Tfap2a (transcription factor AP-2 alpha) - Rat Genome Database

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Gene: Tfap2a (transcription factor AP-2 alpha) Rattus norvegicus
Analyze
Symbol: Tfap2a
Name: transcription factor AP-2 alpha
RGD ID: 1310267
Description: Enables sequence-specific DNA binding activity. Involved in several processes, including Schwann cell development; response to lipopolysaccharide; and response to water deprivation. Located in cytosol and nucleus. Human ortholog(s) of this gene implicated in branchiooculofacial syndrome. Orthologous to human TFAP2A (transcription factor AP-2 alpha); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: activating enhancer-binding protein 2 alpha; activating enhancer-binding protein 2-alpha; activator protein 2; AP-2 transcription factor; AP2-alpha; LOC306862; Tcfap2a; transcription factor AP-2, alpha; transcription factor AP-2-alpha
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21724,028,716 - 24,047,507 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1724,024,432 - 24,047,507 (+)Ensembl
Rnor_6.01724,653,342 - 24,670,457 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1724,654,902 - 24,670,457 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01726,596,839 - 26,634,214 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41730,017,580 - 30,034,852 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11730,020,346 - 30,035,192 (+)NCBI
Celera1723,700,225 - 23,715,767 (+)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dimethylhydrazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (ISO)
15-acetyldeoxynivalenol  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
butanal  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
calcitriol  (ISO)
carboplatin  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
clomiphene  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
cytarabine  (ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gefitinib  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
geraniol  (ISO)
hexestrol  (ISO)
ifosfamide  (ISO)
indinavir  (ISO)
kahweol  (ISO)
L-methionine  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
mercury dibromide  (ISO)
mestranol  (ISO)
methamphetamine  (EXP)
methotrexate  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
mitomycin C  (ISO)
N-[2-(4-bromocinnamylamino)ethyl]isoquinoline-5-sulfonamide  (ISO)
nickel subsulfide  (ISO)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paroxetine  (ISO)
phenylmercury acetate  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
picoxystrobin  (ISO)
pirinixic acid  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
rottlerin  (ISO)
SB 431542  (ISO)
sertraline  (ISO)
stavudine  (ISO)
streptozocin  (EXP)
temozolomide  (ISO)
testosterone  (ISO)
Tetrachlorobisphenol A  (ISO)
trichloroethene  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
troglitazone  (ISO)
tyrphostin AG 1478  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zidovudine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IBA)
anterior neuropore closure  (ISO)
basement membrane organization  (ISO)
bone morphogenesis  (ISO,ISS)
cellular response to iron ion  (ISO,ISS)
cornea development in camera-type eye  (ISO)
embryonic body morphogenesis  (ISO)
embryonic camera-type eye morphogenesis  (ISO)
embryonic cranial skeleton morphogenesis  (ISO,ISS)
embryonic forelimb morphogenesis  (ISO,ISS)
embryonic pattern specification  (ISO)
epidermis morphogenesis  (ISO)
eyelid development in camera-type eye  (ISO,ISS)
face morphogenesis  (ISO)
forebrain neuron development  (ISO)
forelimb morphogenesis  (ISO)
inner ear morphogenesis  (ISO,ISS)
keratinocyte development  (ISO)
kidney development  (ISO,ISS)
lens induction in camera-type eye  (ISO)
lens morphogenesis in camera-type eye  (ISO)
metanephric nephron development  (ISO)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of epidermal growth factor receptor signaling pathway  (ISO)
negative regulation of neuron apoptotic process  (ISO)
negative regulation of reactive oxygen species metabolic process  (ISO,ISS)
negative regulation of transcription by competitive promoter binding  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (ISO,ISS)
negative regulation of transcription, DNA-templated  (ISO)
nervous system development  (ISO)
neural crest cell development  (ISO)
neural tube closure  (ISO)
oculomotor nerve formation  (ISO,ISS)
optic cup structural organization  (ISO,ISS)
optic vesicle morphogenesis  (ISO,ISS)
outflow tract morphogenesis  (ISO)
positive regulation of bone mineralization  (ISO,ISS)
positive regulation of cell migration  (ISO)
positive regulation of gene expression  (ISO,ISS)
positive regulation of neuron apoptotic process  (ISO)
positive regulation of tooth mineralization  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IEA,IMP,ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO,ISS)
regulation of cell differentiation  (ISO)
regulation of cell population proliferation  (IBA)
regulation of neuron differentiation  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
regulation of transcription, DNA-templated  (IEA,ISO)
response to lipopolysaccharide  (IDA)
response to organic substance  (IEP)
response to water deprivation  (IEP)
retina layer formation  (ISO)
roof of mouth development  (ISO,ISS)
Schwann cell development  (IEP)
sensory organ development  (ISO)
sensory perception of sound  (ISO,ISS)
skeletal system morphogenesis  (ISO)
skin development  (ISO)
sympathetic nervous system development  (ISO)
trigeminal nerve development  (ISO,ISS)

Cellular Component
clathrin-coated pit  (ISO)
cytosol  (IDA)
nucleoplasm  (ISO)
nucleus  (IBA,IDA,IEA,ISO)

References

Additional References at PubMed
PMID:1998122   PMID:7555706   PMID:7559606   PMID:8321221   PMID:8622765   PMID:8622766   PMID:9520389   PMID:9811866   PMID:9858544   PMID:9918694   PMID:10068641   PMID:10571739  
PMID:10803593   PMID:10842061   PMID:10847586   PMID:11205881   PMID:11278550   PMID:11522791   PMID:11694877   PMID:11744375   PMID:12072434   PMID:15013802   PMID:15475956   PMID:16186342  
PMID:16236267   PMID:16449191   PMID:17670746   PMID:17984226   PMID:18224708   PMID:18718911   PMID:18723448   PMID:18824566   PMID:19115315   PMID:19463168   PMID:19578371   PMID:19750005  
PMID:19943855   PMID:20066163   PMID:20150232   PMID:20351096   PMID:20448150   PMID:20607706   PMID:20808827   PMID:21084835   PMID:21204207   PMID:21539825   PMID:21829553   PMID:22306374  
PMID:23393395   PMID:26437238   PMID:27053364   PMID:33264079  


Genomics

Comparative Map Data
Tfap2a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21724,028,716 - 24,047,507 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1724,024,432 - 24,047,507 (+)Ensembl
Rnor_6.01724,653,342 - 24,670,457 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1724,654,902 - 24,670,457 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01726,596,839 - 26,634,214 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41730,017,580 - 30,034,852 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11730,020,346 - 30,035,192 (+)NCBI
Celera1723,700,225 - 23,715,767 (+)NCBICelera
Cytogenetic Map17p12NCBI
TFAP2A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl610,393,186 - 10,419,659 (-)EnsemblGRCh38hg38GRCh38
GRCh38610,396,677 - 10,419,897 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37610,396,910 - 10,419,892 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36610,504,902 - 10,527,783 (-)NCBINCBI36hg18NCBI36
Build 34610,506,384 - 10,523,252NCBI
Celera611,625,394 - 11,648,276 (-)NCBI
Cytogenetic Map6p24.3NCBI
HuRef610,272,671 - 10,295,552 (-)NCBIHuRef
CHM1_1610,399,160 - 10,422,046 (-)NCBICHM1_1
Tfap2a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391340,867,278 - 40,891,715 (-)NCBIGRCm39mm39
GRCm39 Ensembl1340,868,778 - 40,891,852 (-)Ensembl
GRCm381340,713,802 - 40,738,238 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1340,715,302 - 40,738,376 (-)EnsemblGRCm38mm10GRCm38
MGSCv371340,811,044 - 40,829,192 (-)NCBIGRCm37mm9NCBIm37
MGSCv361340,727,706 - 40,745,894 (-)NCBImm8
Celera1341,797,334 - 41,815,714 (-)NCBICelera
Cytogenetic Map13A3.3NCBI
cM Map1320.01NCBI
Tfap2a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554653,882,549 - 3,898,929 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554653,877,896 - 3,900,259 (+)NCBIChiLan1.0ChiLan1.0
TFAP2A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1610,519,625 - 10,541,898 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0610,237,834 - 10,260,843 (-)NCBIMhudiblu_PPA_v0panPan3
TFAP2A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13510,157,043 - 10,180,484 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3510,157,882 - 10,180,270 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3510,170,458 - 10,197,631 (-)NCBI
ROS_Cfam_1.03510,260,835 - 10,284,005 (-)NCBI
UMICH_Zoey_3.13510,091,163 - 10,114,276 (-)NCBI
UNSW_CanFamBas_1.03510,131,471 - 10,154,557 (-)NCBI
UU_Cfam_GSD_1.03511,458,363 - 11,481,509 (-)NCBI
Tfap2a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494614,212,794 - 14,243,177 (+)NCBI
SpeTri2.0NW_0049365342,481,804 - 2,518,573 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TFAP2A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl77,221,656 - 7,244,477 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.177,221,654 - 7,244,626 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.277,534,956 - 7,556,586 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TFAP2A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11761,750,757 - 61,769,041 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604410,406,413 - 10,425,011 (-)NCBIVero_WHO_p1.0
Tfap2a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475615,413,950 - 15,436,037 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
TFAP2A  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21724,031,723 - 24,032,003 (+)MAPPERmRatBN7.2
Rnor_6.01724,654,659 - 24,654,938NCBIRnor6.0
Rnor_5.01726,596,596 - 26,596,875UniSTSRnor5.0
RGSC_v3.41730,017,337 - 30,017,616UniSTSRGSC3.4
Celera1723,699,982 - 23,700,261UniSTS
Cytogenetic Map17p12UniSTS
AI013304  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21724,046,528 - 24,046,645 (+)MAPPERmRatBN7.2
Rnor_6.01724,669,462 - 24,669,578NCBIRnor6.0
Rnor_5.01726,611,399 - 26,611,515UniSTSRnor5.0
RGSC_v3.41730,032,198 - 30,032,314UniSTSRGSC3.4
Celera1723,714,785 - 23,714,901UniSTS
RH 3.4 Map17280.8UniSTS
Cytogenetic Map17p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:359
Count of miRNA genes:194
Interacting mature miRNAs:221
Transcripts:ENSRNOT00000041960
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 nervous system renal system reproductive system respiratory system
High
Medium 17 6
Low 2 2 2 2 24 22 18
Below cutoff 2 27 4 2 2 2 29 7 17 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000041960   ⟹   ENSRNOP00000040925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,031,967 - 24,047,507 (+)Ensembl
Rnor_6.0 Ensembl1724,654,902 - 24,670,457 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000102035   ⟹   ENSRNOP00000078814
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,024,432 - 24,047,507 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103008   ⟹   ENSRNOP00000082537
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,029,869 - 24,047,507 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000105131   ⟹   ENSRNOP00000076636
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,029,746 - 24,047,507 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107954   ⟹   ENSRNOP00000088142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,030,646 - 24,047,507 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109680   ⟹   ENSRNOP00000081532
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,028,667 - 24,047,507 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110879   ⟹   ENSRNOP00000094618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1724,033,357 - 24,047,507 (+)Ensembl
RefSeq Acc Id: NM_001107345   ⟹   NP_001100815
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21724,031,967 - 24,047,507 (+)NCBI
Rnor_6.01724,654,902 - 24,670,457 (+)NCBI
Rnor_5.01726,596,839 - 26,634,214 (+)NCBI
RGSC_v3.41730,017,580 - 30,034,852 (+)RGD
Celera1723,700,225 - 23,715,767 (+)RGD
Sequence:
RefSeq Acc Id: XM_039095687   ⟹   XP_038951615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21724,028,716 - 24,046,727 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100815   ⟸   NM_001107345
- UniProtKB: G3V9A8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040925   ⟸   ENSRNOT00000041960
RefSeq Acc Id: XP_038951615   ⟸   XM_039095687
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000094618   ⟸   ENSRNOT00000110879
RefSeq Acc Id: ENSRNOP00000081532   ⟸   ENSRNOT00000109680
RefSeq Acc Id: ENSRNOP00000082537   ⟸   ENSRNOT00000103008
RefSeq Acc Id: ENSRNOP00000088142   ⟸   ENSRNOT00000107954
RefSeq Acc Id: ENSRNOP00000078814   ⟸   ENSRNOT00000102035
RefSeq Acc Id: ENSRNOP00000076636   ⟸   ENSRNOT00000105131
Protein Domains
TF_AP-2

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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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)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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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)
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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
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310267 AgrOrtholog
Ensembl Genes ENSRNOG00000015522 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000040925 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000041960 UniProtKB/TrEMBL
InterPro TF_AP2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_AP2_alpha_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_AP2_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306862 UniProtKB/TrEMBL
NCBI Gene 306862 ENTREZGENE
PANTHER PTHR10812 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TF_AP-2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tfap2a PhenoGen
PRINTS AP2ATNSCPFCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  AP2TNSCPFCT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt AP2A_RAT UniProtKB/Swiss-Prot
  G3V9A8 ENTREZGENE, UniProtKB/TrEMBL
  P58197 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-09 Tfap2a  transcription factor AP-2 alpha  Tcfap2a  transcription factor AP-2, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Tcfap2a  transcription factor AP-2, alpha   Tcfap2a_predicted  transcription factor AP-2, alpha (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Tcfap2a_predicted  transcription factor AP-2, alpha (predicted)      Symbol and Name status set to approved 70820 APPROVED