Gata1 (GATA binding protein 1) - Rat Genome Database

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Gene: Gata1 (GATA binding protein 1) Rattus norvegicus
Analyze
Symbol: Gata1
Name: GATA binding protein 1
RGD ID: 2663
Description: Enables chromatin binding activity and sequence-specific DNA binding activity. Involved in several processes, including Sertoli cell development; cellular response to cAMP; and cellular response to follicle-stimulating hormone stimulus. Located in nucleus. Biomarker of mental depression and polycythemia. Human ortholog(s) of this gene implicated in several diseases, including Down syndrome; X-linked recessive disease (multiple); bone marrow cancer (multiple); colon adenocarcinoma; and myeloid leukemia associated with Down Syndrome. Orthologous to human GATA1 (GATA binding protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Eryf1; erythroid transcription factor; GATA-1; GATA-binding factor 1; GATA-binding protein 1 (globin transcription factor 1); GF-1; LOC108348091; NF-E1 DNA-binding protein
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
mRatBN7.2X14,529,706 - 14,537,530 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,529,702 - 14,537,530 (+)Ensembl
Rnor_6.0X15,273,937 - 15,281,759 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,378,789 - 15,382,066 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,273,933 - 15,281,759 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,054,178 - 16,062,000 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,564,259 - 26,572,081 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,617,727 - 26,625,550 (+)NCBI
CeleraX14,614,331 - 14,622,295 (+)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
animal organ regeneration  (IDA)
basophil differentiation  (ISO)
cell development  (ISO)
cell fate commitment  (IBA)
cell-cell signaling  (ISO)
cellular response to cAMP  (IEP)
cellular response to follicle-stimulating hormone stimulus  (IEP)
cellular response to lipopolysaccharide  (IDA)
cellular response to thyroid hormone stimulus  (ISO)
dendritic cell differentiation  (ISO)
embryonic hemopoiesis  (ISO)
eosinophil differentiation  (ISO)
eosinophil fate commitment  (ISO)
erythrocyte development  (ISO)
erythrocyte differentiation  (ISO)
homeostasis of number of cells within a tissue  (ISO)
in utero embryonic development  (ISO)
male gonad development  (ISO)
megakaryocyte differentiation  (ISO)
myeloid cell differentiation  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of bone mineralization  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
negative regulation of transcription regulatory region DNA binding  (ISO)
platelet aggregation  (ISO)
platelet formation  (ISO)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of erythrocyte differentiation  (ISO)
positive regulation of mast cell degranulation  (IMP)
positive regulation of osteoblast proliferation  (ISO)
positive regulation of peptidyl-tyrosine phosphorylation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO,ISS)
regulation of definitive erythrocyte differentiation  (ISO)
regulation of glycoprotein biosynthetic process  (ISO)
regulation of primitive erythrocyte differentiation  (ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (TAS)
Sertoli cell development  (IEP)

Cellular Component

References

References - curated
1. Akimova T, etal., JCI Insight. 2017 Aug 17;2(16). pii: 94075. doi: 10.1172/jci.insight.94075. eCollection 2017 Aug 17.
2. Birger Y, etal., Blood. 2013 Aug 8;122(6):988-98. doi: 10.1182/blood-2012-10-460998. Epub 2013 May 29.
3. Choi M, etal., PLoS One. 2014 Oct 23;9(10):e109253. doi: 10.1371/journal.pone.0109253. eCollection 2014.
4. El Gazzar MA Inflamm Res. 2007 Aug;56(8):345-51.
5. Fadilah SA, etal., Leukemia. 2002 Aug;16(8):1563-5.
6. Freson K, etal., Blood. 2001 Jul 1;98(1):85-92.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. GOA data from the GO Consortium
9. Greene ME, etal., Blood Cells Mol Dis. 2003 Nov-Dec;31(3):351-6.
10. Ishijima Y, etal., Genes Cells. 2012 Apr;17(4):285-301. doi: 10.1111/j.1365-2443.2012.01588.x. Epub 2012 Mar 5.
11. Juskeviciute E, etal., BMC Genomics. 2008 Nov 6;9:527.
12. Kang HJ, etal., Nat Med. 2012 Aug 12. doi: 10.1038/nm.2886.
13. Li JP, etal., Zhonghua Xue Ye Xue Za Zhi. 2007 Aug;28(8):537-40.
14. Liu F, etal., Zhonghua Xue Ye Xue Za Zhi. 2016 Aug 14;37(8):696-701. doi: 10.3760/cma.j.issn.0253-2727.2016.08.013.
15. Liu YM, etal., Zhong Xi Yi Jie He Xue Bao. 2006 May;4(3):247-50.
16. Majewski IJ, etal., Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14146-51. Epub 2006 Sep 11.
17. Maratheftis CI, etal., Am J Hematol. 2007 Oct;82(10):887-92.
18. Matsuda K, etal., FEBS Lett 1994 Oct 24;353(3):269-72.
19. Mehaffey MG, etal., Blood. 2001 Nov 1;98(9):2681-8.
20. MGD data from the GO Consortium
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Nichols KE, etal., Nat Genet. 2000 Mar;24(3):266-70.
23. OMIM Disease Annotation Pipeline
24. Online Mendelian Inheritance in Man, OMIM (TM).
25. Onodera K, etal., J Biochem. 1997 Feb;121(2):251-63.
26. Peters I, etal., Target Oncol. 2015 Jun;10(2):267-75. doi: 10.1007/s11523-014-0335-8. Epub 2014 Sep 19.
27. RGD automated data pipeline
28. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
29. RGD automated import pipeline for gene-chemical interactions
30. RGD comprehensive gene curation
31. Shakib K, etal., Proteomics. 2005 Jul;5(11):2819-38.
32. Shimamoto T, etal., Blood. 1995 Oct 15;86(8):3173-80.
33. Shimizu R, etal., Mol Cell Biol. 2004 Dec;24(24):10814-25.
34. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
35. Vannucchi AM, etal., Am J Pathol. 2005 Sep;167(3):849-58.
36. Vannucchi AM, etal., Blood. 2002 Aug 15;100(4):1123-32.
37. Vannucchi AM, etal., Blood. 2005 May 1;105(9):3493-501. Epub 2005 Jan 21.
38. Yu C, etal., Blood. 2002 Sep 15;100(6):2040-5.
39. Yu J, etal., Mol Cell Biochem. 2019 Jul;457(1-2):191-199. doi: 10.1007/s11010-019-03523-w. Epub 2019 May 9.
40. Zhang Z, etal., Endocrinology. 2002 Mar;143(3):829-36.
Additional References at PubMed
PMID:1302015   PMID:1987478   PMID:2467208   PMID:7568185   PMID:7678994   PMID:7867497   PMID:7896801   PMID:7924983   PMID:8195185   PMID:8507862   PMID:8524811   PMID:8628290  
PMID:8901585   PMID:9139715   PMID:9230307   PMID:9233806   PMID:9427697   PMID:9576834   PMID:9787185   PMID:10773455   PMID:12023274   PMID:12045236   PMID:12483298   PMID:12609092  
PMID:14504093   PMID:15005853   PMID:15613485   PMID:15644435   PMID:15701726   PMID:15920471   PMID:15993847   PMID:17167422   PMID:17505015   PMID:18063754   PMID:19011221   PMID:19375645  
PMID:19398553   PMID:19411634   PMID:20133935   PMID:20855530   PMID:21245044   PMID:21436399   PMID:22235304   PMID:22835905   PMID:24245781  


Genomics

Comparative Map Data
Gata1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X14,529,706 - 14,537,530 (+)NCBImRatBN7.2
mRatBN7.2 EnsemblX14,529,702 - 14,537,530 (+)Ensembl
Rnor_6.0X15,273,937 - 15,281,759 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,378,789 - 15,382,066 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 EnsemblX15,273,933 - 15,281,759 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X16,054,178 - 16,062,000 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X26,564,259 - 26,572,081 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X26,617,727 - 26,625,550 (+)NCBI
CeleraX14,614,331 - 14,622,295 (+)NCBICelera
Cytogenetic MapXq12NCBI
GATA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX48,786,562 - 48,794,311 (+)EnsemblGRCh38hg38GRCh38
GRCh38X48,786,590 - 48,794,311 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X48,644,998 - 48,652,718 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X48,529,906 - 48,537,662 (+)NCBINCBI36hg18NCBI36
Build 34X48,401,209 - 48,408,964NCBI
CeleraX53,010,810 - 53,018,547 (-)NCBI
Cytogenetic MapXp11.23NCBI
HuRefX46,304,230 - 46,311,086 (+)NCBIHuRef
CHM1_1X48,676,125 - 48,683,862 (+)NCBICHM1_1
Gata1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X7,825,499 - 7,842,902 (-)NCBIGRCm39mm39
GRCm39 EnsemblX7,825,499 - 7,844,310 (-)Ensembl
GRCm38X7,959,260 - 7,976,663 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX7,959,260 - 7,978,071 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X7,536,386 - 7,544,941 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X7,116,219 - 7,124,774 (-)NCBImm8
CeleraX3,501,753 - 3,509,992 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.59NCBI
Gata1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955543334,061 - 342,061 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955543334,581 - 342,042 (+)NCBIChiLan1.0ChiLan1.0
GATA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X48,945,394 - 48,953,126 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX48,945,394 - 48,953,126 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X41,088,724 - 41,092,190 (+)NCBIMhudiblu_PPA_v0panPan3
GATA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X41,991,321 - 41,998,319 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX41,971,582 - 41,998,303 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX16,366,765 - 16,373,724 (+)NCBI
ROS_Cfam_1.0X42,127,527 - 42,134,488 (+)NCBI
UMICH_Zoey_3.1X42,113,779 - 42,120,737 (+)NCBI
UNSW_CanFamBas_1.0X42,102,035 - 42,108,995 (+)NCBI
UU_Cfam_GSD_1.0X42,196,190 - 42,203,150 (+)NCBI
Gata1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X34,488,565 - 34,510,496 (+)NCBI
SpeTri2.0NW_004936721742,862 - 750,843 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GATA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX42,898,442 - 42,905,976 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X42,898,431 - 42,905,939 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X47,745,326 - 47,752,876 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GATA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X45,912,638 - 45,920,415 (+)NCBI
ChlSab1.1 EnsemblX45,917,231 - 45,920,268 (+)Ensembl
Vero_WHO_p1.0NW_02366607611,392,674 - 11,400,428 (+)NCBI
Gata1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624893595,948 - 602,980 (+)NCBI

Position Markers
RH129447  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,537,012 - 14,537,210 (+)MAPPERmRatBN7.2
Rnor_6.0X15,382,055 - 15,382,252NCBIRnor6.0
Rnor_6.0X15,281,242 - 15,281,439NCBIRnor6.0
Rnor_5.0X16,163,290 - 16,163,487UniSTSRnor5.0
Rnor_5.0X16,061,483 - 16,061,680UniSTSRnor5.0
RGSC_v3.4X26,571,564 - 26,571,761UniSTSRGSC3.4
CeleraX14,621,778 - 14,621,975UniSTS
RH 3.4 MapX165.4UniSTS
Cytogenetic MapXq12UniSTS
RH130040  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,537,245 - 14,537,445 (+)MAPPERmRatBN7.2
Rnor_6.0X15,382,288 - 15,382,487NCBIRnor6.0
Rnor_6.0X15,281,475 - 15,281,674NCBIRnor6.0
Rnor_5.0X16,061,716 - 16,061,915UniSTSRnor5.0
Rnor_5.0X16,163,523 - 16,163,722UniSTSRnor5.0
RGSC_v3.4X26,571,797 - 26,571,996UniSTSRGSC3.4
CeleraX14,622,011 - 14,622,210UniSTS
Cytogenetic MapXq12UniSTS
Gata1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X14,533,837 - 14,534,724 (+)MAPPERmRatBN7.2
Rnor_6.0X15,378,880 - 15,379,766NCBIRnor6.0
Rnor_6.0X15,278,067 - 15,278,953NCBIRnor6.0
Rnor_5.0X16,058,308 - 16,059,194UniSTSRnor5.0
Rnor_5.0X16,160,115 - 16,161,001UniSTSRnor5.0
RGSC_v3.4X26,568,389 - 26,569,275UniSTSRGSC3.4
CeleraX14,618,603 - 14,619,489UniSTS
Cytogenetic MapXq12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:259
Count of miRNA genes:167
Interacting mature miRNAs:195
Transcripts:ENSRNOT00000029272
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 4 18 18 3 18
Low 16 6 6 8 6 11 10 31 3
Below cutoff 2 18 13 6 5 6 1 2 38 9 11 8 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029272   ⟹   ENSRNOP00000038111
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX15,378,789 - 15,382,066 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075082   ⟹   ENSRNOP00000067336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX14,529,702 - 14,537,530 (+)Ensembl
Rnor_6.0 EnsemblX15,273,933 - 15,281,759 (+)Ensembl
RefSeq Acc Id: NM_012764   ⟹   NP_036896
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X14,529,706 - 14,537,530 (+)NCBI
Rnor_6.0X15,273,937 - 15,281,759 (+)NCBI
Rnor_5.0X16,054,178 - 16,062,000 (+)NCBI
RGSC_v3.4X26,564,259 - 26,572,081 (+)RGD
CeleraX14,614,331 - 14,622,295 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_036896 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA02735 (Get FASTA)   NCBI Sequence Viewer  
  EDL83808 (Get FASTA)   NCBI Sequence Viewer  
  P43429 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036896   ⟸   NM_012764
- UniProtKB: P43429 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000038111   ⟸   ENSRNOT00000029272
RefSeq Acc Id: ENSRNOP00000067336   ⟸   ENSRNOT00000075082

Transcriptome

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


Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2663 AgrOrtholog
Ensembl Genes ENSRNOG00000025534 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00000047663 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000038111 UniProtKB/Swiss-Prot
  ENSRNOP00000067336 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000029272 UniProtKB/Swiss-Prot
  ENSRNOT00000075082 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.50.10 UniProtKB/Swiss-Prot
InterPro GATA-1 UniProtKB/Swiss-Prot
  Transcription_factor_GATA UniProtKB/Swiss-Prot
  Znf_GATA UniProtKB/Swiss-Prot
  Znf_NHR/GATA UniProtKB/Swiss-Prot
KEGG Report rno:25172 UniProtKB/Swiss-Prot
NCBI Gene 25172 ENTREZGENE
PANTHER PTHR10071 UniProtKB/Swiss-Prot
  PTHR10071:SF190 UniProtKB/Swiss-Prot
Pfam GATA UniProtKB/Swiss-Prot
PhenoGen Gata1 PhenoGen
PRINTS GATAZNFINGER UniProtKB/Swiss-Prot
PROSITE GATA_ZN_FINGER_1 UniProtKB/Swiss-Prot
  GATA_ZN_FINGER_2 UniProtKB/Swiss-Prot
SMART ZnF_GATA UniProtKB/Swiss-Prot
TIGR TC230471
UniProt GATA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Gata1  GATA binding protein 1  LOC108348091  erythroid transcription factor  Data Merged 737654 PROVISIONAL
2016-08-02 LOC108348091  erythroid transcription factor      Symbol and Name status set to provisional 70820 PROVISIONAL
2002-06-10 Gata1  GATA-binding protein 1 (globin transcription factor 1)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expressed in fetal liver 728595
gene_function binds DNA at the GAT(A/T) motif 728595
gene_process may be involved with transcriptional repression of serine dehydratase 728595