Gfap (glial fibrillary acidic protein) - Rat Genome Database

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Gene: Gfap (glial fibrillary acidic protein) Rattus norvegicus
Analyze
Symbol: Gfap
Name: glial fibrillary acidic protein
RGD ID: 2679
Description: Enables integrin binding activity and kinase binding activity. A structural constituent of cytoskeleton. Involved in positive regulation of glial cell proliferation; regulation of chaperone-mediated autophagy; and response to wounding. Located in astrocyte projection and cytoplasmic side of lysosomal membrane. Biomarker of brain edema and retinal disease. Human ortholog(s) of this gene implicated in Alexander disease. Orthologous to human GFAP (glial fibrillary acidic protein); PARTICIPATES IN chaperone mediated autophagy pathway; INTERACTS WITH (+)-pilocarpine; (R,R,R)-alpha-tocopherol; 1,3,5-trinitro-1,3,5-triazinane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: glial fibrillary acidic protein alpha; glial fibrillary acidic protein delta; intermediate filament
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Gfapem1Ionsz   Gfapem1Mes   Gfapem2Mes  
Genetic Models: SD-Gfapem1Mes /Rrrc SD-Gfapem2Mes /Rrrc SD-Gfapem1(2A-Chr2-EYFP)Ionsz
Is Marker For: Strains:   F344/NRrrc   SD-Tg(Gfap-Tk1)Jog  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21087,852,891 - 87,861,631 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1087,852,890 - 87,861,589 (-)Ensembl
Rnor_6.01090,990,762 - 90,999,435 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,990,762 - 90,999,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01090,763,150 - 90,771,823 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41092,059,881 - 92,068,555 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11092,074,249 - 92,082,949 (-)NCBI
Celera1086,555,367 - 86,564,160 (-)NCBICelera
RH 3.4 Map10920.49RGD
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(R)-lipoic acid  (ISO)
(R,R,R)-alpha-tocopherol  (EXP)
(S)-amphetamine  (ISO)
(S)-nicotine  (ISO)
1,1-bis(2-aminoethyl)-2-hydroxy-3-oxotriazane  (ISO)
1,2-dichloroethane  (ISO)
1,3,5-trinitro-1,3,5-triazinane  (EXP)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
15-deoxy-Delta(12,14)-prostaglandin J2  (EXP,ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2,4-D  (EXP)
2,4-dinitrobenzenesulfonic acid  (ISO)
2,5-hexanedione  (EXP)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (EXP)
2-Ethylhexanoic acid  (ISO)
3',5'-cyclic AMP  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3,5-dichloro-N-[[(2S)-1-ethyl-2-pyrrolidinyl]methyl]-2-hydroxy-6-methoxybenzamide  (ISO)
4'-tert-Butyl-2',6'-dimethyl-3',5'-dinitroacetophenone  (EXP)
5-fluorouracil  (ISO)
6-Cyano-7-nitroquinoxaline-2,3-dione  (EXP)
6-propyl-2-thiouracil  (EXP)
6alpha-methylprednisolone  (ISO)
7-NITROINDAZOLE  (EXP)
8-Br-cAMP  (EXP)
8-OH-DPAT  (ISO)
abacavir  (ISO)
acetamide  (EXP)
acetic acid  (ISO)
acetylsalicylic acid  (EXP,ISO)
acrolein  (EXP)
acrylamide  (ISO)
Aflatoxin B2 alpha  (ISO)
agmatine  (ISO)
agomelatine  (EXP)
all-trans-retinoic acid  (EXP,ISO)
alpha,alpha-trehalose  (ISO)
alpha-D-galactose  (EXP)
aluminium atom  (EXP,ISO)
aluminium(0)  (EXP,ISO)
amentoflavone  (ISO)
aminoguanidine  (EXP)
amiodarone  (EXP)
amitriptyline  (EXP)
ammonia  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP,ISO)
apocynin  (ISO)
aristolochic acid  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
astaxanthin  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
bromochloroacetic acid  (ISO)
cadmium dichloride  (EXP,ISO)
caffeine  (EXP,ISO)
calcidiol  (EXP)
calcitriol  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
calyculin a  (EXP)
cannabidiol  (ISO)
capsaicin  (EXP,ISO)
capsazepine  (EXP,ISO)
captan  (ISO)
carbofuran  (EXP)
carbonyl sulfide  (EXP)
carmustine  (EXP,ISO)
carvacrol  (EXP)
chlordecone  (ISO)
chlorpromazine  (EXP)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
chrysin  (EXP)
Citreoviridin  (ISO)
clofibrate  (ISO)
clotrimazole  (ISO)
clozapine  (EXP)
cobalt dichloride  (EXP)
cocaine  (EXP,ISO)
coenzyme Q10  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
Cuprizon  (EXP,ISO)
curcumin  (EXP,ISO)
Cyanoginosin  (EXP)
cyprodinil  (ISO)
dabigatran  (ISO)
dantrolene  (EXP)
dexamethasone  (ISO)
diazinon  (EXP)
dieldrin  (ISO)
digoxin  (EXP)
dihydrogen  (EXP)
dimethoate  (EXP)
dioxygen  (EXP,ISO)
diprotium  (EXP)
disodium selenite  (EXP,ISO)
dizocilpine maleate  (EXP)
doxorubicin  (EXP)
ebselen  (EXP)
endosulfan  (EXP)
ethanol  (EXP,ISO)
ethylene glycol bis(2-aminoethyl)tetraacetic acid  (EXP)
fenitrothion  (EXP)
finasteride  (EXP)
fisetin  (EXP)
fluoxetine  (ISO)
folic acid  (EXP,ISO)
furan  (EXP)
galactose  (EXP)
gamma-aminobutyric acid  (EXP)
gefitinib  (EXP)
glufosinate  (ISO)
glycidol  (EXP)
haloperidol  (ISO)
hydrogen peroxide  (ISO)
hydrogen sulfide  (ISO)
ibuprofen  (EXP)
ifosfamide  (EXP)
imidacloprid  (EXP)
isoliquiritigenin  (ISO)
isoniazide  (EXP)
ivermectin  (ISO)
kainic acid  (EXP,ISO)
ketamine  (EXP)
KN-93  (EXP)
L-ascorbic acid  (EXP,ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead nitrate  (EXP)
lead(0)  (ISO)
lead(2+)  (ISO)
lead(II) chloride  (EXP)
lipoic acid  (ISO)
lipopolysaccharide  (EXP,ISO)
lithium chloride  (EXP,ISO)
luteolin  (ISO)
lycopene  (EXP,ISO)
Magnolol  (ISO)
maneb  (ISO)
manganese atom  (EXP,ISO)
manganese(0)  (EXP,ISO)
manganese(II) chloride  (EXP,ISO)
melatonin  (EXP,ISO)
memantine  (EXP)
mepanipyrim  (ISO)
metformin  (ISO)
methamphetamine  (EXP,ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methionine sulfoximine  (EXP)
methotrexate  (EXP,ISO)
methylene blue  (ISO)
methylmercury chloride  (EXP,ISO)
microcystin  (EXP)
microcystin LF  (EXP)
monocrotaline  (EXP)
monosodium L-glutamate  (EXP)
morin  (EXP)
morphine  (EXP,ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (EXP,ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
NADP zwitterion  (EXP)
NADP(+)  (EXP)
nicotine  (ISO)
nifedipine  (EXP)
nitric oxide  (EXP)
O-acetyl-L-carnitine  (ISO)
ochratoxin A  (EXP)
olanzapine  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP)
paclitaxel  (EXP,ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP,ISO)
phencyclidine  (ISO)
phenethyl caffeate  (EXP)
Phenoxybenzamine  (EXP)
physostigmine  (ISO)
poly(I:C)  (EXP)
potassium chloride  (EXP)
probenecid  (ISO)
probucol  (EXP)
progesterone  (EXP,ISO)
propiconazole  (EXP)
propionic acid  (EXP)
Pyridostigmine bromide  (ISO)
pyrimethanil  (ISO)
pyrithiamine  (EXP)
pyrroloquinoline quinone  (ISO)
quercetin  (EXP)
reactive oxygen species  (EXP)
resveratrol  (EXP,ISO)
rimonabant  (ISO)
rotenone  (EXP)
ruthenium red  (ISO)
sarin  (EXP,ISO)
SB 431542  (ISO)
SCH 23390  (ISO)
scopolamine  (ISO)
sodium arsenite  (EXP,ISO)
sodium chloride  (EXP)
Soman  (EXP)
staurosporine  (EXP)
sterigmatocystin  (EXP)
streptozocin  (EXP,ISO)
strychnine  (EXP)
tadalafil  (ISO)
tamibarotene  (EXP)
tamoxifen  (ISO)
Tanshinone I  (ISO)
telmisartan  (EXP,ISO)
temozolomide  (ISO)
terbutaline  (EXP)
tert-butyl hydroperoxide  (EXP)
testosterone  (ISO)
tetrachloroethene  (EXP)
tetrachloromethane  (ISO)
thiacloprid  (ISO)
thioacetamide  (EXP,ISO)
thiophanate-methyl  (ISO)
toluene  (EXP,ISO)
tributylstannane  (EXP)
trichostatin A  (EXP)
triclosan  (ISO)
trimethyltin  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
troglitazone  (EXP)
U-73122  (EXP)
valproic acid  (EXP,ISO)
venlafaxine hydrochloride  (EXP)
verapamil  (EXP)
vincristine  (EXP)
vitamin E  (EXP)
warfarin  (ISO)
wogonin  (EXP,ISO)
ziram  (ISO)
zonisamide  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Aamodt AH, etal., J Neurol. 2021 Mar 20. pii: 10.1007/s00415-021-10517-6. doi: 10.1007/s00415-021-10517-6.
2. Ajima H, etal., Arch Histol Cytol 2001 Dec;64(5):503-11.
3. Baldwin SA and Scheff SW, Glia. 1996 Mar;16(3):266-75.
4. Bandyopadhyay U, etal., Mol Cell. 2010 Aug 27;39(4):535-47. doi: 10.1016/j.molcel.2010.08.004.
5. Brouns R, etal., Clin Chem. 2010 Mar;56(3):451-8. Epub 2009 Dec 3.
6. Cuervo AM and Wong E, Cell Res. 2014 Jan;24(1):92-104. doi: 10.1038/cr.2013.153. Epub 2013 Nov 26.
7. Dibas A, etal., Mol Vis. 2008 Sep 25;14:1770-83.
8. GOA data from the GO Consortium
9. Gohara T, etal., J Anesth. 2010 Apr;24(2):225-33. Epub 2010 Jan 29.
10. Kanberg N, etal., Neurology. 2020 Sep 22;95(12):e1754-e1759. doi: 10.1212/WNL.0000000000010111. Epub 2020 Jun 16.
11. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
12. MGD data from the GO Consortium
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Nesic O, etal., J Neurochem. 2005 Nov;95(4):998-1014. Epub 2005 Oct 10.
15. Olave I, etal., Genes Dev. 2002 Oct 1;16(19):2509-17.
16. OMIM Disease Annotation Pipeline
17. Online Mendelian Inheritance in Man, OMIM (TM).
18. Pekny M, etal., J Cell Biol. 1999 May 3;145(3):503-14.
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Roymans D, etal., Exp Cell Res. 2000 Nov 25;261(1):127-38.
22. Rozovsky I, etal., Endocrinology 2002 Feb;143(2):636-46.
23. Toyooka T, etal., J Neurotrauma. 2011 Apr;28(4):607-18. Epub 2011 Mar 24.
24. Triolo D, etal., J Cell Sci. 2006 Oct 1;119(Pt 19):3981-93.
25. Urdzíková LM, etal., Int J Mol Sci. 2014 Jun 25;15(7):11275-93. doi: 10.3390/ijms150711275.
26. Vazquez R, etal., Histol Histopathol 2001 Oct;16(4):1107-16.
27. Xilouri M and Stefanis L, Mol Cell Neurosci. 2015 May;66(Pt A):29-36. doi: 10.1016/j.mcn.2015.01.003. Epub 2015 Feb 25.
28. Yoshimura Y, etal., Biochem Biophys Res Commun 2002 Jan 25;290(3):948-54.
Additional References at PubMed
PMID:1629938   PMID:2153890   PMID:7897704   PMID:8692820   PMID:8793730   PMID:9364068   PMID:10336251   PMID:10816608   PMID:10989258   PMID:11064363   PMID:11283023   PMID:11487638  
PMID:11834298   PMID:12074840   PMID:12177195   PMID:12355421   PMID:12477932   PMID:12533615   PMID:12837269   PMID:12878680   PMID:15135219   PMID:15195688   PMID:15281060   PMID:15378652  
PMID:15476586   PMID:15489334   PMID:15531134   PMID:15656993   PMID:15732097   PMID:15804429   PMID:15840648   PMID:15862905   PMID:15965470   PMID:16048809   PMID:16097052   PMID:16196195  
PMID:16332461   PMID:16374706   PMID:16606365   PMID:16612832   PMID:16806201   PMID:16850587   PMID:16860801   PMID:16879601   PMID:16986516   PMID:17008879   PMID:17203480   PMID:17245710  
PMID:17334943   PMID:17409479   PMID:17443351   PMID:17485853   PMID:17634366   PMID:17684014   PMID:18076286   PMID:18360886   PMID:18443417   PMID:18483855   PMID:18633737   PMID:18707003  
PMID:19000745   PMID:19056393   PMID:19137572   PMID:19141977   PMID:19182904   PMID:19235900   PMID:19383423   PMID:19559073   PMID:19646951   PMID:19661770   PMID:19726345   PMID:19770604  
PMID:20197608   PMID:20423852   PMID:20479526   PMID:20531390   PMID:20578039   PMID:20732387   PMID:20826656   PMID:20876578   PMID:21046809   PMID:21139996   PMID:21168404   PMID:21211284  
PMID:21212183   PMID:21284970   PMID:21343257   PMID:21371476   PMID:21385309   PMID:21470923   PMID:21524663   PMID:21679183   PMID:21683086   PMID:21892662   PMID:21906524   PMID:22475395  
PMID:22610521   PMID:22871113   PMID:23076037   PMID:23110394   PMID:23447615   PMID:23515288   PMID:23861879   PMID:24035762   PMID:24379073   PMID:24481447   PMID:24567055   PMID:24582971  
PMID:24747049   PMID:25110093   PMID:25181319   PMID:25182537   PMID:25282817   PMID:25312986   PMID:25416956   PMID:25448608   PMID:25752945   PMID:25763798   PMID:25798055   PMID:25837926  
PMID:25898931   PMID:25910212   PMID:25931508   PMID:26561800   PMID:26994384   PMID:27003918   PMID:27133445   PMID:27166167   PMID:27579183   PMID:28652433   PMID:28705472   PMID:29350434  
PMID:29476059   PMID:29852171   PMID:30126346   PMID:30334860   PMID:32070010   PMID:32357304   PMID:32910393   PMID:34065959  


Genomics

Comparative Map Data
Gfap
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21087,852,891 - 87,861,631 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1087,852,890 - 87,861,589 (-)Ensembl
Rnor_6.01090,990,762 - 90,999,435 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1090,990,762 - 90,999,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01090,763,150 - 90,771,823 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41092,059,881 - 92,068,555 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11092,074,249 - 92,082,949 (-)NCBI
Celera1086,555,367 - 86,564,160 (-)NCBICelera
RH 3.4 Map10920.49RGD
Cytogenetic Map10q32.1NCBI
GFAP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1744,903,159 - 44,916,937 (-)EnsemblGRCh38hg38GRCh38
GRCh381744,903,159 - 44,915,552 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371742,980,527 - 42,992,868 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361740,338,519 - 40,348,394 (-)NCBINCBI36hg18NCBI36
Build 341740,338,518 - 40,348,394NCBI
Celera1739,693,499 - 39,703,421 (-)NCBI
Cytogenetic Map17q21.31NCBI
HuRef1738,748,049 - 38,758,000 (-)NCBIHuRef
CHM1_11743,219,135 - 43,229,061 (-)NCBICHM1_1
Gfap
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911102,778,162 - 102,791,368 (-)NCBIGRCm39mm39
GRCm39 Ensembl11102,778,162 - 102,791,738 (-)Ensembl
GRCm3811102,887,336 - 102,897,200 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11102,887,336 - 102,900,912 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711102,748,650 - 102,758,514 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611102,704,767 - 102,713,221 (-)NCBImm8
Celera11114,598,382 - 114,608,239 (-)NCBICelera
Cytogenetic Map11E1NCBI
cM Map1166.48NCBI
Gfap
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495545117,695,835 - 17,703,268 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495545117,695,835 - 17,703,894 (-)NCBIChiLan1.0ChiLan1.0
GFAP
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11712,579,754 - 12,589,748 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1712,579,754 - 12,591,961 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01712,407,211 - 12,417,072 (+)NCBIMhudiblu_PPA_v0panPan3
GFAP
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1918,569,868 - 18,579,463 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl918,569,892 - 18,579,461 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha917,955,308 - 17,964,908 (+)NCBI
ROS_Cfam_1.0919,243,310 - 19,252,910 (+)NCBI
ROS_Cfam_1.0 Ensembl919,243,327 - 19,310,887 (+)Ensembl
UMICH_Zoey_3.1918,120,937 - 18,130,529 (+)NCBI
UNSW_CanFamBas_1.0918,299,941 - 18,309,543 (+)NCBI
UU_Cfam_GSD_1.0918,456,787 - 18,466,393 (+)NCBI
LOC101955496
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560217,919,377 - 17,928,684 (+)NCBI
SpeTri2.0NW_0049365411,265,915 - 1,275,232 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GFAP
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1218,456,263 - 18,468,898 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11218,456,268 - 18,466,594 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21218,700,993 - 18,711,304 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103243304
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11661,489,090 - 61,499,672 (+)NCBIChlSab1.1chlSab2
ChlSab1.11661,489,090 - 61,499,672 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607732,238,179 - 32,248,606 (+)NCBIVero_WHO_p1.0
Gfap
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624795395,298 - 400,781 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D10Kyo1   No map positions available.
D10Wox35  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21087,862,024 - 87,862,338 (+)MAPPERmRatBN7.2
Rnor_6.01090,999,895 - 91,000,208NCBIRnor6.0
Rnor_5.01090,772,283 - 90,772,596UniSTSRnor5.0
RGSC_v3.41092,069,015 - 92,069,328UniSTSRGSC3.4
Celera1086,564,620 - 86,564,933UniSTS
Cytogenetic Map10q32.1UniSTS
D10Wox54  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21087,856,969 - 87,857,135 (+)MAPPERmRatBN7.2
Rnor_6.01090,994,841 - 90,995,006NCBIRnor6.0
Rnor_5.01090,767,229 - 90,767,394UniSTSRnor5.0
RGSC_v3.41092,063,960 - 92,064,125UniSTSRGSC3.4
Celera1086,559,446 - 86,559,611UniSTS
Cytogenetic Map10q32.1UniSTS
RH131871  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21087,852,911 - 87,853,116 (+)MAPPERmRatBN7.2
Rnor_6.01090,990,783 - 90,990,987NCBIRnor6.0
Rnor_5.01090,763,171 - 90,763,375UniSTSRnor5.0
RGSC_v3.41092,059,902 - 92,060,106UniSTSRGSC3.4
Celera1086,555,388 - 86,555,592UniSTS
RH 3.4 Map10892.6UniSTS
Cytogenetic Map10q32.1UniSTS
RH142195  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21087,860,798 - 87,860,965 (+)MAPPERmRatBN7.2
Rnor_6.01090,998,669 - 90,998,835NCBIRnor6.0
Rnor_5.01090,771,057 - 90,771,223UniSTSRnor5.0
RGSC_v3.41092,067,789 - 92,067,955UniSTSRGSC3.4
Celera1086,563,394 - 86,563,560UniSTS
RH 3.4 Map10920.49UniSTS
Cytogenetic Map10q32.1UniSTS
PMC125376P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21087,852,916 - 87,853,134 (+)MAPPERmRatBN7.2
Rnor_6.01090,990,788 - 90,991,005NCBIRnor6.0
Rnor_5.01090,763,176 - 90,763,393UniSTSRnor5.0
RGSC_v3.41092,059,907 - 92,060,124UniSTSRGSC3.4
Celera1086,555,393 - 86,555,610UniSTS
Cytogenetic Map10q32.1UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2306793Ean5Experimental allergic neuritis QTL 54.7nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)107255241693995749Rat
1358188Ept9Estrogen-induced pituitary tumorigenesis QTL 93.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
2292617Ept18Estrogen-induced pituitary tumorigenesis QTL 183.9pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)107345313696120911Rat
1579919Bp281Blood pressure QTL 2810.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107437208494965338Rat
10450495Bp383Blood pressure QTL 3830.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)107624608594965338Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
631555Bp134Blood pressure QTL 1340.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)108051528791230079Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
4889948Bss91Bone structure and strength QTL 914tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)108256485692369470Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
12880055Am11Aortic mass QTL 110.004aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)108400727295933025Rat
2301398Kidm38Kidney mass QTL 380.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)108400727295933025Rat
2306792Ean4Experimental allergic neuritis QTL 44nervous system integrity trait (VT:0010566)IFNG-secreting splenocyte count (CMO:0002122)108402232193995963Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
2313856Bp342Blood pressure QTL 3424.40.0001life span trait (VT:0005372)age at time of death (CMO:0001193)108730761796121100Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat


Related Rat Strains
The following Strains have been annotated to Gfap


Genetic Models
This gene Gfap is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:439
Count of miRNA genes:220
Interacting mature miRNAs:272
Transcripts:ENSRNOT00000003948, ENSRNOT00000034401
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 6 12 12 3 12 37
Low 3 11 38 27 16 27 3 3 27 4 33 7 3
Below cutoff 26 7 2 2 5 5 10 30 8 4 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034401   ⟹   ENSRNOP00000032389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,852,890 - 87,861,589 (-)Ensembl
Rnor_6.0 Ensembl1090,990,762 - 90,999,506 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093167   ⟹   ENSRNOP00000076153
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1090,994,104 - 90,994,437 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093266   ⟹   ENSRNOP00000076226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,855,575 - 87,861,589 (-)Ensembl
Rnor_6.0 Ensembl1090,993,446 - 90,995,982 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000113966   ⟹   ENSRNOP00000094303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1087,852,890 - 87,861,589 (-)Ensembl
RefSeq Acc Id: NM_017009   ⟹   NP_058705
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,852,891 - 87,861,565 (-)NCBI
Rnor_6.01090,990,762 - 90,999,435 (-)NCBI
Rnor_5.01090,763,150 - 90,771,823 (-)NCBI
RGSC_v3.41092,059,881 - 92,068,555 (-)RGD
Celera1086,555,367 - 86,564,160 (-)RGD
Sequence:
RefSeq Acc Id: XM_039085178   ⟹   XP_038941106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21087,855,573 - 87,861,631 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_058705   ⟸   NM_017009
- UniProtKB: P47819 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032389   ⟸   ENSRNOT00000034401
RefSeq Acc Id: ENSRNOP00000076153   ⟸   ENSRNOT00000093167
RefSeq Acc Id: ENSRNOP00000076226   ⟸   ENSRNOT00000093266
RefSeq Acc Id: XP_038941106   ⟸   XM_039085178
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000094303   ⟸   ENSRNOT00000113966
Protein Domains
IF rod

Transcriptome

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

Promoters
RGD ID:13697798
Promoter ID:EPDNEW_R8323
Type:single initiation site
Name:Gfap_1
Description:glial fibrillary acidic protein
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01090,999,448 - 90,999,508EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (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)
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)
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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)
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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
LEXF2B/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
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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)
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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)
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/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
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)
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/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
WN/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:2679 AgrOrtholog
Ensembl Genes ENSRNOG00000002919 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000032389 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000076153 UniProtKB/TrEMBL
  ENSRNOP00000076226 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034401 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000093167 UniProtKB/TrEMBL
  ENSRNOT00000093266 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7315338 IMAGE-MGC_LOAD
InterPro GFAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_conserved UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24387 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105466 IMAGE-MGC_LOAD
NCBI Gene 24387 ENTREZGENE
PANTHER PTHR45652:SF9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Filament_head UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gfap PhenoGen
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2Q658_RAT UniProtKB/TrEMBL
  A0A1W2Q6C8_RAT UniProtKB/TrEMBL
  A1E251_RAT UniProtKB/TrEMBL
  A1E252_RAT UniProtKB/TrEMBL
  GFAP_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A7REI0 UniProtKB/Swiss-Prot
  Q7TQ31 UniProtKB/Swiss-Prot
  Q9R1Q3 UniProtKB/Swiss-Prot
  Q9Z2S0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Gfap  Glial fibrillary acidic protein      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease involved in wound healing 70384
gene_other marker for astrogilial cells 70384
gene_other marker for astrogilial cells 70740
gene_process major component of glial intermediate filament 70384
gene_process major component of glial intermediate filament 70740