Per2 (period circadian regulator 2) - Rat Genome Database

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Gene: Per2 (period circadian regulator 2) Rattus norvegicus
Analyze
Symbol: Per2
Name: period circadian regulator 2
RGD ID: 61945
Description: Predicted to have several functions, including enzyme binding activity; nucleic acid binding activity; and transcription factor binding activity. Involved in circadian rhythm and negative regulation of transcription by RNA polymerase II. Localizes to nucleus. Human ortholog(s) of this gene implicated in advanced sleep phase syndrome and advanced sleep phase syndrome 1. Orthologous to human PER2 (period circadian regulator 2); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: circadian clock protein PERIOD 2; period circadian clock 2; period circadian protein homolog 2; period homolog 2; period homolog 2 (Drosophila); rPER2
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
mRatBN7.2992,007,289 - 92,049,551 (-)NCBI
Rnor_6.0 Ensembl998,555,169 - 98,597,359 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0998,555,154 - 98,597,362 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0998,231,202 - 98,273,371 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4990,645,342 - 90,687,509 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1990,850,110 - 90,892,278 (-)NCBI
Celera989,548,336 - 89,590,505 (-)NCBICelera
Cytogenetic Map9q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-epicatechin-3-O-gallate  (ISO)
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(R)-noradrenaline  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-di-tert-butyl-4-methylphenol  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acamprosate  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bexarotene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
capsaicin  (EXP)
carbon nanotube  (ISO)
CGS-21680  (ISO)
chloroprene  (EXP,ISO)
chrysene  (ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
curcumin  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
diethyl maleate  (EXP)
disodium selenite  (ISO)
diuron  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
entinostat  (ISO)
Erionite  (ISO)
ethanol  (ISO)
ferric oxide  (ISO)
flavonoids  (EXP)
fluoranthene  (ISO)
fluoxetine  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gallic acid  (ISO)
gallocatechin  (ISO)
gamma-hexachlorocyclohexane  (EXP)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
leflunomide  (EXP)
linsidomine  (ISO)
manganese(II) chloride  (EXP)
melatonin  (EXP)
menadione  (ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (EXP,ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
milrinone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
morphine  (EXP,ISO)
N-nitrosodiethylamine  (EXP)
orphenadrine  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentanal  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenformin  (EXP)
phenobarbital  (EXP,ISO)
phenol  (ISO)
phenylephrine  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
plumbagin  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
prednisolone  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP,ISO)
propanal  (ISO)
quercetin  (EXP)
raloxifene  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
Se-methyl-L-selenocysteine  (EXP)
Se-methylselenocysteine  (EXP)
sevoflurane  (EXP)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium dodecyl sulfate  (ISO)
Soman  (EXP)
styrene  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
testosterone  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (EXP,ISO)
tetraphene  (ISO)
thapsigargin  (EXP)
titanium dioxide  (EXP,ISO)
torcetrapib  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zalcitabine  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IBA,ISO,ISS)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO)
perinuclear region of cytoplasm  (ISO)

References

References - curated
1. Barnes JW, etal., Science 2003 Oct 17;302(5644):439-42.
2. Chappuis S, etal., Mol Metab. 2013 May 10;2(3):184-93. doi: 10.1016/j.molmet.2013.05.002. eCollection 2013.
3. Dardente H, etal., Brain Res 2002 Dec 27;958(2):261-71.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. GOA data from the GO Consortium
6. Hamaguchi H, etal., Biochem J. 2004 Aug 15;382(Pt 1):43-50.
7. Hirota T, etal., J Biol Chem 2002 Nov 15;277(46):44244-51.
8. Honma S, etal., Nature 2002 Oct 24;419(6909):841-4.
9. Kawamoto T, etal., Biochem Biophys Res Commun. 2004 Jan 2;313(1):117-24.
10. MGD data from the GO Consortium
11. Miyazaki K, etal., Mol Cell Biol 2001 Oct;21(19):6651-9.
12. Muhlbauer E, etal., FEBS Lett. 2004 Apr 23;564(1-2):91-6.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Ohsaki K, etal., J Biochem. 2008 Nov;144(5):609-18. doi: 10.1093/jb/mvn112. Epub 2008 Sep 8.
15. Oishi K, etal., Biochem Biophys Res Commun. 1998 Dec 18;253(2):199-203.
16. OMIM Disease Annotation Pipeline
17. RGD automated data pipeline
18. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
19. RGD automated import pipeline for gene-chemical interactions
20. Sakamoto K, etal., J Biol Chem 1998 Oct 16;273(42):27039-42.
21. Sakamoto S, etal., Biochem Biophys Res Commun. 2000 Dec 9;279(1):131-8.
22. Sanggaard KM, etal., Eur J Neurosci 2003 Mar;17(6):1245-52.
23. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
24. Toh KL, etal., Science. 2001 Feb 9;291(5506):1040-3.
25. Yuferov V, etal., Synapse 2003 Jun 15;48(4):157-69.
Additional References at PubMed
PMID:9989497   PMID:11395012   PMID:11889036   PMID:12710990   PMID:12738229   PMID:12843397   PMID:14593213   PMID:14645221   PMID:14701732   PMID:15193530   PMID:15689618   PMID:15792371  
PMID:15860628   PMID:15864751   PMID:16580135   PMID:16595674   PMID:16675517   PMID:16678973   PMID:16923124   PMID:17310242   PMID:17404161   PMID:17544223   PMID:17915197   PMID:17986006  
PMID:18208549   PMID:18511208   PMID:18810660   PMID:18817849   PMID:19036829   PMID:19103603   PMID:19122877   PMID:19217292   PMID:19222559   PMID:19402751   PMID:19559014   PMID:19605937  
PMID:19740747   PMID:19887760   PMID:19917250   PMID:20096750   PMID:20159955   PMID:20205554   PMID:20424134   PMID:20589906   PMID:20738730   PMID:20962226   PMID:21035761   PMID:21063915  
PMID:21076970   PMID:21182399   PMID:21363938   PMID:21484443   PMID:21547532   PMID:21613214   PMID:21621196   PMID:21680841   PMID:21767615   PMID:21768648   PMID:21775066   PMID:21952132  
PMID:22170608   PMID:22208286   PMID:22274616   PMID:22381761   PMID:22504074   PMID:22767893   PMID:23106436   PMID:23167790   PMID:23418588   PMID:23738784   PMID:23785138   PMID:23850797  
PMID:23850969   PMID:23864491   PMID:23977055   PMID:24124556   PMID:24133102   PMID:24268780   PMID:24413057   PMID:24549704   PMID:24619734   PMID:24737000   PMID:25068868   PMID:25669688  
PMID:25760074   PMID:26213916   PMID:26271538   PMID:26656624   PMID:26892296   PMID:26901093   PMID:27362940   PMID:27365111   PMID:27999821   PMID:28423013   PMID:29165002   PMID:29894471  
PMID:30627637  


Genomics

Comparative Map Data
Per2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2992,007,289 - 92,049,551 (-)NCBI
Rnor_6.0 Ensembl998,555,169 - 98,597,359 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0998,555,154 - 98,597,362 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0998,231,202 - 98,273,371 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4990,645,342 - 90,687,509 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1990,850,110 - 90,892,278 (-)NCBI
Celera989,548,336 - 89,590,505 (-)NCBICelera
Cytogenetic Map9q36NCBI
PER2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2238,244,044 - 238,290,102 (-)EnsemblGRCh38hg38GRCh38
GRCh382238,244,038 - 238,290,102 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372239,152,685 - 239,197,251 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362238,817,418 - 238,861,946 (-)NCBINCBI36hg18NCBI36
Build 342238,934,685 - 238,979,092NCBI
Celera2232,865,233 - 232,909,762 (-)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2230,943,837 - 230,988,232 (-)NCBIHuRef
CHM1_12239,158,528 - 239,203,056 (-)NCBICHM1_1
Per2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39191,343,699 - 91,387,072 (-)NCBIGRCm39mm39
GRCm39 Ensembl191,343,704 - 91,387,046 (-)Ensembl
GRCm38191,415,977 - 91,459,351 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl191,415,982 - 91,459,324 (-)EnsemblGRCm38mm10GRCm38
MGSCv37193,312,559 - 93,355,905 (-)NCBIGRCm37mm9NCBIm37
MGSCv36193,246,388 - 93,289,702 (-)NCBImm8
Celera194,353,350 - 94,396,834 (-)NCBICelera
Cytogenetic Map1DNCBI
Per2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555422,338,099 - 2,371,274 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555422,331,547 - 2,369,011 (+)NCBIChiLan1.0ChiLan1.0
PER2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B244,328,122 - 244,371,040 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B244,328,122 - 244,371,040 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B125,477,021 - 125,521,577 (-)NCBIMhudiblu_PPA_v0panPan3
PER2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12548,716,499 - 48,761,617 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2548,717,173 - 48,758,755 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2549,211,912 - 49,257,033 (-)NCBI
ROS_Cfam_1.02549,102,140 - 49,147,315 (-)NCBI
UMICH_Zoey_3.12548,977,242 - 49,022,398 (-)NCBI
UNSW_CanFamBas_1.02548,765,877 - 48,806,293 (-)NCBI
UU_Cfam_GSD_1.02548,998,242 - 49,043,270 (-)NCBI
Per2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303190,676,406 - 190,718,243 (-)NCBI
SpeTri2.0NW_004936525221,601 - 263,284 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PER2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15137,793,419 - 137,837,236 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115137,793,419 - 137,837,854 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215152,264,819 - 152,284,153 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PER2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110124,270,917 - 124,316,031 (-)NCBI
ChlSab1.1 Ensembl10124,269,543 - 124,315,904 (-)Ensembl
Per2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248473,359,174 - 3,399,584 (-)NCBI

Position Markers
AW524487  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2992,035,203 - 92,035,384 (+)MAPPER
Rnor_6.0998,583,068 - 98,583,248NCBIRnor6.0
Rnor_5.0998,259,116 - 98,259,296UniSTSRnor5.0
RGSC_v3.4990,673,254 - 90,673,434UniSTSRGSC3.4
Celera989,576,250 - 89,576,430UniSTS
Cytogenetic Map9q36UniSTS
BI276674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2992,034,821 - 92,034,960 (+)MAPPER
Rnor_6.0998,582,686 - 98,582,824NCBIRnor6.0
Rnor_5.0998,258,734 - 98,258,872UniSTSRnor5.0
RGSC_v3.4990,672,872 - 90,673,010UniSTSRGSC3.4
Celera989,575,868 - 89,576,006UniSTS
RH 3.4 Map9785.49UniSTS
Cytogenetic Map9q36UniSTS
PMC124275P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2992,008,649 - 92,009,153 (+)MAPPER
Rnor_6.0998,556,510 - 98,557,013NCBIRnor6.0
Rnor_5.0998,232,558 - 98,233,061UniSTSRnor5.0
RGSC_v3.4990,646,696 - 90,647,199UniSTSRGSC3.4
Celera989,549,690 - 89,550,193UniSTS
Cytogenetic Map9q36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95417754299177542Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)961186278106186278Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)963270073107878387Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)966757444112943287Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96745166499920892Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96745166499920892Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)970241351115241351Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)970942881115942881Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)983686153111609081Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)990024661107199079Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)99274129798606834Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:281
Count of miRNA genes:174
Interacting mature miRNAs:220
Transcripts:ENSRNOT00000027506
Prediction methods:Miranda, 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 18 9 3 3 3 3 46 15 17 6
Low 25 48 38 16 38 8 8 28 20 24 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027506   ⟹   ENSRNOP00000027507
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl998,555,169 - 98,597,359 (-)Ensembl
RefSeq Acc Id: NM_031678   ⟹   NP_113866
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,007,296 - 92,049,459 (-)NCBI
Rnor_6.0998,555,156 - 98,597,323 (-)NCBI
Rnor_5.0998,231,202 - 98,273,371 (-)NCBI
RGSC_v3.4990,645,342 - 90,687,509 (-)RGD
Celera989,548,336 - 89,590,505 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245476   ⟹   XP_006245538
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,007,289 - 92,049,353 (-)NCBI
Rnor_6.0998,555,154 - 98,597,225 (-)NCBI
Rnor_5.0998,231,202 - 98,273,371 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596618   ⟹   XP_017452107
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,007,289 - 92,049,551 (-)NCBI
Rnor_6.0998,555,154 - 98,597,362 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039084159   ⟹   XP_038940087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,007,289 - 92,049,551 (-)NCBI
RefSeq Acc Id: XM_039084160   ⟹   XP_038940088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2992,007,289 - 92,029,049 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113866   ⟸   NM_031678
- UniProtKB: Q9Z301 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006245538   ⟸   XM_006245476
- Peptide Label: isoform X1
- UniProtKB: Q9Z301 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017452107   ⟸   XM_017596618
- Peptide Label: isoform X1
- UniProtKB: Q9Z301 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000027507   ⟸   ENSRNOT00000027506
RefSeq Acc Id: XP_038940087   ⟸   XM_039084159
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038940088   ⟸   XM_039084160
- Peptide Label: isoform X3
Protein Domains
PAC   PAS

Transcriptome

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

Promoters
RGD ID:13696861
Promoter ID:EPDNEW_R7386
Type:initiation region
Name:Per2_1
Description:period circadian regulator 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_6.0998,597,372 - 98,597,432EPDNEW

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
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 90655995 90655996 C A snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61945 AgrOrtholog
Ensembl Genes ENSRNOG00000020254 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027507 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027506 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro PAS UniProtKB/Swiss-Prot
  PAS-like_dom_sf UniProtKB/Swiss-Prot
  PAS_fold_3 UniProtKB/Swiss-Prot
  Period_circadian-like_C UniProtKB/Swiss-Prot
KEGG Report rno:63840 UniProtKB/Swiss-Prot
NCBI Gene 63840 ENTREZGENE
Pfam PAS_3 UniProtKB/Swiss-Prot
  Period_C UniProtKB/Swiss-Prot
PhenoGen Per2 PhenoGen
PROSITE PAS UniProtKB/Swiss-Prot
SMART PAS UniProtKB/Swiss-Prot
Superfamily-SCOP SSF55785 UniProtKB/Swiss-Prot
TIGR TC231261
UniProt PER2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-10-09 Per2  period circadian regulator 2  Per2  period circadian clock 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-02 Per2  period circadian clock 2  Per2  period homolog 2 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Per2  period homolog 2 (Drosophila)    period homolog 2   Name updated 1299863 APPROVED
2002-06-10 Per2  period homolog 2       Name updated 70585 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains a nucleus localization signal in the central domain; has PAS domians near the N-terminal which can interact with and regulate the activity of PAS domain transcriptional factors, such as CLOCK and BMAL 61691
gene_domains contains a nucleus localization signal in the central domain; has PAS domians near the N-terminal which can interact with and regulate the activity of PAS domain transcriptional factors, such as CLOCK and BMAL 69505
gene_domains contains PAS (PER-ARNT-SIM) domains near the N-terminus which regulate PAS domain transcriptional factors 631232
gene_process controls circadian rhythms 61691
gene_process controls circadian rhythms 631232