Mecp2 (methyl CpG binding protein 2) - Rat Genome Database

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Gene: Mecp2 (methyl CpG binding protein 2) Rattus norvegicus
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Symbol: Mecp2
Name: methyl CpG binding protein 2
RGD ID: 3075
Description: Enables several functions, including DNA binding activity; histone deacetylase binding activity; and promoter-specific chromatin binding activity. Involved in several processes, including nervous system development; positive regulation of dense core granule transport; and regulation of dendrite extension. Located in chromatin; cytosol; and nucleus. Part of protein-containing complex. Is active in glutamatergic synapse. Used to study Rett syndrome. Biomarker of hepatocellular carcinoma; transient cerebral ischemia; and visual epilepsy. Human ortholog(s) of this gene implicated in Rett syndrome; X-linked intellectual disability-psychosis-macroorchidism syndrome; autistic disorder; severe congenital encephalopathy due to MECP2 mutation; and syndromic X-linked intellectual disability Lubs type. Orthologous to human MECP2 (methyl-CpG binding protein 2); PARTICIPATES IN DNA modification pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: meCP-2 protein; methyl-CpG-binding protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Mecp2em1Sage  
Genetic Models: SD-Mecp2em1Sage
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,781,177 - 151,844,687 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX151,789,930 - 151,844,689 (-)Ensembl
Rnor_6.0X156,650,389 - 156,713,813 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,655,960 - 156,705,233 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,390,961 - 152,461,647 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,980,599 - 160,035,260 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X160,055,071 - 160,104,134 (-)NCBI
Celera1136,055,782 - 136,105,104 (+)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5-aza-2'-deoxycytidine  (EXP,ISO)
5-azacytidine  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alpha-pinene  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenous acid  (EXP)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bicuculline  (EXP,ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
butanal  (ISO)
C60 fullerene  (EXP)
carbon nanotube  (ISO)
cocaine  (EXP,ISO)
copper(II) sulfate  (ISO)
curcumin  (ISO)
diarsenic trioxide  (EXP)
dichlorine  (EXP)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
flavonoids  (EXP)
fluoxetine  (EXP)
formaldehyde  (EXP)
genistein  (ISO)
gentamycin  (ISO)
guggulsterone  (ISO)
homocysteine  (ISO)
L-methionine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP,ISO)
lead(2+)  (EXP,ISO)
melittin  (ISO)
methapyrilene  (ISO)
methylmercury chloride  (EXP)
mitomycin C  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethyl-N-nitrosourea  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (EXP,ISO)
paracetamol  (ISO)
paraquat  (ISO)
permethrin  (EXP)
phenobarbital  (EXP)
potassium chloride  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
trichostatin A  (ISO)
triclosan  (ISO)
tungsten  (ISO)
valproic acid  (EXP,ISO)
withaferin A  (ISO)
zebularine  (ISO)
zolpidem  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult locomotory behavior  (IEA,ISO)
associative learning  (ISO)
behavioral fear response  (IEA,ISO)
brain development  (ISO)
cardiolipin metabolic process  (IEA,ISO)
cellular biogenic amine metabolic process  (IEA,ISO)
cellular response to isoquinoline alkaloid  (IDA)
cellular response to potassium ion  (IDA)
cerebellum development  (IEA,IEP,ISO)
cerebral cortex development  (IEP)
chemical synaptic transmission  (ISO)
dendrite development  (IEA,ISO)
excitatory postsynaptic potential  (IEA,ISO)
glucocorticoid metabolic process  (IEA,ISO)
glutamine metabolic process  (IEA,ISO)
heart development  (IEP)
heterochromatin assembly  (IEA,ISO)
hippocampus development  (IEP)
histone acetylation  (IEA,ISO)
histone methylation  (IEA,ISO)
inositol metabolic process  (IEA,ISO)
learning  (ISO)
long-term memory  (IEA,ISO)
long-term synaptic potentiation  (IEA,ISO)
lung alveolus development  (IEP)
memory  (ISO)
mitotic spindle organization  (IEA,ISO)
multicellular organismal response to stress  (ISO)
negative regulation of angiogenesis  (IEA,ISO)
negative regulation of astrocyte differentiation  (IDA)
negative regulation of blood vessel endothelial cell migration  (IEA,ISO)
negative regulation of dendrite extension  (IMP)
negative regulation of dendritic spine development  (IMP)
negative regulation of gene expression  (IMP,ISO)
negative regulation of locomotion involved in locomotory behavior  (IMP)
negative regulation of neuron apoptotic process  (IEA,ISO)
negative regulation of primary miRNA processing  (IMP)
negative regulation of protein binding  (IMP)
negative regulation of respiratory gaseous exchange  (IMP)
negative regulation of smooth muscle cell differentiation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IDA,IMP,ISO)
negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation  (IEA,ISO)
negative regulation of transcription, DNA-templated  (IDA,ISO)
nervous system process involved in regulation of systemic arterial blood pressure  (IEA,ISO)
neuromuscular process  (ISO)
neuromuscular process controlling posture  (ISO)
neuron differentiation  (IEP,ISO)
neuron maturation  (IEA,ISO)
neuron projection development  (ISO)
olfactory bulb development  (IEP)
oligodendrocyte development  (IEP)
oligodendrocyte differentiation  (IEP)
phosphatidylcholine metabolic process  (IEA,ISO)
positive regulation of anterograde dense core granule transport  (IMP)
positive regulation of branching morphogenesis of a nerve  (IMP)
positive regulation of cell population proliferation  (IEA,ISO)
positive regulation of dendrite extension  (IMP)
positive regulation of dendritic spine development  (IMP)
positive regulation of DNA methylation  (IEA,ISO)
positive regulation of G2/M transition of mitotic cell cycle  (IEA,ISO)
positive regulation of gene expression  (IMP)
positive regulation of histone H3-K9 trimethylation  (IEA,ISO)
positive regulation of microtubule nucleation  (IEA,ISO)
positive regulation of retrograde dense core granule transport  (IMP)
positive regulation of synaptic plasticity  (IMP)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
post-embryonic development  (IEA,ISO)
principal sensory nucleus of trigeminal nerve development  (IEP)
proprioception  (IEA,ISO)
protein localization  (IEA,ISO)
regulation of action potential firing threshold  (IMP)
regulation of DNA methylation  (IEP,IMP)
regulation of gene expression  (ISO)
regulation of gene expression by genetic imprinting  (IEA,ISO)
regulation of gene expression, epigenetic  (ISO)
regulation of histone H3-K9 methylation  (ISO)
regulation of respiratory gaseous exchange by nervous system process  (IEA,ISO)
regulation of synapse organization  (IDA,IMP)
regulation of synaptic plasticity  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
respiratory gaseous exchange by respiratory system  (IEA,ISO)
response to cocaine  (IDA,IEP)
response to estradiol  (IEP)
response to hypoxia  (IEA,ISO)
response to ionizing radiation  (IEP)
response to lead ion  (IEP)
response to organic cyclic compound  (IEP)
response to other organism  (IEA,ISO)
sensory perception of pain  (IEA,ISO)
social behavior  (IEA,IMP,ISO)
spinal cord development  (IEP)
startle response  (IEA,ISO)
striatum development  (IEP)
synapse assembly  (IEA,ISO)
thalamus development  (IEP)
triglyceride metabolic process  (ISO)
ventricular system development  (IEA,ISO)
visual learning  (IEA,ISO)

Cellular Component
centrosome  (IEA,ISO)
chromatin  (IDA)
cytoplasm  (ISO)
cytosol  (IDA,IEA,ISO)
glutamatergic synapse  (IDA,IMP)
heterochromatin  (IBA,IEA,ISO)
nucleoplasm  (IEA,ISO,TAS)
nucleus  (IBA,IDA,ISO)
postsynapse  (IEA)
protein-containing complex  (IDA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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17. GOA data from the GO Consortium
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33. MGD data from the GO Consortium
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39. NCBI rat LocusLink and RefSeq merged data July 26, 2002
40. OMIM Disease Annotation Pipeline
41. Patterson KC, etal., Hum Mol Genet. 2016 Aug 1;25(15):3303-3320. doi: 10.1093/hmg/ddw179. Epub 2016 Jun 21.
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45. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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Additional References at PubMed
PMID:8563762   PMID:10888872   PMID:11441023   PMID:11809720   PMID:12949043   PMID:14519686   PMID:14593184   PMID:15006690   PMID:15034150   PMID:15322089   PMID:15342650   PMID:15345242  
PMID:15519245   PMID:15608638   PMID:15757975   PMID:15939091   PMID:15975715   PMID:16087343   PMID:16199017   PMID:16354910   PMID:16399702   PMID:16467389   PMID:16763620   PMID:16782889  
PMID:17046689   PMID:17050729   PMID:17108082   PMID:17237885   PMID:17532643   PMID:17544925   PMID:17546630   PMID:17553988   PMID:17920015   PMID:17997046   PMID:18203756   PMID:18295506  
PMID:18321864   PMID:18334558   PMID:18511691   PMID:18550052   PMID:18571096   PMID:18952054   PMID:19225110   PMID:19382685   PMID:19692427   PMID:20211261   PMID:21435439   PMID:21782149  
PMID:22056649   PMID:22369085   PMID:22658674   PMID:22664934   PMID:22848609   PMID:23200852   PMID:23333245   PMID:23935992   PMID:23960241   PMID:23980619   PMID:24269336   PMID:24936739  
PMID:25409090   PMID:25511996   PMID:25527496   PMID:25617893   PMID:25716866   PMID:25722434   PMID:26093272   PMID:26239616   PMID:26511729   PMID:26842955   PMID:26975406   PMID:27245166  
PMID:27312406   PMID:27350269   PMID:27365498   PMID:27995568   PMID:28074855   PMID:28573530   PMID:28655627   PMID:29090669   PMID:29155278   PMID:29286317   PMID:29476059   PMID:29540297  
PMID:29738885   PMID:29992497   PMID:30053369   PMID:30137367   PMID:31398393   PMID:32634579   PMID:33932163  


Genomics

Comparative Map Data
Mecp2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X151,781,177 - 151,844,687 (-)NCBImRatBN7.2
mRatBN7.2 EnsemblX151,789,930 - 151,844,689 (-)Ensembl
Rnor_6.0X156,650,389 - 156,713,813 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,655,960 - 156,705,233 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,390,961 - 152,461,647 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X159,980,599 - 160,035,260 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X160,055,071 - 160,104,134 (-)NCBI
Celera1136,055,782 - 136,105,104 (+)NCBICelera
Cytogenetic MapXq37NCBI
MECP2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX154,021,573 - 154,137,103 (-)EnsemblGRCh38hg38GRCh38
GRCh38X154,021,573 - 154,097,717 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X153,287,024 - 153,363,174 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X152,940,458 - 153,016,323 (-)NCBINCBI36hg18NCBI36
Build 34X152,808,110 - 152,883,976NCBI
CeleraX153,520,969 - 153,596,868 (-)NCBI
Cytogenetic MapXq28NCBI
HuRefX141,928,231 - 142,007,659 (-)NCBIHuRef
CHM1_1X153,161,670 - 153,237,718 (-)NCBICHM1_1
Mecp2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,070,198 - 73,129,296 (-)NCBIGRCm39mm39
GRCm39 EnsemblX73,070,198 - 73,178,969 (-)Ensembl
GRCm38X74,026,592 - 74,085,690 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,026,592 - 74,135,363 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X71,272,160 - 71,330,975 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X70,279,550 - 70,338,313 (-)NCBImm8
CeleraX65,279,211 - 65,338,021 (-)NCBICelera
Cytogenetic MapXA7.3NCBI
cM MapX37.63NCBI
Mecp2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955580679,109 - 735,288 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955580674,014 - 737,586 (-)NCBIChiLan1.0ChiLan1.0
MECP2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X153,458,248 - 153,527,854 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX153,465,204 - 153,527,854 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X143,571,864 - 143,647,192 (-)NCBIMhudiblu_PPA_v0panPan3
MECP2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X121,866,721 - 121,876,088 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX121,873,218 - 121,932,994 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX107,201,895 - 107,204,829 (-)NCBI
ROS_Cfam_1.0X125,014,436 - 125,017,609 (-)NCBI
UMICH_Zoey_3.1X120,783,667 - 120,786,824 (-)NCBI
UNSW_CanFamBas_1.0X123,299,346 - 123,302,280 (-)NCBI
UU_Cfam_GSD_1.0X123,060,405 - 123,063,561 (-)NCBI
Mecp2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X119,165,167 - 119,228,780 (-)NCBI
SpeTri2.0NW_004936809902,938 - 967,771 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MECP2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX124,735,656 - 124,789,110 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X124,735,523 - 124,789,063 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X142,295,001 - 142,349,438 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MECP2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X128,445,028 - 128,519,892 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 EnsemblX128,453,577 - 128,455,785 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606566,318,831 - 66,395,535 (-)NCBIVero_WHO_p1.0
Mecp2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624946620,581 - 685,339 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
BE114216  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,791,231 - 151,791,428 (-)MAPPERmRatBN7.2
Rnor_6.0X156,703,562 - 156,703,758NCBIRnor6.0
Rnor_5.01152,451,396 - 152,451,592UniSTSRnor5.0
RGSC_v3.4X159,981,891 - 159,982,087UniSTSRGSC3.4
Celera1136,103,616 - 136,103,812UniSTS
Cytogenetic MapXq37UniSTS
Mecp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,788,800 - 151,790,347 (-)MAPPERmRatBN7.2
Rnor_6.0X156,704,643 - 156,706,189NCBIRnor6.0
Rnor_5.01152,452,477 - 152,454,023UniSTSRnor5.0
RGSC_v3.4X159,979,460 - 159,981,006UniSTSRGSC3.4
Celera1136,104,697 - 136,106,243UniSTS
Cytogenetic MapXq37UniSTS
REN88597  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,789,797 - 151,790,042 (-)MAPPERmRatBN7.2
Rnor_6.0X156,704,948 - 156,705,192NCBIRnor6.0
Rnor_5.01152,452,782 - 152,453,026UniSTSRnor5.0
RGSC_v3.4X159,980,457 - 159,980,701UniSTSRGSC3.4
Celera1136,105,002 - 136,105,246UniSTS
Cytogenetic MapXq37UniSTS
REN88598  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,789,984 - 151,790,233 (-)MAPPERmRatBN7.2
Rnor_6.0X156,704,757 - 156,705,005NCBIRnor6.0
Rnor_5.01152,452,591 - 152,452,839UniSTSRnor5.0
RGSC_v3.4X159,980,644 - 159,980,892UniSTSRGSC3.4
Celera1136,104,811 - 136,105,059UniSTS
Cytogenetic MapXq37UniSTS
REN88847  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,838,647 - 151,838,884 (-)MAPPERmRatBN7.2
Rnor_6.0X156,656,111 - 156,656,347NCBIRnor6.0
Rnor_5.01152,403,946 - 152,404,182UniSTSRnor5.0
RGSC_v3.4X160,029,302 - 160,029,538UniSTSRGSC3.4
Celera1136,055,934 - 136,056,170UniSTS
Cytogenetic MapXq37UniSTS
Mecp2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,790,522 - 151,790,830 (-)MAPPERmRatBN7.2
Rnor_6.0X156,704,160 - 156,704,467NCBIRnor6.0
Rnor_5.01152,451,994 - 152,452,301UniSTSRnor5.0
RGSC_v3.4X159,981,182 - 159,981,489UniSTSRGSC3.4
Celera1136,104,214 - 136,104,521UniSTS
Cytogenetic MapXq37UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat


Genetic Models
This gene Mecp2 is modified in the following models/strains
miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
Mir132rno-miR-132-3pMirtarbaseexternal_infoWestern blotFunctional MTI17994015

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:84
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000056327
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 1 26 19 4 19 4 1 1 74 25 34 11 1
Low 2 17 38 37 37 7 10 10 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000085723   ⟹   ENSRNOP00000069913
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,789,940 - 151,839,036 (-)Ensembl
Rnor_6.0 EnsemblX156,655,960 - 156,705,233 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106335   ⟹   ENSRNOP00000094658
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,789,930 - 151,844,689 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000118226   ⟹   ENSRNOP00000088700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,789,930 - 151,792,256 (-)Ensembl
RefSeq Acc Id: NM_022673   ⟹   NP_073164
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,789,940 - 151,844,604 (-)NCBI
Rnor_6.0X156,650,389 - 156,705,050 (+)NCBI
Rnor_5.01152,390,961 - 152,461,647 (+)NCBI
RGSC_v3.4X159,980,599 - 160,035,260 (-)RGD
Celera1136,055,782 - 136,105,104 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006229567   ⟹   XP_006229629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,781,177 - 151,844,414 (-)NCBI
Rnor_6.0X156,655,516 - 156,713,813 (+)NCBI
Rnor_5.01152,390,961 - 152,461,647 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601935   ⟹   XP_017457424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,781,177 - 151,844,413 (-)NCBI
Rnor_6.0X156,655,516 - 156,713,813 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099534   ⟹   XP_038955462
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X151,781,177 - 151,844,687 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_073164   ⟸   NM_022673
- UniProtKB: Q00566 (UniProtKB/Swiss-Prot),   A0A0G2JWK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006229629   ⟸   XM_006229567
- Peptide Label: isoform X2
- UniProtKB: Q00566 (UniProtKB/Swiss-Prot),   A0A0G2JWK2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457424   ⟸   XM_017601935
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSRNOP00000069913   ⟸   ENSRNOT00000085723
RefSeq Acc Id: XP_038955462   ⟸   XM_039099534
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000094658   ⟸   ENSRNOT00000106335
RefSeq Acc Id: ENSRNOP00000088700   ⟸   ENSRNOT00000118226
Protein Domains
MBD

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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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)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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