Cdk5r1 (cyclin-dependent kinase 5 regulatory subunit 1) - Rat Genome Database

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Gene: Cdk5r1 (cyclin-dependent kinase 5 regulatory subunit 1) Rattus norvegicus
Analyze
Symbol: Cdk5r1
Name: cyclin-dependent kinase 5 regulatory subunit 1
RGD ID: 629472
Description: Enables several functions, including cadherin binding activity; cyclin-dependent protein serine/threonine kinase activator activity; and ephrin receptor binding activity. Involved in several processes, including G protein-coupled acetylcholine receptor signaling pathway; nervous system development; and regulation of synaptic vesicle cycle. Located in several cellular components, including dendritic spine; growth cone; and postsynaptic density. Part of protein kinase 5 complex. Is active in presynapse. Biomarker of hypothyroidism and trigeminal neuralgia. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human CDK5R1 (cyclin dependent kinase 5 regulatory subunit 1); PARTICIPATES IN Reelin signaling pathway; Alzheimer's disease pathway; INTERACTS WITH (S)-amphetamine; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CDK5 activator 1; Cdk5r; cyclin-dependent kinase 5 activator 1; cyclin-dependent kinase 5, regulatory subunit 1; cyclin-dependent kinase 5, regulatory subunit 1 (p35); p23; p35; tau protein kinase II 23 kDa subunit; TPKII regulatory subunit
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21065,484,266 - 65,485,467 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1065,483,941 - 65,488,456 (+)Ensembl
Rnor_6.01067,862,054 - 67,863,255 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1067,862,054 - 67,863,255 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01067,515,764 - 67,516,965 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41068,715,844 - 68,717,045 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11068,729,476 - 68,730,668 (+)NCBI
Celera1064,442,587 - 64,443,788 (+)NCBICelera
Cytogenetic Map10q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
(S)-amphetamine  (EXP)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (EXP)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
Calpeptin  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
cisplatin  (ISO)
clozapine  (ISO)
cobalt dichloride  (ISO)
cocaine  (EXP,ISO)
copper atom  (ISO)
copper(0)  (ISO)
cytarabine  (ISO)
deguelin  (ISO)
dexmedetomidine  (EXP)
diarsenic trioxide  (EXP)
diclofenac  (EXP)
diiodine  (EXP)
disodium selenite  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenpyroximate  (ISO)
formaldehyde  (ISO)
gamma-tocopherol  (ISO)
gentamycin  (EXP)
hydroxyurea  (ISO)
ionomycin  (EXP)
lead diacetate  (ISO)
Licochalcone B  (ISO)
maneb  (ISO)
mercury atom  (ISO)
mercury(0)  (ISO)
metformin  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylmercury(1+)  (ISO)
methylphenidate  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N-nitrosourea  (EXP)
nickel atom  (ISO)
ochratoxin A  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (EXP)
paraquat  (ISO)
phencyclidine  (ISO)
phenylmercury acetate  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propofol  (EXP)
pyrimidifen  (ISO)
quercetin  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
tamoxifen  (ISO)
tebufenpyrad  (ISO)
tocopherol  (ISO)
tributylstannane  (ISO)
Tributyltin oxide  (ISO)
trichloroethene  (EXP,ISO)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
tungsten  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
axon extension  (TAS)
axon guidance  (ISO,ISS)
axonal fasciculation  (ISO,ISS)
brain development  (IEP,ISO,ISS)
cerebellum development  (ISO)
cerebral cortex radially oriented cell migration  (ISO)
embryo development ending in birth or egg hatching  (IDA)
ephrin receptor signaling pathway  (ISO,ISS)
G protein-coupled acetylcholine receptor signaling pathway  (IDA)
G1 to G0 transition involved in cell differentiation  (ISO)
hippocampus development  (ISO)
ionotropic glutamate receptor signaling pathway  (IDA)
layer formation in cerebral cortex  (ISO)
negative regulation of axon extension  (ISO)
negative regulation of transcription, DNA-templated  (ISO)
neuron cell-cell adhesion  (ISO,ISS)
neuron differentiation  (IDA)
neuron migration  (ISO,ISS)
neuron projection development  (IMP)
peptidyl-serine phosphorylation  (ISO)
peptidyl-threonine phosphorylation  (ISO)
positive regulation of cyclin-dependent protein serine/threonine kinase activity  (IEA)
positive regulation of MHC class II biosynthetic process  (ISO)
positive regulation of neuron apoptotic process  (IDA)
positive regulation of protein kinase activity  (ISO)
positive regulation of protein targeting to membrane  (ISO)
positive regulation of signaling receptor activity  (ISO)
regulation of actin cytoskeleton organization  (ISO)
regulation of dendritic spine morphogenesis  (ISO,ISS)
regulation of microtubule cytoskeleton organization  (ISO)
regulation of synaptic vesicle cycle  (IDA,IMP)
rhythmic process  (IEA)
serine phosphorylation of STAT protein  (ISO)
superior olivary nucleus maturation  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Chang WS, etal., Med Sci Monit. 2017 Jun 4;23:2721-2731.
2. Cheng K, etal., J Biol Chem 2002 Aug 30;277(35):31988-93.
3. Cheung ZH, etal., PLoS Biol. 2007 Apr;5(4):e63.
4. Dhavan R, etal., J Neurosci. 2002 Sep 15;22(18):7879-91.
5. Fu AK, etal., Nat Neurosci. 2001 Apr;4(4):374-81.
6. Fu WY, etal., Nat Neurosci. 2007 Jan;10(1):67-76. Epub 2006 Dec 3.
7. GOA data from the GO Consortium
8. Hsiao K, etal., Dev Neurobiol. 2014 Mar;74(3):351-64. doi: 10.1002/dneu.22154. Epub 2013 Dec 14.
9. Kesavapany S, etal., J Neurosci. 2003 Jun 15;23(12):4975-83.
10. Kwon YT, etal., Curr Biol. 2000 Apr 6;10(7):363-72.
11. Li W, etal., Shanghai Kou Qiang Yi Xue. 2010 Oct;19(5):545-8.
12. Maestre C, etal., EMBO J. 2008 Oct 22;27(20):2736-45. doi: 10.1038/emboj.2008.195. Epub 2008 Sep 25.
13. Mateo I, etal., Acta Neurol Scand. 2009 Aug;120(2):130-3. doi: 10.1111/j.1600-0404.2008.01128.x. Epub 2008 Dec 22.
14. MGD data from the GO Consortium
15. Nikolic M, etal., Genes Dev. 1996 Apr 1;10(7):816-25.
16. O'Hare MJ, etal., J Neurosci. 2005 Sep 28;25(39):8954-66.
17. Pipeline to import KEGG annotations from KEGG into RGD
18. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
19. Pruitt KD and Maglott DR, Nucleic Acids Res. 2001 Jan 1;29(1):137-40.
20. RGD automated data pipeline
21. RGD automated import pipeline for gene-chemical interactions
22. Sahlgren CM, etal., EMBO J. 2006 Oct 18;25(20):4808-19. Epub 2006 Oct 12.
23. Sahlgren CM, etal., Mol Cell Biol 2003 Jul;23(14):5090-106.
24. Saito T, etal., J Neurosci 2003 Feb 15;23(4):1189-97.
25. Sakaue F, etal., J Biol Chem. 2005 Sep 9;280(36):31522-9. Epub 2005 Jul 1.
26. Sato K, etal., J Neurosci Res. 2007 Nov 1;85(14):3071-8. doi: 10.1002/jnr.21438.
27. Seo J, etal., Cell. 2014 Apr 10;157(2):486-498. doi: 10.1016/j.cell.2014.01.065.
28. Sun D, etal., J Biol Chem 1996 Jun 14;271(24):14245-51.
29. Tan X, etal., Neuroscience. 2015 Apr 2;290:552-60. doi: 10.1016/j.neuroscience.2015.01.054. Epub 2015 Feb 7.
30. Tian F, etal., Neurosci Lett. 2015 Jan 1;584:50-5. doi: 10.1016/j.neulet.2014.09.049. Epub 2014 Oct 7.
31. Yu F, etal., Environ Toxicol. 2014 Aug;29(8):847-55. doi: 10.1002/tox.21811. Epub 2012 Sep 15.
32. Zhu WL, etal., Int J Neuropsychopharmacol. 2012 Jul;15(6):795-809. doi: 10.1017/S1461145711000915. Epub 2011 Jun 20.
Additional References at PubMed
PMID:9010203   PMID:10545161   PMID:10903889   PMID:11113134   PMID:11226314   PMID:11517264   PMID:12393264   PMID:14521924   PMID:14976144   PMID:15051507   PMID:15096606   PMID:15123626  
PMID:15592431   PMID:17121855   PMID:17334225   PMID:17498664   PMID:17517623   PMID:17591690   PMID:17728463   PMID:18054859   PMID:18247371   PMID:18289510   PMID:18385322   PMID:18771616  
PMID:18991853   PMID:19118186   PMID:19141975   PMID:19304511   PMID:19638632   PMID:19965374   PMID:20033852   PMID:20357208   PMID:20624590   PMID:21554958   PMID:21566658   PMID:21873635  
PMID:22106156   PMID:22573681   PMID:22801079   PMID:22870316   PMID:25864429   PMID:26788519   PMID:28559121   PMID:29020624   PMID:29388152   PMID:31314915   PMID:33456665  


Genomics

Candidate Gene Status
Cdk5r1 is a candidate Gene for QTL Eau9
Comparative Map Data
Cdk5r1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21065,484,266 - 65,485,467 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1065,483,941 - 65,488,456 (+)Ensembl
Rnor_6.01067,862,054 - 67,863,255 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1067,862,054 - 67,863,255 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01067,515,764 - 67,516,965 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41068,715,844 - 68,717,045 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11068,729,476 - 68,730,668 (+)NCBI
Celera1064,442,587 - 64,443,788 (+)NCBICelera
Cytogenetic Map10q26NCBI
CDK5R1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1732,486,993 - 32,491,253 (+)EnsemblGRCh38hg38GRCh38
GRCh381732,485,028 - 32,491,256 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371730,814,011 - 30,818,271 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361727,838,218 - 27,842,384 (+)NCBINCBI36hg18NCBI36
Build 341727,838,217 - 27,842,383NCBI
Celera1727,724,307 - 27,728,473 (+)NCBI
Cytogenetic Map17q11.2NCBI
HuRef1727,000,601 - 27,004,486 (+)NCBIHuRef
CHM1_11730,876,567 - 30,880,733 (+)NCBICHM1_1
Cdk5r1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391180,367,849 - 80,372,010 (+)NCBIGRCm39mm39
GRCm39 Ensembl1180,367,849 - 80,372,010 (+)Ensembl
GRCm381180,477,023 - 80,481,184 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1180,477,023 - 80,481,184 (+)EnsemblGRCm38mm10GRCm38
MGSCv371180,290,548 - 80,294,681 (+)NCBIGRCm37mm9NCBIm37
MGSCv361180,293,241 - 80,297,376 (+)NCBImm8
Celera1190,115,053 - 90,119,186 (+)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1147.94NCBI
Cdk5r1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554817,408,205 - 7,409,128 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554817,408,089 - 7,411,813 (+)NCBIChiLan1.0ChiLan1.0
CDK5R1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11724,575,561 - 24,579,226 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1724,577,537 - 24,579,232 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01724,285,069 - 24,289,311 (-)NCBIMhudiblu_PPA_v0panPan3
CDK5R1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1940,481,111 - 40,502,689 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl940,501,646 - 40,502,569 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha939,645,753 - 39,661,533 (-)NCBI
ROS_Cfam_1.0941,302,927 - 41,318,699 (-)NCBI
ROS_Cfam_1.0 Ensembl941,314,917 - 41,318,708 (-)Ensembl
UMICH_Zoey_3.1940,089,089 - 40,104,860 (-)NCBI
UNSW_CanFamBas_1.0940,383,316 - 40,399,074 (-)NCBI
UU_Cfam_GSD_1.0940,458,001 - 40,473,768 (-)NCBI
Cdk5r1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560239,533,255 - 39,537,114 (-)NCBI
SpeTri2.0NW_0049365382,411,194 - 2,415,106 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDK5R1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1242,493,321 - 42,494,659 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11242,456,063 - 42,494,494 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21244,209,897 - 44,253,700 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CDK5R1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11626,044,751 - 26,048,920 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1626,045,061 - 26,049,101 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660753,994,491 - 4,000,484 (-)NCBIVero_WHO_p1.0
Cdk5r1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624875538,752 - 542,874 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
PMC30213P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21065,484,808 - 65,485,468 (+)MAPPERmRatBN7.2
Rnor_6.01067,862,597 - 67,863,256NCBIRnor6.0
Rnor_5.01067,516,307 - 67,516,966UniSTSRnor5.0
RGSC_v3.41068,716,387 - 68,717,046UniSTSRGSC3.4
Celera1064,443,130 - 64,443,789UniSTS
Cytogenetic Map10q26UniSTS
CDK5R1_1797  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21065,484,627 - 65,485,459 (+)MAPPERmRatBN7.2
Rnor_6.01067,862,416 - 67,863,247NCBIRnor6.0
Rnor_5.01067,516,126 - 67,516,957UniSTSRnor5.0
RGSC_v3.41068,716,206 - 68,717,037UniSTSRGSC3.4
Celera1064,442,949 - 64,443,780UniSTS
Cytogenetic Map10q26UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
1331839Eae18bExperimental allergic encephalomyelitis QTL 18b5.80.03nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)106124830367785171Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
631526Bp76Blood pressure QTL 760.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106134541366743655Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:26
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000031746
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 72
Low 2 22 28 12 19 12 8 9 2 27 41 11 8
Below cutoff 1 19 29 29 29 2 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031746   ⟹   ENSRNOP00000062473
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1067,862,054 - 67,863,255 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119428   ⟹   ENSRNOP00000079807
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1065,483,941 - 65,488,456 (+)Ensembl
RefSeq Acc Id: NM_053891   ⟹   NP_446343
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21065,484,266 - 65,485,467 (+)NCBI
Rnor_6.01067,862,054 - 67,863,255 (+)NCBI
Rnor_5.01067,515,764 - 67,516,965 (+)NCBI
RGSC_v3.41068,715,844 - 68,717,045 (+)RGD
Celera1064,442,587 - 64,443,788 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446343 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC52611 (Get FASTA)   NCBI Sequence Viewer  
  EDM05425 (Get FASTA)   NCBI Sequence Viewer  
  P61810 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446343   ⟸   NM_053891
- UniProtKB: P61810 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062473   ⟸   ENSRNOT00000031746
RefSeq Acc Id: ENSRNOP00000079807   ⟸   ENSRNOT00000119428

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 (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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)
FHL/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
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
10 67516376 67516377 G A snv ACI/EurMcwi (MCW), ACI/N (KNAW), ACI/EurMcwi (KNAW), BUF/N (KNAW), DA/BklArbNsi (KNAW), F344/NRrrc (SOLiD) (KNAW), F344/Jcl (KyushuU), F344/NHsd (KNAW), M520/N (KNAW), F344/NRrrc (Illumina) (KNAW), F344/DuCrlCrlj (KyushuU), F344/NSlc (KyushuU), F344/Stm (KyushuU), F344/NCrl (KNAW)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 65484878 65484879 G A snv ACI/EurMcwi (2019), M520/N (2020), BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), ACI/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 67862666 67862667 G A snv ACI/EurMcwi (MCW), M520/N (2020), Buf/N (MCW), ACI/EurMcwi (RGD), F344/NCrl (RGD), ACI/EurMcwi (2019), ACI/N (2020), BUF/N (2020), DA/OlaHsd (2019), F344/DuCrl (2019), F344/NCrl (2019), F344/N (2020), F344/Stm (2019), FXLE16/Stm (2020), FXLE18/Stm (2020), LEXF2B/Stm (2019), LEXF3/Stm (2020), LEXF10A/StmMcwi (2020), M520/NRrrcMcwi (2019), ACI/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 68716456 68716457 G A snv ACI/EurMcwi (MCW), ACI/N (KNAW), BUF/N (KNAW), ACI/EurMcwi (ICL), F344/NCrl (ICL), F344/NHsd (ICAHN), LCR/1Mco (UMich), HCR/2Mco (UMich), LCR/2Mco (UMich), DA/BklArbNsi (ICAHN), HCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:629472 AgrOrtholog
Ensembl Genes ENSRNOG00000021685 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000068243 Ensembl, ENTREZGENE
Ensembl Protein ENSRNOP00000062473 UniProtKB/Swiss-Prot
  ENSRNOP00000079807 ENTREZGENE
Ensembl Transcript ENSRNOT00000031746 UniProtKB/Swiss-Prot
  ENSRNOT00000119428 ENTREZGENE
InterPro CDK5_activator UniProtKB/Swiss-Prot
  Cyclin-like_sf UniProtKB/Swiss-Prot
KEGG Report rno:116671 UniProtKB/Swiss-Prot
NCBI Gene 116671 ENTREZGENE
PANTHER PTHR23401 UniProtKB/Swiss-Prot
Pfam CDK5_activator UniProtKB/Swiss-Prot
PhenoGen Cdk5r1 PhenoGen
PIRSF Cdk5_activator UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47954 UniProtKB/Swiss-Prot
UniProt CD5R1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q62938 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Cdk5r1  cyclin-dependent kinase 5 regulatory subunit 1  Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1 (p35)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-29 Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1 (p35)  Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-11-05 Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1  Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1 (p35)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 Cdk5r1  cyclin-dependent kinase 5, regulatory subunit 1 (p35)  Cdk5r    Symbol updated 1299863 APPROVED
2005-01-20 Cdk5r  cyclin-dependent kinase 5, regulatory subunit 1 (p35)      Symbol and Name status set to approved 1299863 APPROVED
2003-04-06 Cdk5r  cyclin-dependent kinase 5, regulatory subunit 1 (p35)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation activity depends on its regulatory partners, p35 or p39 632377