Clock (clock circadian regulator) - Rat Genome Database

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Gene: Clock (clock circadian regulator) Rattus norvegicus
Analyze
Symbol: Clock
Name: clock circadian regulator
RGD ID: 620271
Description: Predicted to have DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and histone acetyltransferase activity. Involved in several processes, including entrainment of circadian clock; female pregnancy; and positive regulation of transcription, DNA-templated. Localizes to nucleolus; perichromatin fibrils; and rough endoplasmic reticulum. Biomarker of cholestasis and hypertension. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human CLOCK (clock circadian regulator); INTERACTS WITH 4,4'-diaminodiphenylmethane; ammonium chloride; amphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: circadian locomoter output cycles kaput; circadian locomoter output cycles protein kaput; clock homolog (mouse); rCLOCK
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
Rnor_6.0 Ensembl1434,446,616 - 34,502,218 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01434,418,226 - 34,502,218 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01434,233,721 - 34,289,468 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41434,218,472 - 34,258,054 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11434,218,471 - 34,258,054 (+)NCBI
Celera1431,247,422 - 31,293,707 (+)NCBICelera
Cytogenetic Map14p11NCBI
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
(+)-epicatechin-3-O-gallate  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-amino-2-deoxy-D-glucopyranose  (ISO)
20-HETE  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP,ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
Aroclor 1254  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-D-glucosamine  (ISO)
beta-naphthoflavone  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
cadmium dichloride  (EXP)
cannabidiol  (ISO)
cannabigerol  (ISO)
carbon nanotube  (ISO)
CGS-21680  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
cocaine  (ISO)
crocidolite asbestos  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dibenz[a,h]anthracene  (ISO)
dichloromethane  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
fluoxetine  (ISO)
folic acid  (ISO)
furan  (ISO)
gallic acid  (ISO)
gallocatechin  (ISO)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
manganese(II) chloride  (EXP)
melatonin  (EXP)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
ozone  (ISO)
pentanal  (ISO)
perfluorooctanoic acid  (ISO)
phenethyl caffeate  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
rotenone  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
styrene  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
trichloroethene  (EXP)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
1. Abe H, etal., Brain Res Mol Brain Res 1999 Mar 20;66(1-2):104-10.
2. Chen HF, etal., Arch Med Res. 2013 Apr;44(3):203-7. doi: 10.1016/j.arcmed.2013.01.002. Epub 2013 Jan 26.
3. Chen Q, etal., J Int Med Res. 2013 Apr;41(2):340-6. doi: 10.1177/0300060513476430.
4. Dubrovsky YV, etal., Aging (Albany NY). 2010 Dec;2(12):936-44.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Ghorbel MT, etal., Mol Cell Neurosci 2003 Mar;22(3):396-404.
7. GOA data from the GO Consortium
8. Li YF, etal., Zhongguo Dang Dai Er Ke Za Zhi. 2013 Jan;15(1):62-6.
9. Malatesta M, etal., Microsc Res Tech. 2005 Sep;68(1):45-50.
10. Matagne V, etal., J Neuroendocrinol. 2012 Jun;24(6):916-29. doi: 10.1111/j.1365-2826.2012.02302.x.
11. MGD data from the GO Consortium
12. Miyazaki M, etal., PLoS One. 2011;6(11):e27168. doi: 10.1371/journal.pone.0027168. Epub 2011 Nov 4.
13. Nakagami K, etal., Jpn J Cancer Res. 1999 Apr;90(4):419-24.
14. Namihira M, etal., Neurosci Lett. 1999 Aug 13;271(1):1-4.
15. NCBI rat LocusLink and RefSeq merged data July 26, 2002
16. Renzi A, etal., Am J Physiol Gastrointest Liver Physiol. 2011 Oct;301(4):G634-43. doi: 10.1152/ajpgi.00206.2011. Epub 2011 Jul 14.
17. RGD automated import pipeline for gene-chemical interactions
18. Wharfe MD, etal., Endocrinology. 2011 Sep;152(9):3552-60. doi: 10.1210/en.2011-0081. Epub 2011 Jul 19.
19. Yang YK, etal., J Investig Med. 2013 Oct;61(7):1084-7. doi: 10.231/JIM.0b013e31829f91c0.
Additional References at PubMed
PMID:8171325   PMID:9576906   PMID:11441146   PMID:12024206   PMID:12397359   PMID:12738229   PMID:12897057   PMID:14645221   PMID:14672706   PMID:15094047   PMID:15147242   PMID:15193144  
PMID:15560782   PMID:15719143   PMID:15774559   PMID:15864751   PMID:15944262   PMID:16373438   PMID:16376516   PMID:16603678   PMID:16606840   PMID:17097616   PMID:17310242   PMID:17364576  
PMID:18316400   PMID:18375864   PMID:18411297   PMID:18662546   PMID:19141540   PMID:19217292   PMID:19299583   PMID:19387896   PMID:19605937   PMID:19633447   PMID:19887760   PMID:20106950  
PMID:20430893   PMID:20562852   PMID:20861012   PMID:21113167   PMID:21613214   PMID:21659603   PMID:21768648   PMID:21775066   PMID:21980503   PMID:22208286   PMID:22653727   PMID:22894897  
PMID:22895791   PMID:22900038   PMID:22960268   PMID:23263459   PMID:23395176   PMID:23785138   PMID:23864491   PMID:24005054   PMID:24043798   PMID:24051492   PMID:24089055   PMID:24378737  
PMID:24385426   PMID:24610784   PMID:24736997   PMID:26975828   PMID:28985504   PMID:30012868   PMID:30815822   PMID:32448507  


Genomics

Comparative Map Data
Clock
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
Rnor_6.0 Ensembl1434,446,616 - 34,502,218 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01434,418,226 - 34,502,218 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01434,233,721 - 34,289,468 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41434,218,472 - 34,258,054 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11434,218,471 - 34,258,054 (+)NCBI
Celera1431,247,422 - 31,293,707 (+)NCBICelera
Cytogenetic Map14p11NCBI
CLOCK
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl455,427,903 - 55,546,909 (-)EnsemblGRCh38hg38GRCh38
GRCh38455,427,903 - 55,547,138 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37456,294,070 - 56,413,076 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36455,993,417 - 56,107,754 (-)NCBINCBI36hg18NCBI36
Build 34456,139,587 - 56,253,925NCBI
Celera453,800,517 - 53,915,033 (-)NCBI
Cytogenetic Map4q12NCBI
HuRef452,243,062 - 52,362,368 (-)NCBIHuRef
CHM1_1456,329,197 - 56,448,202 (-)NCBICHM1_1
Clock
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39576,357,715 - 76,452,675 (-)NCBIGRCm39mm39
GRCm39 Ensembl576,357,715 - 76,452,639 (-)Ensembl
GRCm38576,209,868 - 76,305,603 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl576,209,868 - 76,304,792 (-)EnsemblGRCm38mm10GRCm38
MGSCv37576,641,202 - 76,733,573 (-)NCBIGRCm37mm9NCBIm37
MGSCv36577,286,952 - 77,379,323 (-)NCBImm8
Celera573,483,631 - 73,569,902 (-)NCBICelera
Cytogenetic Map5C3.3NCBI
cM Map540.63NCBI
Clock
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544715,454,630 - 15,530,906 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544715,394,496 - 15,537,969 (+)NCBIChiLan1.0ChiLan1.0
CLOCK
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1474,954,284 - 75,071,210 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl475,018,898 - 75,066,726 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0468,391,310 - 68,509,813 (+)NCBIMhudiblu_PPA_v0panPan3
CLOCK
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11347,684,409 - 47,825,733 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1347,691,709 - 47,758,784 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1347,641,539 - 47,782,815 (-)NCBI
ROS_Cfam_1.01348,295,259 - 48,436,678 (-)NCBI
UMICH_Zoey_3.11347,970,216 - 48,111,463 (-)NCBI
UNSW_CanFamBas_1.01347,498,942 - 47,640,139 (-)NCBI
UU_Cfam_GSD_1.01348,447,647 - 48,588,918 (-)NCBI
Clock
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528528,397,879 - 28,511,737 (+)NCBI
SpeTri2.0NW_00493648217,789,834 - 17,900,371 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLOCK
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl854,788,864 - 54,910,146 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1854,793,323 - 54,910,192 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2858,659,297 - 58,720,896 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLOCK
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1713,015,198 - 13,134,741 (+)NCBI
ChlSab1.1 Ensembl713,051,454 - 13,127,240 (+)Ensembl
Clock
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476113,915,277 - 14,038,596 (+)NCBI

Position Markers
RH137478  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01434,483,667 - 34,483,879NCBIRnor6.0
Rnor_5.01434,270,917 - 34,271,129UniSTSRnor5.0
RGSC_v3.41434,246,205 - 34,246,417UniSTSRGSC3.4
Celera1431,275,155 - 31,275,367UniSTS
Cytogenetic Map14p11UniSTS
D14S292  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01434,486,941 - 34,488,004NCBIRnor6.0
Rnor_5.01434,319,777 - 34,320,840UniSTSRnor5.0
Rnor_5.01434,274,191 - 34,275,254UniSTSRnor5.0
RGSC_v3.41434,249,479 - 34,250,542UniSTSRGSC3.4
Celera1431,278,428 - 31,279,493UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14141333960Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14141333960Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14142766285Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14975643572854397Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin141053997755539977Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)141053997755539977Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)141072926861873323Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1412680424106641756Rat
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141915991938289187Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141916189343957503Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141919154143957628Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)142018938665189386Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)142026622343957628Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)142145756566457565Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143259392686191589Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143303991261783215Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143316331673391571Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:97
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000002976, ENSRNOT00000002981
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.


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 2 29 30 14 16 14 8 8 62 34 32 11 8
Low 1 14 27 27 3 27 3 12 1 9
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001289832 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001389254 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_021856 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006250870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599363 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017599364 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092372 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092373 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092376 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092378 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092379 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092381 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092384 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092385 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039092387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB019258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB019259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC116236 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002976   ⟹   ENSRNOP00000002976
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1434,446,616 - 34,495,713 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000002981   ⟹   ENSRNOP00000002981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1434,455,934 - 34,502,218 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085991   ⟹   ENSRNOP00000074670
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1434,455,934 - 34,502,218 (+)Ensembl
RefSeq Acc Id: NM_001289832   ⟹   NP_001276761
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,946,340 - 31,992,673 (+)NCBI
Rnor_6.01434,455,934 - 34,502,218 (+)NCBI
Celera1431,247,422 - 31,293,707 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001389254   ⟹   NP_001376183
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,546 - 31,992,673 (+)NCBI
RefSeq Acc Id: NM_021856   ⟹   NP_068628
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,946,340 - 31,992,673 (+)NCBI
Rnor_6.01434,455,934 - 34,502,218 (+)NCBI
Rnor_5.01434,233,721 - 34,289,468 (+)NCBI
RGSC_v3.41434,218,472 - 34,258,054 (+)RGD
Celera1431,247,422 - 31,293,707 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250869   ⟹   XP_006250931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01434,431,958 - 34,502,215 (+)NCBI
Rnor_5.01434,233,721 - 34,289,468 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006250870   ⟹   XP_006250932
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01434,418,226 - 34,502,215 (+)NCBI
Rnor_5.01434,233,721 - 34,289,468 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599361   ⟹   XP_017454850
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
Rnor_6.01434,418,226 - 34,502,215 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599362   ⟹   XP_017454851
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01434,418,226 - 34,502,215 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599363   ⟹   XP_017454852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
Rnor_6.01434,418,226 - 34,502,215 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017599364   ⟹   XP_017454853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
Rnor_6.01434,418,226 - 34,502,215 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092371   ⟹   XP_038948299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,838 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092372   ⟹   XP_038948300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,838 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092373   ⟹   XP_038948301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092374   ⟹   XP_038948302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,838 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092375   ⟹   XP_038948303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092376   ⟹   XP_038948304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092377   ⟹   XP_038948305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092378   ⟹   XP_038948306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,933,883 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092379   ⟹   XP_038948307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092380   ⟹   XP_038948308
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092381   ⟹   XP_038948309
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,943,132 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092382   ⟹   XP_038948310
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,945,969 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092383   ⟹   XP_038948311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092384   ⟹   XP_038948312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092385   ⟹   XP_038948313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092386   ⟹   XP_038948314
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,908,542 - 31,992,673 (+)NCBI
RefSeq Acc Id: XM_039092387   ⟹   XP_038948315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21431,950,133 - 31,992,673 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001276761 (Get FASTA)   NCBI Sequence Viewer  
  NP_001376183 (Get FASTA)   NCBI Sequence Viewer  
  NP_068628 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454850 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454852 (Get FASTA)   NCBI Sequence Viewer  
  XP_017454853 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948299 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948300 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948301 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948302 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948303 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948304 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948305 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948306 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948307 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948308 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948309 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948310 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948311 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948312 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948313 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948314 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948315 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA81819 (Get FASTA)   NCBI Sequence Viewer  
  BAB68768 (Get FASTA)   NCBI Sequence Viewer  
  EDL89909 (Get FASTA)   NCBI Sequence Viewer  
  EDL89910 (Get FASTA)   NCBI Sequence Viewer  
  Q9WVS9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_068628   ⟸   NM_021856
- Peptide Label: isoform 1
- Sequence:
RefSeq Acc Id: XP_006250931   ⟸   XM_006250869
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006250932   ⟸   XM_006250870
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001276761   ⟸   NM_001289832
- Peptide Label: isoform S
- Sequence:
RefSeq Acc Id: XP_017454853   ⟸   XM_017599364
- Peptide Label: isoform X1
- UniProtKB: G3V697 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454852   ⟸   XM_017599363
- Peptide Label: isoform X1
- UniProtKB: G3V697 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454850   ⟸   XM_017599361
- Peptide Label: isoform X1
- UniProtKB: G3V697 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454851   ⟸   XM_017599362
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000002981   ⟸   ENSRNOT00000002981
RefSeq Acc Id: ENSRNOP00000002976   ⟸   ENSRNOT00000002976
RefSeq Acc Id: ENSRNOP00000074670   ⟸   ENSRNOT00000085991
RefSeq Acc Id: XP_038948308   ⟸   XM_039092380
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948301   ⟸   XM_039092373
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948307   ⟸   XM_039092379
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948304   ⟸   XM_039092376
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948303   ⟸   XM_039092375
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948305   ⟸   XM_039092377
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948311   ⟸   XM_039092383
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038948313   ⟸   XM_039092385
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948314   ⟸   XM_039092386
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038948312   ⟸   XM_039092384
- Peptide Label: isoform X3
RefSeq Acc Id: NP_001376183   ⟸   NM_001389254
- Peptide Label: isoform 3
RefSeq Acc Id: XP_038948302   ⟸   XM_039092374
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948300   ⟸   XM_039092372
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948299   ⟸   XM_039092371
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948306   ⟸   XM_039092378
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948309   ⟸   XM_039092381
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948310   ⟸   XM_039092382
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038948315   ⟸   XM_039092387
- Peptide Label: isoform X6
Protein Domains
bHLH   PAC   PAS

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/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)
ACI/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
ACI/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
BBDP/Wor (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620271 AgrOrtholog
Ensembl Genes ENSRNOG00000002175 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002976 UniProtKB/TrEMBL
  ENSRNOP00000002981 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074670 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002976 UniProtKB/TrEMBL
  ENSRNOT00000002981 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000085991 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro bHLH_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nuc_translocat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60447 UniProtKB/Swiss-Prot
NCBI Gene 60447 ENTREZGENE
Pfam HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Clock PhenoGen
PRINTS NCTRNSLOCATR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE BHLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HLH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PAS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47459 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF55785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K8N0_RAT UniProtKB/TrEMBL
  CLOCK_RAT UniProtKB/Swiss-Prot
  D4A4R8_RAT UniProtKB/TrEMBL
  G3V697 ENTREZGENE, UniProtKB/TrEMBL
  Q9WVS9 ENTREZGENE
UniProt Secondary Q920Y1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-12-18 Clock  clock circadian regulator  Clock  clock homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-24 Clock  clock homolog (mouse)  Clock  circadian locomoter output cycles kaput  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Clock  circadian locomoter output cycles kaput  Clock  clock homolog (mouse)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Clock  clock homolog (mouse)    circadian locomoter output cycles kaput  Name updated 1299863 APPROVED
2004-12-07   circadian locomoter output cycles kaput  Clock  clock gene  Name updated 1299863 APPROVED
2002-08-07 Clock  clock gene      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the suprachiasmatic nucleus 632379
gene_regulation mRNA level increased by light exposure in a phase dependent manner 632379