Agrn (agrin) - Rat Genome Database

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Gene: Agrn (agrin) Rattus norvegicus
Analyze
Symbol: Agrn
Name: agrin
RGD ID: 2067
Description: Enables calcium ion binding activity; cytokine binding activity; and dystroglycan binding activity. Involved in several processes, including positive regulation of filopodium assembly; positive regulation of nitrogen compound metabolic process; and synapse organization. Acts upstream of or within receptor clustering. Located in axonal growth cone; basement membrane; and synapse. Is active in glutamatergic synapse. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 8. Orthologous to human AGRN (agrin); PARTICIPATES IN acetylcholine signaling pathway via nicotinic acetylcholine receptor; cell-extracellular matrix signaling pathway; INTERACTS WITH (+)-pilocarpine; 17beta-estradiol; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: AGR
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
mRatBN7.25166,749,306 - 166,782,212 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5166,749,310 - 166,786,003 (-)Ensembl
Rnor_6.05173,589,910 - 173,622,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,589,819 - 173,622,645 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05177,063,797 - 177,096,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,999,420 - 173,020,764 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15173,009,918 - 173,031,259 (-)NCBI
Celera5164,949,181 - 164,970,209 (-)NCBICelera
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrolein  (ISO)
acrylamide  (ISO)
all-trans-retinoic acid  (EXP)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
biochanin A  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bortezomib  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
cadmium dichloride  (EXP,ISO)
camptothecin  (ISO)
chlordecone  (ISO)
chloroacetaldehyde  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
clofibrate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (EXP,ISO)
daunorubicin  (ISO)
dexamethasone  (ISO)
dioxygen  (ISO)
elemental selenium  (ISO)
endosulfan  (EXP)
ethanol  (EXP,ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fenofibrate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
hypochlorous acid  (ISO)
ifosfamide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
linsidomine  (EXP)
mercury dichloride  (ISO)
metformin  (EXP)
methamphetamine  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctanoic acid  (EXP,ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP)
reactive oxygen species  (EXP)
sarin  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
troglitazone  (EXP)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vitamin E  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ morphogenesis  (IBA)
cell differentiation  (IEA)
chemical synaptic transmission  (IMP,ISO)
G protein-coupled acetylcholine receptor signaling pathway  (IEA)
negative regulation of catalytic activity  (IEA)
negative regulation of P-type sodium:potassium-exchanging transporter activity  (ISO)
negative regulation of sodium ion export across plasma membrane  (ISO)
neuromuscular junction development  (IBA,ISO,TAS)
neurotransmitter receptor metabolic process  (ISO)
plasma membrane organization  (ISO)
positive regulation of filopodium assembly  (IDA)
positive regulation of GTPase activity  (IDA)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (IDA)
positive regulation of protein binding  (ISO)
positive regulation of protein geranylgeranylation  (ISO)
positive regulation of protein phosphorylation  (IMP,ISO)
positive regulation of protein tyrosine kinase activity  (ISO)
positive regulation of synaptic assembly at neuromuscular junction  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IDA,ISO)
receptor clustering  (IBA,IDA,IEA,ISO,ISS)
regulation of axon guidance  (IDA)
regulation of cardiac muscle cell membrane potential  (ISO)
regulation of cardiac muscle contraction  (ISO)
regulation of GTPase activity  (ISO)
regulation of microtubule cytoskeleton organization  (IDA)
regulation of protein phosphorylation  (IDA)
regulation of synapse organization  (IDA,IMP)
regulation of synaptic assembly at neuromuscular junction  (ISO)
skeletal muscle acetylcholine-gated channel clustering  (IDA,IMP)
synapse assembly  (IMP)
tissue development  (IBA)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Banyai L, etal., PLoS One. 2010 May 21;5(5):e10758. doi: 10.1371/journal.pone.0010758.
2. Bergstrom RA, etal., Neuroscience. 2007 Nov 9;149(3):527-36. Epub 2007 Aug 14.
3. Erasso D, etal., Exp Neurol. 2014 Nov;261:646-53. doi: 10.1016/j.expneurol.2014.08.014. Epub 2014 Aug 21.
4. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Gee SH, etal., Cell. 1994 Jun 3;77(5):675-86.
6. Gingras J, etal., Cell Tissue Res. 2005 Apr;320(1):115-25. Epub 2005 Feb 16.
7. Glass DJ, etal., Cell 1996 May 17;85(4):513-23.
8. Hilgenberg LG, etal., Cell. 2006 Apr 21;125(2):359-69.
9. Hoover CL, etal., J Cell Biol. 2003 Jun 9;161(5):923-32.
10. Kim N, etal., Cell. 2008 Oct 17;135(2):334-42. doi: 10.1016/j.cell.2008.10.002. Epub 2008 Oct 9.
11. Lin L, etal., Exp Cell Res. 2010 Aug 15;316(14):2260-77. doi: 10.1016/j.yexcr.2010.05.006. Epub 2010 May 13.
12. Martin AO, etal., J Cell Biol. 2005 May 9;169(3):503-14.
13. McCroskery S, etal., Neuroscience. 2009 Sep 29;163(1):168-79. doi: 10.1016/j.neuroscience.2009.06.012. Epub 2009 Jun 10.
14. MGD data from the GO Consortium
15. Moransard M, etal., J Biol Chem. 2003 Feb 28;278(9):7350-9. Epub 2002 Dec 16.
16. NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. Neuhuber B and Daniels MP, Mol Cell Neurosci. 2003 Dec;24(4):1180-96.
18. O'Toole JJ, etal., Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7369-74.
19. OMIM Disease Annotation Pipeline
20. Pipeline to import KEGG annotations from KEGG into RGD
21. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. RGD automated import pipeline for gene-chemical interactions
23. Rupp F, etal., Neuron 1991 May;6(5):811-23.
24. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
25. Trinidad JC and Cohen JB, J Biol Chem. 2004 Jul 23;279(30):31622-8. Epub 2004 May 20.
26. Tseng CN, etal., J Biol Chem. 2010 Sep 3;285(36):27641-51. doi: 10.1074/jbc.M110.130625. Epub 2010 Jun 21.
27. Witzemann V, etal., Mech Dev. 2013 Jun-Aug;130(6-8):402-11. doi: 10.1016/j.mod.2012.09.004. Epub 2012 Sep 29.
28. Zhang B, etal., Neuron. 2008 Oct 23;60(2):285-97. doi: 10.1016/j.neuron.2008.10.006.
29. Zong Y, etal., Genes Dev. 2012 Feb 1;26(3):247-58. doi: 10.1101/gad.180885.111.
Additional References at PubMed
PMID:1326608   PMID:7670489   PMID:8653788   PMID:9151673   PMID:9405491   PMID:9422725   PMID:10402191   PMID:11018052   PMID:11312299   PMID:11395002   PMID:12165471   PMID:12773545  
PMID:12955494   PMID:14622576   PMID:15210115   PMID:15340048   PMID:16274639   PMID:16635246   PMID:16860570   PMID:17119023   PMID:17628813   PMID:18003748   PMID:18230682   PMID:18627255  
PMID:18639611   PMID:18757743   PMID:19199708   PMID:19285050   PMID:19376779   PMID:19940118   PMID:20458337   PMID:20551380   PMID:21068333   PMID:21969364   PMID:23056392   PMID:23117006  
PMID:23376485   PMID:23533145   PMID:23658023   PMID:24006456   PMID:27068509   PMID:27559042   PMID:31055156   PMID:31454080  


Genomics

Comparative Map Data
Agrn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25166,749,306 - 166,782,212 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl5166,749,310 - 166,786,003 (-)Ensembl
Rnor_6.05173,589,910 - 173,622,813 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5173,589,819 - 173,622,645 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05177,063,797 - 177,096,674 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45172,999,420 - 173,020,764 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15173,009,918 - 173,031,259 (-)NCBI
Celera5164,949,181 - 164,970,209 (-)NCBICelera
Cytogenetic Map5q36NCBI
AGRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11,020,120 - 1,056,118 (+)EnsemblGRCh38hg38GRCh38
GRCh3811,020,102 - 1,056,119 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371955,500 - 991,496 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361945,366 - 981,355 (+)NCBINCBI36hg18NCBI36
Celera11,597,136 - 1,631,462 (-)NCBI
Cytogenetic Map1p36.33NCBI
HuRef1226,888 - 263,237 (+)NCBIHuRef
CHM1_11942,522 - 978,540 (+)NCBICHM1_1
Agrn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394156,249,747 - 156,281,997 (-)NCBIGRCm39mm39
GRCm39 Ensembl4156,249,747 - 156,281,945 (-)Ensembl
GRCm384156,165,290 - 156,197,533 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4156,165,290 - 156,197,488 (-)EnsemblGRCm38mm10GRCm38
MGSCv374155,539,399 - 155,559,244 (-)NCBIGRCm37mm9NCBIm37
MGSCv364155,009,090 - 155,028,935 (-)NCBImm8
Celera4158,419,989 - 158,441,614 (-)NCBICelera
Cytogenetic Map4E2NCBI
cM Map488.55NCBI
Agrn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554869,675,214 - 9,704,991 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554869,674,103 - 9,704,994 (-)NCBIChiLan1.0ChiLan1.0
AGRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11953,977 - 967,946 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1936,000 - 966,808 (+)Ensemblpanpan1.1panPan2
AGRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1556,239,621 - 56,273,679 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl556,239,701 - 56,272,745 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha556,317,660 - 56,351,511 (+)NCBI
ROS_Cfam_1.0556,443,168 - 56,477,026 (+)NCBI
UMICH_Zoey_3.1556,434,207 - 56,468,062 (+)NCBI
UNSW_CanFamBas_1.0556,326,114 - 56,359,961 (+)NCBI
UU_Cfam_GSD_1.0556,716,182 - 56,750,025 (+)NCBI
Agrn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505827,426,638 - 27,455,302 (+)NCBI
SpeTri2.0NW_0049367372,010,647 - 2,041,401 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AGRN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,365,983 - 63,398,311 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,366,017 - 63,398,311 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2657,851,241 - 57,880,816 (-)NCBISscrofa10.2Sscrofa10.2susScr3
AGRN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120130,383,226 - 130,416,926 (-)NCBI
ChlSab1.1 Ensembl20130,383,220 - 130,416,933 (-)Ensembl
Vero_WHO_p1.0NW_02366605435,009,405 - 35,044,463 (-)NCBI
Agrn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248188,475,453 - 8,508,818 (-)NCBI

Position Markers
RH127796  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,749,466 - 166,749,656 (+)MAPPERmRatBN7.2
Rnor_6.05173,590,071 - 173,590,260NCBIRnor6.0
Rnor_5.05177,063,958 - 177,064,147UniSTSRnor5.0
RGSC_v3.45172,999,581 - 172,999,770UniSTSRGSC3.4
Celera5164,949,342 - 164,949,531UniSTS
RH 3.4 Map51172.9UniSTS
Cytogenetic Map5q36UniSTS
RH94447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25166,750,028 - 166,750,202 (+)MAPPERmRatBN7.2
Rnor_6.05173,590,633 - 173,590,806NCBIRnor6.0
Rnor_5.05177,064,520 - 177,064,693UniSTSRnor5.0
RGSC_v3.45173,000,143 - 173,000,316UniSTSRGSC3.4
Celera5164,949,904 - 164,950,077UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
631272Lanf1Left ventricular atrial natriuretic factor QTL 112heart left ventricle natriuretic peptide A amount (VT:0010596)heart left ventricle natriuretic peptide A level (CMO:0002165)5151113452166875058Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1549904Neuinf1Neuroinflammation QTL 130nervous system integrity trait (VT:0010566)blood T lymphocyte count (CMO:0000110)5154828214166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1178
Count of miRNA genes:262
Interacting mature miRNAs:325
Transcripts:ENSRNOT00000042726, ENSRNOT00000045678, ENSRNOT00000046315, ENSRNOT00000047854
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 39 16 6 8 6 1 1 74 35 34 11 1
Low 1 4 41 35 11 35 7 10 6 7
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045678   ⟹   ENSRNOP00000050623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,749,310 - 166,786,003 (-)Ensembl
Rnor_6.0 Ensembl5173,589,819 - 173,622,645 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000047854   ⟹   ENSRNOP00000040828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5166,749,310 - 166,786,003 (-)Ensembl
Rnor_6.0 Ensembl5173,589,914 - 173,611,202 (-)Ensembl
RefSeq Acc Id: NM_175754   ⟹   NP_786930
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,770,603 (-)NCBI
Rnor_6.05173,589,910 - 173,611,202 (-)NCBI
Rnor_5.05177,063,797 - 177,096,674 (-)NCBI
RGSC_v3.45172,999,420 - 173,020,764 (-)RGD
Celera5164,949,181 - 164,970,209 (-)RGD
Sequence:
RefSeq Acc Id: XM_006239541   ⟹   XP_006239603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,211 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Rnor_5.05177,063,797 - 177,096,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006239542   ⟹   XP_006239604
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,211 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Rnor_5.05177,063,797 - 177,096,674 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593166   ⟹   XP_017448655
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,211 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593167   ⟹   XP_017448656
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,211 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593168   ⟹   XP_017448657
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,211 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593169   ⟹   XP_017448658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,782,212 (-)NCBI
Rnor_6.05173,589,910 - 173,622,813 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593170   ⟹   XP_017448659
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,771,490 (-)NCBI
Rnor_6.05173,589,910 - 173,612,677 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109320   ⟹   XP_038965248
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25166,749,306 - 166,763,068 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_786930   ⟸   NM_175754
- Sequence:
RefSeq Acc Id: XP_006239604   ⟸   XM_006239542
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_006239603   ⟸   XM_006239541
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017448658   ⟸   XM_017593169
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017448656   ⟸   XM_017593167
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017448657   ⟸   XM_017593168
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017448655   ⟸   XM_017593166
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017448659   ⟸   XM_017593170
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: ENSRNOP00000040828   ⟸   ENSRNOT00000047854
RefSeq Acc Id: ENSRNOP00000050623   ⟸   ENSRNOT00000045678
RefSeq Acc Id: XP_038965248   ⟸   XM_039109320
- Peptide Label: isoform X8
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)
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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
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)
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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 (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
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-Lx/CubMcwi (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
BN/NHsdMcwi (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
BN/NHsdMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (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
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 (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
BXH2/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
DA/OlaHsd (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: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (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
F344/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
F344/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
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
F344/Stm (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
FHH/EurMcwi (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
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
FXLE16/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (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
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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
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)
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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
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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (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
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)
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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
LEXF4/Stm (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: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
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)
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
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)
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
MNS/Gib (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
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)
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
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)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
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)
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
SHRSP/Gcrc (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
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)
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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (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
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)
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2067 AgrOrtholog
Ensembl Genes ENSRNOG00000020205 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040828 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000050623 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045678 UniProtKB/TrEMBL
  ENSRNOT00000047854 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.40.50.120 UniProtKB/TrEMBL
  3.30.70.960 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Agrin_NtA UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FacI_MAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fol_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kazal_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kazal_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEA_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEA_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIMP-like_OB-fold UniProtKB/TrEMBL
KEGG Report rno:25592 UniProtKB/Swiss-Prot
NCBI Gene 25592 ENTREZGENE
Pfam EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kazal_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Kazal_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Agrn PhenoGen
PROSITE EGF_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_LAM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_LAM_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KAZAL_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NTA UniProtKB/TrEMBL
  SEA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_CA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF_Lam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIMAC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FOLN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KAZAL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LamG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SEA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF100895 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF82671 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TIMP_like UniProtKB/TrEMBL
TIGR TC229521
UniProt AGRIN_RAT UniProtKB/Swiss-Prot
  D4A2F1_RAT UniProtKB/TrEMBL
  F1LPF2_RAT UniProtKB/TrEMBL
  P25304 ENTREZGENE
UniProt Secondary Q63034 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Agrn  Agrin      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
null contains141 cysteine residues 632164
gene_cellular_localization localized to synapses 632164
gene_expression expressed in embryonic spinal cord and muscle 632164
gene_process may play a role in synaptic development and regeneration 632164
gene_protein protein sequence contains1940 amino acid residues 632164