Gata6 (GATA binding protein 6) - Rat Genome Database

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Gene: Gata6 (GATA binding protein 6) Rattus norvegicus
Analyze
Symbol: Gata6
Name: GATA binding protein 6
RGD ID: 2666
Description: Enables cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of BMP signaling pathway; positive regulation of cardiac muscle cell apoptotic process; and regulation of transcription by RNA polymerase II. Located in nucleus. Biomarker of congenital diaphragmatic hernia and pulmonary hypertension. Human ortholog(s) of this gene implicated in adenocarcinoma (multiple); congenital heart disease (multiple); and pancreatic hypoplasia-diabetes-congenital heart disease syndrome. Orthologous to human GATA6 (GATA binding protein 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-ethoxyethanol; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: DNA-binding protein GATA-GT2; GATA-binding factor 6; GATA-binding protein 6; transcription factor GATA-6
RGD Orthologs
Human
Mouse
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
mRatBN7.2182,188,121 - 2,219,532 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl182,188,121 - 2,219,532 (+)Ensembl
Rnor_6.0182,415,821 - 2,447,087 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl182,416,552 - 2,446,338 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,436,500 - 2,465,966 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4182,504,264 - 2,534,648 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1182,504,263 - 2,534,648 (+)NCBI
Celera182,065,111 - 2,096,513 (+)NCBICelera
RH 3.4 Map1810.8RGD
Cytogenetic Map18p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3-methylcholanthrene  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (ISO)
8'-apo-beta,psi-caroten-8'-al  (ISO)
9-cis-retinoic acid  (ISO)
acetic acid  (ISO)
aflatoxin B1  (ISO)
all-trans-4-oxoretinoic acid  (ISO)
all-trans-4-oxoretinol  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (ISO)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
beta-carotene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bromochloroacetic acid  (ISO)
cadmium dichloride  (ISO)
calciol  (ISO)
carbon nanotube  (ISO)
CHIR 99021  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt dichloride  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
dichromium trioxide  (ISO)
diclofenac  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinous acid  (ISO)
divanadium pentaoxide  (ISO)
dorsomorphin  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
indometacin  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (EXP)
menadione  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
N-ethyl-N-nitrosourea  (ISO)
nickel atom  (ISO)
nickel dichloride  (ISO)
nicotine  (ISO)
nimesulide  (EXP)
nitrofen  (EXP)
NS-398  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (EXP)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
quercetin  (ISO)
quinolin-8-ol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (EXP)
sodium arsenite  (ISO)
sulindac sulfone  (ISO)
sunitinib  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (ISO)
trimellitic anhydride  (ISO)
uranium atom  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
warfarin  (ISO)
zinc atom  (EXP,ISO)
zinc sulfate  (EXP)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ formation  (IEA,ISO)
cardiac muscle cell differentiation  (IEA,ISO)
cardiac muscle hypertrophy in response to stress  (IEA,ISO)
cardiac muscle tissue development  (ISO)
cardiac vascular smooth muscle cell differentiation  (IEA,ISO)
cell fate commitment  (IBA)
cellular response to BMP stimulus  (IEA,ISO)
cellular response to gonadotropin stimulus  (IEA,ISO)
cellular response to hypoxia  (IEA,ISO)
club cell differentiation  (IEA,ISO)
endodermal cell differentiation  (ISO)
endodermal cell fate determination  (IEA,ISO)
epithelial cell differentiation  (IBA,ISO)
gene expression  (ISO)
heart contraction  (ISO)
in utero embryonic development  (IEA,ISO)
intestinal epithelial cell differentiation  (IEA,ISO)
liver development  (IEA,ISO)
lung saccule development  (IEA,ISO)
male gonad development  (IEA,ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of pri-miRNA transcription by RNA polymerase II  (IMP)
negative regulation of sebum secreting cell proliferation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
negative regulation of transcription, DNA-templated  (ISO)
negative regulation of transforming growth factor beta1 production  (IEA,ISO)
negative regulation of transforming growth factor beta2 production  (IEA,ISO)
odontogenesis of dentin-containing tooth  (IEP)
outflow tract septum morphogenesis  (IEA,ISO)
pancreas development  (ISO)
pancreatic A cell differentiation  (IEA,ISO)
phospholipid metabolic process  (IEA,ISO)
positive regulation of angiogenesis  (IEA,ISO)
positive regulation of apoptotic process  (IMP)
positive regulation of BMP signaling pathway  (IDA)
positive regulation of cardiac muscle cell apoptotic process  (IMP)
positive regulation of cardiac muscle cell proliferation  (IEA,ISO)
positive regulation of cardiac muscle myoblast proliferation  (IEA,ISO)
positive regulation of cardioblast differentiation  (IEA,ISO)
positive regulation of transcription by RNA polymerase II  (IEA,IMP,ISO)
positive regulation of transcription, DNA-templated  (IEA,ISO,ISS)
positive regulation of transforming growth factor beta activation  (IEA,ISO)
regulation of antimicrobial humoral response  (IEA,ISO)
regulation of cell cycle  (IEA,ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (IBA,IEA)
response to cAMP  (IEP)
response to estrogen  (IEA,ISO)
response to growth factor  (ISO)
response to retinoic acid  (IEA,ISO)
response to toxic substance  (IEP)
response to xenobiotic stimulus  (IEA,IEP,ISO)
sebaceous gland cell differentiation  (IEA,ISO)
sinoatrial node development  (ISO)
skin epidermis development  (IEA,ISO)
smooth muscle cell differentiation  (ISO)
tube morphogenesis  (IEA,ISO)
type B pancreatic cell differentiation  (IEA,ISO)
type II pneumocyte differentiation  (IEA,ISO)

Cellular Component
nuclear membrane  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,IEA,ISO)
transcription regulator complex  (IEA,ISO)

References

References - curated
1. Charron F, etal., Mol Cell Biol. 1999 Jun;19(6):4355-65.
2. Feng F, etal., Int J Clin Oncol. 2021 Apr;26(4):717-727. doi: 10.1007/s10147-020-01846-z. Epub 2021 Jan 2.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Ghatnekar A, etal., Am J Pathol. 2013 Jun;182(6):2391-406. doi: 10.1016/j.ajpath.2013.02.039. Epub 2013 Apr 11.
5. GOA data from the GO Consortium
6. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
7. Lan SJ, etal., J Craniofac Surg. 2016 Sep;27(6):1600-5. doi: 10.1097/SCS.0000000000002844.
8. Lepore JJ, etal., Arterioscler Thromb Vasc Biol. 2005 Feb;25(2):309-14. Epub 2004 Dec 9.
9. Lin X, etal., J Hum Genet. 2010 Oct;55(10):662-7. doi: 10.1038/jhg.2010.84. Epub 2010 Jul 15.
10. Liu B, etal., Exp Lung Res. 2009 Jun;35(5):411-26.
11. MGD data from the GO Consortium
12. Nakagawa R, etal., FEBS Lett. 1997 May 26;408(3):301-5.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Nemer G and Nemer M, Dev Biol. 2003 Feb 1;254(1):131-48.
15. OMIM Disease Annotation Pipeline
16. Online Mendelian Inheritance in Man, OMIM (TM).
17. Pavlov K, etal., Dig Liver Dis. 2015 Jan;47(1):73-80. doi: 10.1016/j.dld.2014.09.014. Epub 2014 Oct 16.
18. Potvin E, etal., Mol Cell Biol. 2010 Nov;30(22):5348-63. doi: 10.1128/MCB.00353-09. Epub 2010 Sep 20.
19. RGD automated data pipeline
20. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
21. RGD automated import pipeline for gene-chemical interactions
22. Roca-Alonso L, etal., Cell Death Dis. 2015 May 7;6:e1754. doi: 10.1038/cddis.2015.89.
23. Takayasu H, etal., J Pediatr Surg. 2008 Feb;43(2):362-6. doi: 10.1016/j.jpedsurg.2007.10.047.
24. Tamura S, etal., Proc Natl Acad Sci U S A 1993 Nov 15;90(22):10876-80.
25. Tan NY, etal., Circ Res. 2009 Aug 28;105(5):422-30. Epub 2009 Jul 23.
26. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
27. Tsuji S, etal., Nat Commun. 2014;5:3150. doi: 10.1038/ncomms4150.
28. Wada H, etal., J Biol Chem. 2000 Aug 18;275(33):25330-5.
29. Wang J, etal., DNA Cell Biol. 2012 Nov;31(11):1610-7. doi: 10.1089/dna.2012.1814. Epub 2012 Sep 28.
30. Xing X, etal., Biochem Biophys Res Commun. 2007 Nov 30;363(4):994-1000. Epub 2007 Oct 1.
31. Zheng GF, etal., Int J Mol Med. 2012 Jun;29(6):1065-71. doi: 10.3892/ijmm.2012.930. Epub 2012 Mar 7.
Additional References at PubMed
PMID:8083222   PMID:8183957   PMID:8660897   PMID:8889548   PMID:9231805   PMID:9566909   PMID:9593712   PMID:9738004   PMID:9832509   PMID:11733512   PMID:11889139   PMID:11914369  
PMID:12130579   PMID:12530967   PMID:12615657   PMID:14988427   PMID:15016828   PMID:15539431   PMID:15767668   PMID:15987774   PMID:16137232   PMID:16199866   PMID:16293227   PMID:16510470  
PMID:16621466   PMID:16887115   PMID:16912278   PMID:16940177   PMID:17164424   PMID:17626241   PMID:17785913   PMID:17848411   PMID:18177748   PMID:18303859   PMID:18400219   PMID:18671946  
PMID:18768929   PMID:19084512   PMID:19497978   PMID:19666519   PMID:20123909   PMID:20206639   PMID:20308546   PMID:20501701   PMID:20705924   PMID:20864106   PMID:21127043   PMID:21350014  
PMID:21828274   PMID:22695114   PMID:22750565   PMID:22824924   PMID:23824537   PMID:24036311   PMID:25015078   PMID:25068583   PMID:25332186   PMID:27511375   PMID:27756709   PMID:29859221  
PMID:31949236  


Genomics

Comparative Map Data
Gata6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2182,188,121 - 2,219,532 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl182,188,121 - 2,219,532 (+)Ensembl
Rnor_6.0182,415,821 - 2,447,087 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl182,416,552 - 2,446,338 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,436,500 - 2,465,966 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4182,504,264 - 2,534,648 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1182,504,263 - 2,534,648 (+)NCBI
Celera182,065,111 - 2,096,513 (+)NCBICelera
RH 3.4 Map1810.8RGD
Cytogenetic Map18p13NCBI
GATA6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1822,169,589 - 22,202,528 (+)EnsemblGRCh38hg38GRCh38
GRCh381822,169,589 - 22,202,528 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371819,749,550 - 19,782,491 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361818,003,414 - 18,036,225 (+)NCBINCBI36hg18NCBI36
Build 341818,003,413 - 18,036,225NCBI
Celera1816,555,843 - 16,588,650 (+)NCBI
Cytogenetic Map18q11.2NCBI
HuRef1816,596,234 - 16,629,323 (+)NCBIHuRef
CHM1_11819,676,426 - 19,709,511 (+)NCBICHM1_1
Gata6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391811,052,510 - 11,085,636 (+)NCBIGRCm39mm39
GRCm39 Ensembl1811,052,064 - 11,085,635 (+)Ensembl
GRCm381811,052,510 - 11,085,636 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1811,052,064 - 11,085,635 (+)EnsemblGRCm38mm10GRCm38
MGSCv371811,052,508 - 11,085,633 (+)NCBIGRCm37mm9NCBIm37
MGSCv361811,052,506 - 11,085,628 (+)NCBImm8
Celera1811,079,782 - 11,114,690 (+)NCBICelera
Cytogenetic Map18A1NCBI
cM Map185.63NCBI
GATA6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11819,046,132 - 19,078,398 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01815,411,764 - 15,444,402 (+)NCBIMhudiblu_PPA_v0panPan3
GATA6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1765,932,114 - 65,962,574 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha765,386,151 - 65,418,363 (-)NCBI
ROS_Cfam_1.0765,995,800 - 66,028,019 (-)NCBI
UMICH_Zoey_3.1765,662,867 - 65,695,075 (-)NCBI
UNSW_CanFamBas_1.0765,685,301 - 65,716,538 (-)NCBI
UU_Cfam_GSD_1.0765,985,181 - 66,017,395 (-)NCBI
Gata6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494461,971,676 - 62,001,620 (-)NCBI
SpeTri2.0NW_0049365501,814,336 - 1,844,399 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GATA6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6107,282,847 - 107,314,634 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16107,282,709 - 107,314,725 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2699,758,773 - 99,790,688 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GATA6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11858,312,328 - 58,345,472 (-)NCBI
ChlSab1.1 Ensembl1858,311,482 - 58,343,746 (-)Ensembl
Vero_WHO_p1.0NW_02366605033,085,880 - 33,119,030 (-)NCBI
Gata6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247709,772,818 - 9,799,837 (-)NCBI

Position Markers
RH94728  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2182,218,434 - 2,218,617 (+)MAPPERmRatBN7.2
Rnor_6.0182,445,990 - 2,446,172NCBIRnor6.0
Rnor_5.0182,465,618 - 2,465,800UniSTSRnor5.0
RGSC_v3.4182,534,300 - 2,534,482UniSTSRGSC3.4
Celera182,095,416 - 2,095,598UniSTS
RH 3.4 Map1810.8UniSTS
Cytogenetic Map18p13UniSTS
RH124933  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2182,218,920 - 2,219,067 (+)MAPPERmRatBN7.2
Rnor_6.0182,446,476 - 2,446,622NCBIRnor6.0
Rnor_5.0182,466,104 - 2,466,250UniSTSRnor5.0
RGSC_v3.4182,534,786 - 2,534,932UniSTSRGSC3.4
Celera182,095,902 - 2,096,048UniSTS
Cytogenetic Map18p13UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125758124Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125758124Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:240
Count of miRNA genes:171
Interacting mature miRNAs:181
Transcripts:ENSRNOT00000030726
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 43 16 8 8 14 33 11
Low 1 41 33 19 33 3 3 7 21 8 3
Below cutoff 5 8 65 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030726   ⟹   ENSRNOP00000036967
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl182,416,552 - 2,445,941 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000081399   ⟹   ENSRNOP00000070439
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl182,188,121 - 2,219,532 (+)Ensembl
Rnor_6.0 Ensembl182,416,871 - 2,446,338 (+)Ensembl
RefSeq Acc Id: NM_019185   ⟹   NP_062058
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2182,188,121 - 2,219,532 (+)NCBI
Rnor_6.0182,415,821 - 2,447,087 (+)NCBI
Rnor_5.0182,436,500 - 2,465,966 (+)NCBI
RGSC_v3.4182,504,264 - 2,534,648 (+)RGD
Celera182,065,111 - 2,096,513 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_062058 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA92577 (Get FASTA)   NCBI Sequence Viewer  
  EDL86681 (Get FASTA)   NCBI Sequence Viewer  
  P46153 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062058   ⟸   NM_019185
- UniProtKB: P46153 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070439   ⟸   ENSRNOT00000081399
RefSeq Acc Id: ENSRNOP00000036967   ⟸   ENSRNOT00000030726
Protein Domains
GATA-type

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)
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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)
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)
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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)
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)
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)
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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)
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)
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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)
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)
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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)
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)
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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)
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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
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
LEXF1A/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
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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
LEXF4/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
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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
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)
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
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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/OlalpcvMcwi (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
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)
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: 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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (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: 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)
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
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)
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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:2666 AgrOrtholog
Ensembl Genes ENSRNOG00000023433 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036967 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070439 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030726 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000081399 UniProtKB/TrEMBL
Gene3D-CATH 3.30.50.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GATA_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TF_GATA_4/5/6 UniProtKB/TrEMBL
  TF_GATA_6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transcription_factor_GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29300 UniProtKB/Swiss-Prot
NCBI Gene 29300 ENTREZGENE
PANTHER PTHR10071 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10071:SF23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GATA-N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Gata6 PhenoGen
PIRSF TF_GATA_4/5/6 UniProtKB/TrEMBL
PRINTS GATAZNFINGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GATA_ZN_FINGER_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GATA_ZN_FINGER_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_GATA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC217732
UniProt A0A0G2JXX6_RAT UniProtKB/TrEMBL
  F1M7P7_RAT UniProtKB/TrEMBL
  GATA6_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Gata6  GATA-binding protein 6      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains tandem zinc-finger domains 728607
gene_expression mRNA expressed in the gastric mucosa, and at lower levels in the intestine 728607