,348 - 28,002,578 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11227,855,700 - 27,866,156 (+)NCBI
Celera1228,578,429 - 28,588,659 (-)NCBICelera
Cytogenetic Map12q13NCBI
CCT6A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl756,051,685 - 56,063,989 (+)EnsemblGRCh38hg38GRCh38
GRCh38756,051,765 - 56,063,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37756,119,378 - 56,131,682 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36756,086,872 - 56,099,176 (+)NCBINCBI36hg18NCBI36
Build 34755,893,586 - 55,905,891NCBI
Celera767,172,779 - 67,185,081 (+)NCBI
Cytogenetic Map7p11.2NCBI
HuRef755,933,178 - 55,945,465 (+)NCBIHuRef
CHM1_1756,122,415 - 56,134,705 (+)NCBICHM1_1
CRA_TCAGchr7v2756,123,625 - 56,135,929 (+)NCBI
Cct6a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395129,864,420 - 129,875,284 (+)NCBI
GRCm385129,787,356 - 129,846,443 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5129,786,998 - 129,846,371 (+)EnsemblGRCm38mm10GRCm38
MGSCv375130,320,838 - 130,322,231 (+)NCBIGRCm37mm9NCBIm37
MGSCv375130,293,261 - 130,300,376 (+)NCBIGRCm37mm9NCBIm37
MGSCv365130,102,094 - 130,109,209 (+)NCBImm8
Celera5126,831,958 - 126,842,310 (+)NCBICelera
Cytogenetic Map5G1.3NCBI
Cct6a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554568,223,774 - 8,237,966 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554568,223,785 - 8,236,760 (+)NCBIChiLan1.0ChiLan1.0
CCT6A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1757,087,935 - 57,099,519 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl757,087,072 - 57,098,613 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0756,664,757 - 56,677,000 (+)NCBIMhudiblu_PPA_v0panPan3
CCT6A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl6546,307 - 557,001 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.16546,278 - 556,996 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Cct6a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365437,887,511 - 7,900,174 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCT6A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1316,843,801 - 16,858,819 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2317,180,645 - 17,194,658 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCT6A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl212,718,975 - 2,728,239 (-)Ensembl
ChlSab1.1212,715,990 - 2,728,397 (-)NCBI
Cct6a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247408,247,477 - 8,258,335 (+)NCBI

Position Markers
RH134402  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,491,507 - 30,491,698NCBIRnor6.0
Rnor_5.01232,433,428 - 32,433,619UniSTSRnor5.0
RGSC_v3.458,729,076 - 8,729,267UniSTSRGSC3.4
RGSC_v3.41228,002,464 - 28,002,655UniSTSRGSC3.4
Celera1228,578,352 - 28,578,543UniSTS
Cytogenetic Map12q13UniSTS
Cytogenetic Map9q36UniSTS
RH138649  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01230,500,945 - 30,501,109NCBIRnor6.0
Rnor_5.01232,442,866 - 32,443,030UniSTSRnor5.0
RGSC_v3.41227,993,052 - 27,993,216UniSTSRGSC3.4
Celera1228,587,791 - 28,587,955UniSTS
Cytogenetic Map9q36UniSTS
Cytogenetic Map12q13UniSTS
RH 3.4 Map12453.1UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581516Cm56Cardiac mass QTL 564.20.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)12130749723Rat
1598855Bp294Blood pressure QTL 2943.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12136919844Rat
7387292Kidm42Kidney mass QTL 423.030.0004kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)12138334225Rat
9590086Insglur6Insulin/glucose ratio QTL 618.970.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)1215081045150810Rat
9590147Scort7Serum corticosterone level QTL 713.610.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1215081045150810Rat
7411545Bw128Body weight QTL 1285.20.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
7411586Foco5Food consumption QTL 55.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411660Foco28Food consumption QTL 2810.90.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
7411595Foco9Food consumption QTL 940.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)1215081045150810Rat
8694179Bw150Body weight QTL 1502.90.001body mass (VT:0001259)body weight gain (CMO:0000420)1215081045150810Rat
2303575Insul14Insulin level QTL 144blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)1249257845492578Rat
737979Pia22Pristane induced arthritis QTL 2253.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)12247568747475687Rat
634351Apr5Acute phase response QTL 56.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)12251344247513442Rat
2302042Pia38Pristane induced arthritis QTL 383.50.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)12251344247513442Rat
634350Apr4Acute phase response QTL 46orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)12421005149210051Rat
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
2293086Iddm30Insulin dependent diabetes mellitus QTL 303.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121017588931975590Rat
61331Eau2Experimental allergic uveoretinitis QTL 20.0005uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)121025689031723732Rat
1300157Rf21Renal function QTL 214.4renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)121176499537522089Rat
1331755Bp219Blood pressure QTL 2193.041arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721131723688Rat
1331761Bp218Blood pressure QTL 2182.973arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)121312721150320041Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
61416Pia4Pristane induced arthritis QTL 48.4joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)121571460935964508Rat
61421Cia12Collagen induced arthritis QTL 124.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)121571460941291738Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
631543Bp83Blood pressure QTL 835.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121718558044098244Rat
2293684Bmd26Bone mineral density QTL 264.40.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)121796086538409001Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
737822Alc10Alcohol consumption QTL 102.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)122265070245946937Rat
5684888Pia42Pristane induced arthritis QTL 42joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265070248598906Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
1298081Cia25Collagen induced arthritis QTL 254.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)122265072141291738Rat
70213Niddm27Non-insulin dependent diabetes mellitus QTL 273.72blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)122287629743799153Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
70169Eae13Experimental allergic encephalomyelitis QTL 130.032nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)122719024042196641Rat
1331763Wbc2White blood cell count QTL 23.162leukocyte quantity (VT:0000217)total white blood cell count (CMO:0000365)122728547336161779Rat
8693658Alc33Alcohol consumption QTL 332.10.68drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360949560679Rat
8693635Alc28Alcohol consumption QTL 282.70.439drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)122911360950757185Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:68
Count of miRNA genes:62
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000001227
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.


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: ENSRNOT00000001227   ⟹   ENSRNOP00000001227
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1230,491,416 - 30,501,860 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1230,497,406 - 30,498,864 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093591
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1230,500,927 - 30,501,834 (-)Ensembl
RefSeq Acc Id: NM_001033684   ⟹   NP_001028856
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01230,491,584 - 30,501,813 (-)NCBI
Rnor_5.01232,433,505 - 32,443,734 (-)NCBI
RGSC_v3.41227,992,348 - 28,002,578 (+)RGD
Celera1228,578,429 - 28,588,659 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001028856 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91282 (Get FASTA)   NCBI Sequence Viewer  
  AAI04704 (Get FASTA)   NCBI Sequence Viewer  
  EDM13487 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001028856   ⟸   NM_001033684
- UniProtKB: Q3MHS9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001227   ⟸   ENSRNOT00000001227

Transcriptome

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

Promoters
RGD ID:13698588
Promoter ID:EPDNEW_R9111
Type:initiation region
Name:Cct6a_1
Description:chaperonin containing TCP1 subunit 6A
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_6.01230,501,831 - 30,501,891EPDNEW

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)
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
Buf/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
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
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)
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
F344/NRrrc (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
FHH/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)
FHH/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
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_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 32433901 32433902 G C snv Crl:SD (UDEL), LE/OrlBarth (UDEL), FHL/EurMcwi (MCW), SDLEF7/Barth (UDEL)
12 32433904 32433905 C T snv SDLEF7/Barth (UDEL)
12 32433915 32433916 G C snv SDLEF7/Barth (UDEL)
12 32435076 32435077 A T snv IS/Kyo (KyushuU)
12 32436046 32436047 C G snv GH/OmrMcwi (MCW)
12 32439506 32439507 G A snv BDIX/NemOda (KyushuU)
12 32439741 32439742 A C snv SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)
12 32439745 32439746 C T snv SS/JrHsdMcwi (MCW), ACI/EurMcwi (MCW), FHL/EurMcwi (MCW)
12 32442061 32442062 A T snv FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), BUF/MNa (KyushuU), ZF (KyushuU), KFRS3B/Kyo (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), LEC/Tj (KyushuU), HWY/Slc (KyushuU), F344/Stm (KyushuU), IS-Tlk/Kyo (KyushuU), F344/NSlc (KyushuU), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), ZFDM (KyushuU), IS/Kyo (KyushuU), SBN/Ygl (MCW)
12 32443606 32443607 G C snv KFRS3B/Kyo (KyushuU), COP/CrCrl (MCW & UW), LE/Stm (KyushuU), NIG-III/Hok (KyushuU), LEC/Tj (KyushuU), BDIX/NemOda (KyushuU), GH/OmrMcwi (MCW), ACI/EurMcwi (MCW), DOB/Oda (KyushuU), SBN/Ygl (MCW), SBH/Ygl (MCW)
12 32443649 32443650 T C snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SBH/Ygl (MCW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SR/JrHsd (MCW), IS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), BUF/MNa (KyushuU), LEC/Tj (KyushuU), ZFDM (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), DOB/Oda (KyushuU), RCS/Kyo (KyushuU), BN/SsNSlc (KyushuU), BDIX/NemOda (KyushuU), F344/DuCrlCrlj (KyushuU), NIG-III/Hok (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 30491980 30491981 G C snv SR/JrHsd (MCW), GH/OmrMcwi (MCW), COP/CrCrl (MCW & UW)
12 30494125 30494126 C G snv ACI/EurMcwi (MCW), GH/OmrMcwi (MCW)
12 30497534 30497535 G A snv WKY/N (MCW)
12 30497555 30497556 C T snv WKY/N (MCW)
12 30497558 30497559 C T snv WKY/N (MCW)
12 30497824 30497825 C T snv ACI/EurMcwi (MCW), CDS, SBH/Ygl (MCW)
12 30498066 30498067 G A snv Buf/N (MCW)
12 30500105 30500106 G A snv WKY/N (MCW)
12 30500140 30500141 A T snv GH/OmrMcwi (MCW)
12 30500171 30500172 T C snv COP/CrCrl (MCW & UW)
12 30501685 30501686 G C snv FHL/EurMcwi (MCW), SBH/Ygl (MCW), GH/OmrMcwi (MCW)
12 30501728 30501729 T C snv CDS, SR/JrHsd (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), CDR
12 30501761 30501762 C G snv Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 27992433 27992434 A G snv SR/JrHsd (MCW), LCR/1Mco (UMich), F344/NRrrc (KNAW), WN/N (KNAW), LCR/2Mco (UMich), HCR/1Mco (UMich), FHL/EurMcwi (MCW), COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), FHH/EurMcwi (MCW), HCR/2Mco (UMich)
12 27992476 27992477 C G snv HCR/1Mco (UMich)
12 27993990 27993991 A G snv HCR/2Mco (UMich), LCR/1Mco (UMich), HCR/1Mco (UMich), LCR/2Mco (UMich)
12 27994021 27994022 T A snv FHL/EurMcwi (MCW), ACI/EurMcwi (MCW), WN/N (KNAW), MR/N (KNAW), LE/Stm (KNAW), F344/NRrrc (KNAW), BUF/N (KNAW), ACI/N (KNAW), LCR/2Mco (UMich), HCR/1Mco (UMich), GH/OmrMcwi (MCW), SS/JrHsdMcwi (MCW)
12 27996337 27996338 G A snv FHL/EurMcwi (MCW), MR/N (KNAW), SS/JrHsdMcwi (MCW), WN/N (KNAW), ACI/N (KNAW), ACI/EurMcwi (MCW), FHH/EurMcwi (MCW), F344/NRrrc (KNAW)
12 27996341 27996342 T G snv FHH/EurMcwi (MCW), SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)
12 27998908 27998909 T A snv FHL/EurMcwi (MCW)
12 28000036 28000037 G C snv SR/JrHsd (MCW), ACI/EurMcwi (MCW), GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304763 AgrOrtholog
Ensembl Genes ENSRNOG00000000923 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001227 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001227 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.560.10 UniProtKB/TrEMBL
  3.30.260.10 UniProtKB/TrEMBL
  3.50.7.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7300674 IMAGE-MGC_LOAD
  IMAGE:7300985 IMAGE-MGC_LOAD
InterPro Chap_CCT_zeta UniProtKB/TrEMBL
  Chaperone_TCP-1 UniProtKB/TrEMBL
  Chaperonin_TCP-1_CS UniProtKB/TrEMBL
  Cpn60/TCP-1 UniProtKB/TrEMBL
  GroEL-like_apical_dom UniProtKB/TrEMBL
  GROEL-like_equatorial UniProtKB/TrEMBL
  TCP-1-like_intermed_sf UniProtKB/TrEMBL
KEGG Report rno:288620 UniProtKB/TrEMBL
MGC_CLONE MGC:109172 IMAGE-MGC_LOAD
  MGC:125121 IMAGE-MGC_LOAD
NCBI Gene 288620 ENTREZGENE
Pfam Cpn60_TCP1 UniProtKB/TrEMBL
PhenoGen Cct6a PhenoGen
PRINTS TCOMPLEXTCP1 UniProtKB/TrEMBL
PROSITE TCP1_1 UniProtKB/TrEMBL
  TCP1_2 UniProtKB/TrEMBL
  TCP1_3 UniProtKB/TrEMBL
Superfamily-SCOP SSF48592 UniProtKB/TrEMBL
  SSF52029 UniProtKB/TrEMBL
  SSF54849 UniProtKB/TrEMBL
TIGRFAMs chap_CCT_zeta UniProtKB/TrEMBL
UniGene Rn.33807 ENTREZGENE
UniProt Q3MHS9 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJY2_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Cct6a  chaperonin containing TCP1 subunit 6A  Cct6a  chaperonin containing Tcp1, subunit 6A (zeta 1)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Cct6a  chaperonin containing Tcp1, subunit 6A (zeta 1)  Cct6a  chaperonin subunit 6a (zeta)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Cct6a  chaperonin subunit 6a (zeta)  Cct6a_predicted  chaperonin subunit 6a (zeta) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cct6a_predicted  chaperonin subunit 6a (zeta) (predicted)      Symbol and Name status set to approved 70820 APPROVED