Gdnf (glial cell derived neurotrophic factor) - Rat Genome Database
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Gene: Gdnf (glial cell derived neurotrophic factor) Rattus norvegicus
Analyze
Symbol: Gdnf
Name: glial cell derived neurotrophic factor
RGD ID: 2677
Description: Exhibits protein homodimerization activity and signaling receptor binding activity. Involved in several processes, including animal organ development; cellular response to dexamethasone stimulus; and regulation of mesonephros development. Localizes to extracellular space and receptor complex. Biomarker of sciatic neuropathy. Human ortholog(s) of this gene implicated in Hirschsprung's disease; congenital central hypoventilation syndrome; epilepsy; and pheochromocytoma. Orthologous to human GDNF (glial cell derived neurotrophic factor); INTERACTS WITH (+)-pilocarpine; (R)-Salsolinol; (S)-AMPA.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: astrocyte-derived trophic factor; ATF; glial cell line derived neurotrophic factor; Glial cell line derived neutrophic factor; glial cell line-derived neurotrophic factor; GNDF
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2256,893,992 - 56,919,935 (+)NCBI
Rnor_6.0 Ensembl256,887,987 - 56,910,238 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0256,884,181 - 56,912,964 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0276,896,991 - 76,922,471 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4257,399,312 - 57,424,030 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1257,327,544 - 57,352,263 (+)NCBI
Celera252,510,468 - 52,532,694 (+)NCBICelera
Cytogenetic Map2q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-Salsolinol  (EXP)
(S)-AMPA  (EXP)
(S)-amphetamine  (EXP,ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
13,14-dihydro-Delta(12)-prostaglandin J2  (EXP)
17beta-estradiol  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3',5'-cyclic AMP  (ISO)
4,4'-sulfonyldiphenol  (ISO)
acetamide  (EXP)
actinomycin D  (EXP)
aflatoxin B1  (EXP,ISO)
agathisflavone  (EXP)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP,ISO)
apigenin  (EXP)
apomorphine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (EXP,ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromocriptine  (ISO)
busulfan  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cabergoline  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chondroitin sulfate  (ISO)
chrysin  (ISO)
cisplatin  (ISO)
cocaine  (EXP)
cyclophosphamide  (EXP)
dabigatran  (EXP)
DDE  (EXP)
dermatan sulfate  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dioxygen  (ISO)
disodium selenite  (ISO)
dopamine  (EXP,ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
echinacoside  (ISO)
epoxiconazole  (EXP)
ethanol  (EXP,ISO)
excitatory amino acid agonist  (EXP)
fisetin  (EXP)
fluoranthene  (ISO)
fluoxetine  (EXP)
folpet  (ISO)
furan  (EXP)
genistein  (ISO)
geraniol  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
iron(2+) sulfate (anhydrous)  (ISO)
linuron  (EXP)
lipopolysaccharide  (EXP,ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
manganese(II) chloride  (ISO)
Mazindol  (ISO)
methamphetamine  (ISO)
methylmercury chloride  (EXP,ISO)
methylphenidate  (ISO)
mifepristone  (EXP)
mono(2-ethylhexyl) phthalate  (ISO)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel sulfate  (ISO)
nitrofen  (EXP)
O-methyleugenol  (ISO)
oxidopamine  (EXP,ISO)
paraquat  (ISO)
pergolide  (ISO)
phenethyl caffeate  (EXP)
phenylmercury acetate  (ISO)
potassium chromate  (ISO)
prochloraz  (EXP)
procymidone  (EXP)
progesterone  (ISO)
puerarin  (ISO)
rasagiline  (ISO)
resveratrol  (EXP)
rotenone  (EXP,ISO)
rutin  (EXP)
salvianolic acid B  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
SKF 38393  (ISO)
sodium arsenite  (ISO)
sulfasalazine  (ISO)
telmisartan  (ISO)
testosterone  (ISO)
tetrachloromethane  (EXP)
tetraphene  (ISO)
titanium dioxide  (EXP,ISO)
toluene  (EXP)
trichloroethene  (EXP)
tris(2-butoxyethyl) phosphate  (ISO)
vanoxerine dihydrochloride  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
cell population proliferation  (IDA)
cellular response to dexamethasone stimulus  (IDA)
commissural neuron axon guidance  (IEA,ISO)
dorsal spinal cord development  (IEA,ISO)
embryonic organ development  (IEA,ISO)
enteric nervous system development  (IEA,ISO,ISS)
male gonad development  (IEP)
mesenchymal to epithelial transition involved in metanephros morphogenesis  (IDA,IEA,ISO)
metanephros development  (ISO,ISS)
midbrain development  (IEP)
mRNA stabilization  (IEA,ISO,ISS)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (IEA,ISO)
negative regulation of neuron apoptotic process  (IBA,IEA,ISO,ISS)
nervous system development  (ISO,TAS)
neural crest cell migration  (IEA,ISO,ISS)
neuron differentiation  (IDA)
neuron projection development  (ISO,ISS)
organ induction  (IEA,ISO)
peripheral nervous system development  (IBA,ISO)
peristalsis  (IEA,ISO,ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (IBA,IDA,IEA,IMP,ISO)
positive regulation of cell differentiation  (ISO)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  (IEA,ISO)
positive regulation of monooxygenase activity  (IEA,ISO,ISS)
positive regulation of peptidyl-tyrosine phosphorylation  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO,ISS)
positive regulation of ureteric bud formation  (IEA,ISO,ISS)
postganglionic parasympathetic fiber development  (IEA,ISO,ISS)
postsynaptic membrane organization  (IEA,ISO)
regulation of dopamine uptake involved in synaptic transmission  (IEA,ISO,ISS)
regulation of gene expression  (ISO)
regulation of morphogenesis of a branching structure  (ISO,ISS)
regulation of semaphorin-plexin signaling pathway  (IEA,ISO)
regulation of ureteric bud formation  (IDA)
response to wounding  (IDA)
retina development in camera-type eye  (IEP)
signal transduction  (IEA)
sympathetic nervous system development  (IEA,ISO,ISS)
ureteric bud development  (ISO)
ureteric bud formation  (IEA,ISO)

Cellular Component
extracellular region  (IEA,ISO,ISS,TAS)
extracellular space  (IBA,IDA,IMP)
Golgi apparatus  (IEA,ISO)
receptor complex  (IDA)

Molecular Function

References

References - curated
1. Airavaara M, etal., J Biol Chem. 2011 Dec 30;286(52):45093-102. Epub 2011 Nov 11.
2. Armstrong KJ and Niles LP, Neuroreport 2002 Mar 25;13(4):473-5.
3. Backman CM, etal., Mol Cell Endocrinol. 2006 Jun 27;252(1-2):160-6. Epub 2006 Apr 27.
4. Carmillo P, etal., Biochemistry. 2005 Feb 22;44(7):2545-54.
5. Chao CC, etal., Neurobiol Aging 2003 Jan-Feb;24(1):105-16.
6. Cheng Q, etal., Neurosci Lett. 2008 Jul 4;439(1):24-9. Epub 2008 May 1.
7. Eigenbrot C and Gerber N, Nat Struct Biol. 1997 Jun;4(6):435-8.
8. Eketjäll S, etal., EMBO J. 1999 Nov 1;18(21):5901-10.
9. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
10. GOA data from the GO Consortium
11. Grote D, etal., PLoS Genet. 2008 Dec;4(12):e1000316. doi: 10.1371/journal.pgen.1000316. Epub 2008 Dec 26.
12. Hashimoto M, etal., Neuroreport 2005 Feb 8;16(2):99-102.
13. Hoke A, etal., Neuroreport. 2000 Jun 5;11(8):1651-4.
14. Impellizzeri D, etal., Biochem Pharmacol. 2012 Feb 8.
15. Isajevs S, etal., Medicina (Kaunas). 2011;47(10):552-9.
16. Jin G, etal., Brain Res 2002 Dec 27;958(2):429-33.
17. Jing S, etal., Cell 1996 Jun 28;85(7):1113-24.
18. Kalechman Y, etal., J Am Soc Nephrol 2003 Mar;14(3):620-30.
19. Kanter-Schlifke I, etal., Exp Neurol. 2009 Apr;216(2):413-9. Epub 2009 Jan 7.
20. Kramer F, etal., J Neurooncol. 2010 May;98(1):31-9. doi: 10.1007/s11060-009-0063-6. Epub 2009 Nov 25.
21. Kretz A, etal., Brain Res. 2006 May 23;1090(1):1-14. Epub 2006 May 2.
22. Lei Z, etal., J Neuropathol Exp Neurol. 2011 Sep;70(9):736-47.
23. Lindqvist N, etal., Exp Neurol. 2004 Jun;187(2):487-99.
24. Liu T, etal., Reprod Domest Anim. 2011 Nov 24. doi: 10.1111/j.1439-0531.2011.01950.x.
25. MGD data from the GO Consortium
26. Michos O, etal., Development. 2007 Jul;134(13):2397-405. Epub 2007 May 23.
27. NCBI rat LocusLink and RefSeq merged data July 26, 2002
28. OMIM Disease Annotation Pipeline
29. Online Mendelian Inheritance in Man, OMIM (TM).
30. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
31. RGD automated import pipeline for gene-chemical interactions
32. Sellner J, etal., Brain Res Mol Brain Res. 2005 Jun 13;137(1-2):267-71. Epub 2005 Apr 22.
33. Singh RR, etal., Am J Physiol Renal Physiol. 2007 Aug;293(2):F548-54. Epub 2007 May 30.
34. Sokolov ME, etal., Front Pharmacol. 2018 Feb 15;9:111. doi: 10.3389/fphar.2018.00111. eCollection 2018.
35. Sun M, etal., Brain Res. 2005 Aug 9;1052(2):119-29.
36. Sun ZH, etal., Cell Biol Int 2004;28(4):323-5.
37. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
38. Ubhi K, etal., Exp Neurol. 2012 Jan 16.
39. Yamamoto M, etal., Brain Res. 1998 Nov 2;809(2):175-81.
40. Yamamoto M, etal., Neurochem Res. 1999 Jun;24(6):785-90.
41. Zeng Q, etal., J Int Med Res. 2008 Jul-Aug;36(4):656-64.
42. Zhou W, etal., Zhonghua Yi Xue Za Zhi 2000 Feb;80(2):135-9.
Additional References at PubMed
PMID:7696586   PMID:7867768   PMID:7895811   PMID:8493557   PMID:8657306   PMID:8657307   PMID:8657308   PMID:8988018   PMID:9192898   PMID:9811930   PMID:10322633   PMID:10921886  
PMID:11675876   PMID:11774071   PMID:12125080   PMID:12210384   PMID:12231225   PMID:12358785   PMID:12478607   PMID:12480187   PMID:12712323   PMID:12715924   PMID:12781994   PMID:12832519  
PMID:12832538   PMID:12837245   PMID:12876402   PMID:12957504   PMID:13678594   PMID:14552879   PMID:14552891   PMID:14552902   PMID:14596863   PMID:14598299   PMID:14608602   PMID:14708939  
PMID:14753442   PMID:15033464   PMID:15044553   PMID:15090036   PMID:15130495   PMID:15212950   PMID:15242795   PMID:15381279   PMID:15519246   PMID:15582775   PMID:15618882   PMID:15659589  
PMID:15691764   PMID:15812312   PMID:15905075   PMID:15935064   PMID:15964099   PMID:16086701   PMID:16524382   PMID:16569669   PMID:16584838   PMID:16643884   PMID:16672314   PMID:16766196  
PMID:16841166   PMID:16854632   PMID:16967504   PMID:17113937   PMID:17229286   PMID:17240430   PMID:17298301   PMID:17387333   PMID:17399854   PMID:17537792   PMID:17663984   PMID:17765347  
PMID:17880388   PMID:17888513   PMID:17920149   PMID:17967506   PMID:18003772   PMID:18038430   PMID:18095158   PMID:18194437   PMID:18293415   PMID:18363829   PMID:18465789   PMID:18520583  
PMID:18585464   PMID:18593521   PMID:18668157   PMID:18973572   PMID:19154763   PMID:19238724   PMID:19277011   PMID:19339709   PMID:19362079   PMID:19460370   PMID:19520066   PMID:19524560  
PMID:19530158   PMID:19558709   PMID:19709371   PMID:19741142   PMID:19845157   PMID:19925812   PMID:19944698   PMID:20079213   PMID:20175208   PMID:20305789   PMID:20625988   PMID:20626773  
PMID:20682772   PMID:20739562   PMID:21040239   PMID:21130871   PMID:21174801   PMID:21223624   PMID:21279379   PMID:21281623   PMID:21515689   PMID:21586298   PMID:21653894   PMID:21659885  
PMID:21699926   PMID:21828353   PMID:21871541   PMID:21994944   PMID:22230667   PMID:22251670   PMID:22266674   PMID:22281445   PMID:22282251   PMID:22575563   PMID:22579834   PMID:22672424  
PMID:22704965   PMID:22807215   PMID:22897442   PMID:22985671   PMID:22998873   PMID:23032401   PMID:23151666   PMID:23261589   PMID:23298382   PMID:23373701   PMID:23472740   PMID:23588198  
PMID:23613711   PMID:23694790   PMID:23767459   PMID:23934644   PMID:24312503   PMID:24619502   PMID:24632468   PMID:24706318   PMID:24878766   PMID:25201174   PMID:25220603   PMID:25301495  
PMID:25423132   PMID:25572945   PMID:25655216   PMID:25869129   PMID:25972459   PMID:26318480   PMID:26340267   PMID:26466815   PMID:26709397   PMID:26777664   PMID:26815249   PMID:27230884  
PMID:27519646   PMID:28130107   PMID:28276446   PMID:29018141   PMID:29712778   PMID:30541958   PMID:31112899   PMID:31720997   PMID:32214273  


Genomics

Candidate Gene Status
Gdnf is a candidate Gene for QTL Gdil1
Gdnf is a candidate Gene for QTL Gdil2
Comparative Map Data
Gdnf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2256,893,992 - 56,919,935 (+)NCBI
Rnor_6.0 Ensembl256,887,987 - 56,910,238 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0256,884,181 - 56,912,964 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0276,896,991 - 76,922,471 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4257,399,312 - 57,424,030 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1257,327,544 - 57,352,263 (+)NCBI
Celera252,510,468 - 52,532,694 (+)NCBICelera
Cytogenetic Map2q16NCBI
GDNF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl537,812,677 - 37,840,041 (-)EnsemblGRCh38hg38GRCh38
GRCh38537,812,677 - 37,840,044 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37537,812,779 - 37,840,143 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37537,812,779 - 37,839,782 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36537,851,510 - 37,875,539 (-)NCBINCBI36hg18NCBI36
Build 34537,851,509 - 37,870,655NCBI
Celera537,699,155 - 37,726,173 (-)NCBI
Cytogenetic Map5p13.2NCBI
HuRef537,765,313 - 37,792,316 (-)NCBIHuRef
CHM1_1537,814,804 - 37,841,806 (-)NCBICHM1_1
Gdnf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39157,839,529 - 7,867,061 (+)NCBIGRCm39mm39
GRCm38157,810,048 - 7,837,580 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl157,810,846 - 7,837,575 (+)EnsemblGRCm38mm10GRCm38
MGSCv37157,761,011 - 7,787,575 (+)NCBIGRCm37mm9NCBIm37
MGSCv36157,758,226 - 7,784,790 (+)NCBImm8
Celera157,656,819 - 7,683,345 (+)NCBICelera
Cytogenetic Map15A1NCBI
Gdnf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542622,386,450 - 22,412,324 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542622,386,613 - 22,412,324 (-)NCBIChiLan1.0ChiLan1.0
GDNF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1577,573,466 - 77,600,478 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl577,577,313 - 77,601,362 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0572,539,374 - 72,566,918 (+)NCBIMhudiblu_PPA_v0panPan3
GDNF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl470,971,432 - 70,989,714 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1470,966,694 - 70,991,860 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Gdnf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365184,291,391 - 4,310,752 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GDNF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1622,936,601 - 22,965,886 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11622,936,602 - 22,965,929 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21624,176,604 - 24,179,641 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GDNF
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1436,662,033 - 36,691,761 (-)NCBI
ChlSab1.1 Ensembl436,665,009 - 36,684,257 (-)Ensembl
Gdnf
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475917,263,570 - 17,290,046 (+)NCBI

Position Markers
Gdnf  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.4257,423,774 - 57,424,011UniSTSRGSC3.4
RGSC_v3.4257,423,673 - 57,423,854UniSTSRGSC3.4
RGSC_v3.4257,423,677 - 57,424,014UniSTSRGSC3.4
Celera252,532,337 - 52,532,518UniSTS
Celera252,532,341 - 52,532,678UniSTS
Celera252,532,438 - 52,532,675UniSTS
GDNF_3150  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0256,909,775 - 56,910,250NCBIRnor6.0
Rnor_5.0276,919,282 - 76,919,757UniSTSRnor5.0
RGSC_v3.4257,423,567 - 57,424,042UniSTSRGSC3.4
Celera252,532,231 - 52,532,706UniSTS
Cytogenetic Map2q16UniSTS
Gdnf  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0276,919,388 - 76,919,569UniSTSRnor5.0
RGSC_v3.4257,423,673 - 57,423,854UniSTSRGSC3.4
Celera252,532,337 - 52,532,518UniSTS
Cytogenetic Map2q16UniSTS
Gdnf  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0276,919,489 - 76,919,726UniSTSRnor5.0
RGSC_v3.4257,423,774 - 57,424,011UniSTSRGSC3.4
Celera252,532,438 - 52,532,675UniSTS
Cytogenetic Map2q16UniSTS
Gdnf  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.0276,919,392 - 76,919,729UniSTSRnor5.0
RGSC_v3.4257,423,677 - 57,424,014UniSTSRGSC3.4
Celera252,532,341 - 52,532,678UniSTS
Cytogenetic Map2q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)23127638105149020Rat
1578671Bmd10Bone mineral density QTL 105.4femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)2944467968866454Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21423783059237830Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21901646564016465Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22027698165276981Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22064137165641371Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22261295267612952Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22328064775687607Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)223837491149614623Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491169852800Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)223837491169852800Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)223837491218957222Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)223837719169852670Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)22618609783819822Rat
1354617Bp240Blood pressure QTL 2404arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)22618609783819822Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226186097135654963Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226186097142053534Rat
12879841Cm87Cardiac mass QTL 870.026heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)227161361148295267Rat
12879842Cm88Cardiac mass QTL 880.042heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)227161361148295267Rat
12879843Am3Aortic mass QTL 30.016aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)227161361148295267Rat
12879844Kidm62Kidney mass QTL 620.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227161361148295267Rat
9590095Sffal3Serum free fatty acids level QTL 36.780.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)22776030172760301Rat
10755434Coatc7Coat color QTL 70.04794coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23127237976272379Rat
61371Edpm1Estrogen-dependent pituitary mass QTL 140.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)23408817591101903Rat
10755436Coatc8Coat color QTL 80.02431coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)23513320280133202Rat
2306903Bp336Blood pressure QTL 3360.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)236245223112175725Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)240171834105089682Rat
70174BpQTLCluster2Blood pressure QTL cluster 24.24arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)240171834105089682Rat
1300155Bp174Blood pressure QTL 1744.09arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)24277691662238534Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916169852800Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242776916195645082Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242776916217498710Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243133606217498545Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243133606217498545Rat
2293676Bmd19Bone mineral density QTL 1910.70.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)243141290114164944Rat
2293682Bmd24Bone mineral density QTL 248.90.0001femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)243141290114164944Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243141290154583160Rat
631208Bw1Body weight QTL15.09mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight as a percentage of body weight (CMO:0000654)24314978885642672Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243149788198704485Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246537589217498710Rat
1354592Rf50Renal function QTL 503.5urine output (VT:0003620)timed urine volume (CMO:0000260)25443669875687607Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256244671217498710Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)25673640160325686Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:34
Interacting mature miRNAs:36
Transcripts:ENSRNOT00000041288
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 1 1 1 14 9
Low 3 20 18 4 18 1 1 21 4 30 11 1
Below cutoff 28 16 8 10 8 5 7 45 8 2 5

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_019139 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006232011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008760757 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC141975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF205713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF205714 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF205715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF497634 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ011432 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068467 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068469 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EU068472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000066 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L15305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S75583 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X92495 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000041288   ⟹   ENSRNOP00000044012
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl256,887,987 - 56,910,238 (+)Ensembl
RefSeq Acc Id: NM_019139   ⟹   NP_062012
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2256,895,048 - 56,917,209 (+)NCBI
Rnor_6.0256,887,987 - 56,910,238 (+)NCBI
Rnor_5.0276,896,991 - 76,922,471 (+)NCBI
RGSC_v3.4257,399,312 - 57,424,030 (+)RGD
Celera252,510,468 - 52,532,694 (+)RGD
Sequence:
RefSeq Acc Id: XM_006232010   ⟹   XP_006232072
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0256,884,181 - 56,912,964 (+)NCBI
Rnor_5.0276,896,991 - 76,922,471 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006232011   ⟹   XP_006232073
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2256,893,992 - 56,919,935 (+)NCBI
Rnor_6.0256,884,181 - 56,912,964 (+)NCBI
Rnor_5.0276,896,991 - 76,922,471 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760756   ⟹   XP_008758978
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2256,898,358 - 56,919,935 (+)NCBI
Rnor_6.0256,892,164 - 56,912,964 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008760757   ⟹   XP_008758979
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2256,898,278 - 56,919,935 (+)NCBI
Rnor_6.0256,892,164 - 56,912,964 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_062012   ⟸   NM_019139
- Peptide Label: precursor
- UniProtKB: Q07731 (UniProtKB/Swiss-Prot),   A7UGJ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006232072   ⟸   XM_006232010
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006232073   ⟸   XM_006232011
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008758978   ⟸   XM_008760756
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008758979   ⟸   XM_008760757
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000044012   ⟸   ENSRNOT00000041288
Protein Domains
TGF_BETA_2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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
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/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
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 (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
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
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
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
M520/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
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 (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
SBH/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: 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)
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
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 (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 (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2677 AgrOrtholog
Ensembl Genes ENSRNOG00000012819 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000044012 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041288 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.10.90.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cystine-knot_cytokine UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GDNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GDNF_fam UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TGF-b_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25453 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 25453 ENTREZGENE
PANTHER PTHR12173 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12173:SF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TGF_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gdnf PhenoGen
PIRSF GDNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TGF_BETA_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57501 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC222344
UniProt A7UGI9_RAT UniProtKB/TrEMBL
  A7UGJ1 ENTREZGENE, UniProtKB/TrEMBL
  F8WFL7_RAT UniProtKB/TrEMBL
  GDNF_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q63214 UniProtKB/Swiss-Prot
  Q64062 UniProtKB/Swiss-Prot
  Q64063 UniProtKB/Swiss-Prot
  Q8R485 UniProtKB/Swiss-Prot
  Q9QX94 UniProtKB/Swiss-Prot
  Q9QX95 UniProtKB/Swiss-Prot
  Q9QXJ7 UniProtKB/Swiss-Prot
  Q9QXJ8 UniProtKB/Swiss-Prot
  Q9QXJ9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-17 Gdnf  glial cell derived neurotrophic factor  Gdnf  glial cell line derived neurotrophic factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Gdnf  Glial cell line derived neutrophic factor      Symbol and Name status set to approved 70586 APPROVED