Yy1 (YY1 transcription factor) - Rat Genome Database

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Gene: Yy1 (YY1 transcription factor) Rattus norvegicus
Analyze
Symbol: Yy1
Name: YY1 transcription factor
RGD ID: 3982
Description: Enables sequence-specific DNA binding activity. Involved in several processes, including cellular response to interleukin-1; negative regulation of cell growth involved in cardiac muscle cell development; and regulation of transcription by RNA polymerase II. Located in cytoplasm and nuclear matrix. Part of transcription regulator complex. Used to study type 1 diabetes mellitus. Biomarker of type 1 diabetes mellitus. Human ortholog(s) of this gene implicated in congestive heart failure. Orthologous to human YY1 (YY1 transcription factor); PARTICIPATES IN INO80 family mediated chromatin remodeling pathway; mTOR signaling pathway; Notch signaling pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene; 2-ethoxyethanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: NF-E1; NMP-1; NMP1; transcriptional repressor protein YY1; UCRBP
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
mRatBN7.26127,706,739 - 127,731,907 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6127,707,596 - 127,732,747 (+)Ensembl
Rnor_6.06132,702,443 - 132,726,848 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6132,702,448 - 132,727,046 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06141,872,505 - 141,896,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46133,132,419 - 133,156,686 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16133,138,605 - 133,162,873 (+)NCBI
Celera6125,273,530 - 125,282,803 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-arachidonoylglycerol  (ISO)
2-ethoxyethanol  (EXP)
2-methoxyethanol  (EXP)
2-methylcholine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (ISO)
acrolein  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
AM-251  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
artesunate  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (ISO)
cadmium sulfate  (ISO)
calyculin a  (ISO)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
decabromodiphenyl ether  (EXP)
diarsenic trioxide  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
enzyme inhibitor  (ISO)
ethanol  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
isoprenaline  (ISO)
ketamine  (EXP)
L-methionine  (ISO)
lead diacetate  (EXP)
lead(II) chloride  (ISO)
manganese atom  (EXP)
manganese(0)  (EXP)
melatonin  (ISO)
methapyrilene  (ISO)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenethyl caffeate  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
potassium chloride  (ISO)
rotenone  (EXP)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
thioacetamide  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior/posterior pattern specification  (ISO)
B cell differentiation  (ISO)
camera-type eye morphogenesis  (ISO)
cell development  (ISO)
cellular response to DNA damage stimulus  (ISO)
cellular response to interleukin-1  (IDA)
cellular response to UV  (ISO)
chromatin remodeling  (ISO)
chromosome organization  (ISO)
double-strand break repair via homologous recombination  (ISO)
gene expression  (ISO)
immunoglobulin heavy chain V-D-J recombination  (ISO)
negative regulation of cell growth involved in cardiac muscle cell development  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of interferon-beta production  (ISO)
negative regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
negative regulation of transcription by RNA polymerase II  (IMP,ISO)
nucleosome mobilization  (ISO)
positive regulation of DNA repair  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of telomere maintenance in response to DNA damage  (ISO)
positive regulation of transcription by RNA polymerase II  (IMP)
positive regulation of transcription, DNA-templated  (ISO)
regulation of cell cycle  (IEA,ISO)
regulation of chromosome organization  (ISO)
regulation of DNA repair  (ISO)
regulation of DNA replication  (IEA,ISO)
regulation of DNA strand elongation  (ISO)
regulation of embryonic development  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (IDA,ISO)
response to prostaglandin F  (IEP)
response to UV-C  (ISO)
RNA localization  (ISO)
spermatogenesis  (ISO)
telomere maintenance  (IEA,ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Beck K, etal., Circ Res. 2010 Dec 10;107(12):1490-7. doi: 10.1161/CIRCRESAHA.110.231985. Epub 2010 Oct 28.
2. Bergad PL, etal., J Biol Chem. 2000 Mar 17;275(11):8114-20.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Karki P, etal., Mol Cell Biol. 2014 Apr;34(7):1280-9. doi: 10.1128/MCB.01176-13. Epub 2014 Jan 27.
6. Kloting N and Kloting I, Mol Genet Metab. 2004 Jul;82(3):255-9.
7. Kloting N, etal., Diabetes Metab Res Rev. 2005 May-Jun;21(3):281-7.
8. Lindenmuth DM, etal., J Cell Biochem. 1997 Jul 1;66(1):123-32.
9. Mariner PD, etal., Biochem Biophys Res Commun. 2005 Jan 7;326(1):79-86.
10. MGD data from the GO Consortium
11. Mizuno D, etal., Biochim Biophys Acta 2003 Jun 19;1627(2-3):121-8.
12. Nackley AC, etal., Endocrinology 2002 Mar;143(3):1085-96.
13. Nowak K, etal., J Neurochem. 2006 Mar;96(6):1696-707.
14. Patten M, etal., J Mol Cell Cardiol. 2000 Jul;32(7):1341-52.
15. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Santiago FS, etal., J Biol Chem 2001 Nov 2;276(44):41143-9.
20. Sucharov CC, etal., J Biol Chem. 2003 Aug 15;278(33):31233-9. Epub 2003 May 16.
21. Sucharov CC, etal., Mol Biol Cell. 2008 Oct;19(10):4141-53. doi: 10.1091/mbc.E07-12-1217. Epub 2008 Jul 16.
22. Watanabe S and Peterson CL, Cold Spring Harb Symp Quant Biol. 2010;75:35-42. doi: 10.1101/sqb.2010.75.063. Epub 2011 Apr 18.
Additional References at PubMed
PMID:9857059   PMID:10791971   PMID:11861914   PMID:12527199   PMID:12723621   PMID:15161869   PMID:15329343   PMID:15369764   PMID:15574595   PMID:16099430   PMID:16260628   PMID:16624538  
PMID:17001316   PMID:17107999   PMID:17556661   PMID:17702849   PMID:18026119   PMID:18584324   PMID:18940814   PMID:19139378   PMID:19786570   PMID:20720167   PMID:20843790   PMID:21303910  
PMID:21729784   PMID:22005459   PMID:22065573   PMID:23531880   PMID:23555743   PMID:23942234   PMID:24101522   PMID:24137001   PMID:24675724   PMID:26269591   PMID:26658965   PMID:28065881  
PMID:30998979   PMID:32590621   PMID:33300076   PMID:33498722  


Genomics

Comparative Map Data
Yy1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26127,706,739 - 127,731,907 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl6127,707,596 - 127,732,747 (+)Ensembl
Rnor_6.06132,702,443 - 132,726,848 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6132,702,448 - 132,727,046 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06141,872,505 - 141,896,924 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46133,132,419 - 133,156,686 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16133,138,605 - 133,162,873 (+)NCBI
Celera6125,273,530 - 125,282,803 (+)NCBICelera
Cytogenetic Map6q32NCBI
YY1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl14100,238,298 - 100,282,788 (+)EnsemblGRCh38hg38GRCh38
GRCh3814100,239,144 - 100,282,788 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3714100,705,481 - 100,749,125 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361499,774,855 - 99,814,557 (+)NCBINCBI36hg18NCBI36
Build 341499,774,854 - 99,814,557NCBI
Celera1480,759,739 - 80,799,431 (+)NCBI
Cytogenetic Map14q32.2NCBI
HuRef1480,888,079 - 80,926,725 (+)NCBIHuRef
CHM1_114100,642,915 - 100,683,150 (+)NCBICHM1_1
Yy1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912108,758,841 - 108,786,074 (+)NCBIGRCm39mm39
GRCm39 Ensembl12108,758,899 - 108,786,074 (+)Ensembl
GRCm3812108,792,945 - 108,820,148 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12108,792,973 - 108,820,148 (+)EnsemblGRCm38mm10GRCm38
MGSCv3712110,031,521 - 110,054,842 (+)NCBIGRCm37mm9NCBIm37
MGSCv3612109,241,118 - 109,264,439 (+)NCBImm8
Celera12110,029,534 - 110,052,930 (+)NCBICelera
Cytogenetic Map12F1NCBI
cM Map1259.58NCBI
Yy1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543821,341,374 - 21,377,674 (+)NCBIChiLan1.0ChiLan1.0
YY1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.114100,173,287 - 100,217,651 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01480,859,491 - 80,903,651 (+)NCBIMhudiblu_PPA_v0panPan3
YY1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1868,539,511 - 68,572,796 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl868,539,353 - 68,568,058 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha868,058,331 - 68,091,508 (+)NCBI
ROS_Cfam_1.0868,823,410 - 68,856,669 (+)NCBI
UMICH_Zoey_3.1868,485,332 - 68,518,533 (+)NCBI
UNSW_CanFamBas_1.0868,551,498 - 68,584,736 (+)NCBI
UU_Cfam_GSD_1.0868,948,873 - 68,982,099 (+)NCBI
Yy1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244086406,137,064 - 6,171,061 (-)NCBI
SpeTri2.0NW_0049366043,911,407 - 3,945,405 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YY1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl7121,131,917 - 121,170,697 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.17121,132,168 - 121,170,699 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.27128,602,231 - 128,613,935 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YY1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12478,199,172 - 78,243,081 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2478,199,039 - 78,237,165 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605365,338,296 - 65,383,353 (+)NCBIVero_WHO_p1.0
Yy1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247343,846,753 - 3,875,294 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
AW488674  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,734,241 - 127,734,334 (+)MAPPERmRatBN7.2
Rnor_6.06132,729,183 - 132,729,275NCBIRnor6.0
Rnor_5.06141,899,259 - 141,899,351UniSTSRnor5.0
RGSC_v3.46133,159,021 - 133,159,113UniSTSRGSC3.4
Celera6125,285,138 - 125,285,230UniSTS
Cytogenetic Map6q32UniSTS
RH131280  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,706,741 - 127,706,961 (+)MAPPERmRatBN7.2
Rnor_6.06132,701,686 - 132,701,905NCBIRnor6.0
Rnor_5.06141,871,762 - 141,871,981UniSTSRnor5.0
RGSC_v3.46133,131,523 - 133,131,742UniSTSRGSC3.4
Celera6125,258,019 - 125,258,238UniSTS
Cytogenetic Map6q32UniSTS
RH139545  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,734,146 - 127,734,334 (+)MAPPERmRatBN7.2
Rnor_6.06132,729,088 - 132,729,275NCBIRnor6.0
Rnor_5.06141,899,164 - 141,899,351UniSTSRnor5.0
RGSC_v3.46133,158,926 - 133,159,113UniSTSRGSC3.4
Celera6125,285,043 - 125,285,230UniSTS
RH 3.4 Map6788.1UniSTS
Cytogenetic Map6q32UniSTS
RH140410  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,705,978 - 127,706,172 (+)MAPPERmRatBN7.2
Rnor_6.06132,700,923 - 132,701,116NCBIRnor6.0
Rnor_5.06141,870,999 - 141,871,192UniSTSRnor5.0
RGSC_v3.46133,130,760 - 133,130,953UniSTSRGSC3.4
Celera6125,257,256 - 125,257,449UniSTS
RH 3.4 Map6787.5UniSTS
Cytogenetic Map6q32UniSTS
AI231795  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,736,071 - 127,736,204 (+)MAPPERmRatBN7.2
Rnor_6.06132,731,013 - 132,731,145NCBIRnor6.0
Rnor_5.06141,901,089 - 141,901,221UniSTSRnor5.0
RGSC_v3.46133,160,851 - 133,160,983UniSTSRGSC3.4
Celera6125,286,968 - 125,287,100UniSTS
RH 3.4 Map6787.0UniSTS
Cytogenetic Map6q32UniSTS
G36215  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,722,669 - 127,722,765 (+)MAPPERmRatBN7.2
Rnor_6.06132,717,611 - 132,717,706NCBIRnor6.0
Rnor_5.06141,887,687 - 141,887,782UniSTSRnor5.0
RGSC_v3.46133,147,449 - 133,147,544UniSTSRGSC3.4
Celera6125,273,566 - 125,273,661UniSTS
Cytogenetic Map6q32UniSTS
PMC84716P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26127,707,884 - 127,708,096 (+)MAPPERmRatBN7.2
Rnor_6.06132,702,828 - 132,703,039NCBIRnor6.0
Rnor_5.06141,872,904 - 141,873,115UniSTSRnor5.0
RGSC_v3.46133,132,666 - 133,132,877UniSTSRGSC3.4
Cytogenetic Map6q32UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)672202632130729475Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)672202632130919985Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)672227641130729205Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)672227641130729205Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)684130881129130881Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)685140138130140138Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)685140138130140138Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)693701310128713626Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
1331797Bp213Blood pressure QTL 2133.291arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6104085867128713626Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1298087Iddm18Insulin dependent diabetes mellitus QTL 180.0001urine glucose amount (VT:0001758)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)6116506292130245370Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2312560Pur20Proteinuria QTL 202.10.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6125628133137801795Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:39
Count of miRNA genes:33
Interacting mature miRNAs:39
Transcripts:ENSRNOT00000005743
Prediction methods: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 3 43 57 41 19 41 8 10 74 35 41 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005743   ⟹   ENSRNOP00000005743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6127,707,596 - 127,731,999 (+)Ensembl
Rnor_6.0 Ensembl6132,702,448 - 132,727,046 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000097604   ⟹   ENSRNOP00000089643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl6127,707,596 - 127,732,747 (+)Ensembl
RefSeq Acc Id: NM_173290   ⟹   NP_775412
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26127,707,638 - 127,731,907 (+)NCBI
Rnor_6.06132,702,581 - 132,726,848 (+)NCBI
Rnor_5.06141,872,505 - 141,896,924 (+)NCBI
RGSC_v3.46133,132,419 - 133,156,686 (+)RGD
Celera6125,273,530 - 125,282,803 (+)RGD
Sequence:
RefSeq Acc Id: XM_006240537   ⟹   XP_006240599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26127,706,739 - 127,730,923 (+)NCBI
Rnor_6.06132,702,443 - 132,725,702 (+)NCBI
Rnor_5.06141,872,505 - 141,896,924 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_775412   ⟸   NM_173290
- UniProtKB: Q8CHJ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240599   ⟸   XM_006240537
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000005743   ⟸   ENSRNOT00000005743
RefSeq Acc Id: ENSRNOP00000089643   ⟸   ENSRNOT00000097604
Protein Domains
C2H2-type

Transcriptome

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

Promoters
RGD ID:13694821
Promoter ID:EPDNEW_R5345
Type:initiation region
Name:Yy1_1
Description:YY1 transcription factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06132,702,480 - 132,702,540EPDNEW

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)
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)
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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)
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)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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)
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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)
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)
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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)
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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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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:3982 AgrOrtholog
Ensembl Genes ENSRNOG00000004339 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005743 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005743 UniProtKB/TrEMBL
InterPro YY-1-like UniProtKB/TrEMBL
  Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:24919 UniProtKB/TrEMBL
NCBI Gene 24919 ENTREZGENE
Pfam zf-C2H2 UniProtKB/TrEMBL
PharmGKB YY1 RGD
PhenoGen Yy1 PhenoGen
PIRSF TF_Yin_yang UniProtKB/TrEMBL
PROSITE ZINC_FINGER_C2H2_1 UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/TrEMBL
SMART ZnF_C2H2 UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL
UniProt Q8CHJ4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Yy1  YY1 transcription factor      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the rat vascular smooth muscle cells after injury 628455
gene_function GL1-Kruppel-type zinc finger nuclear factor 628455
gene_process represses or activates the expression of many growth factors and inhibits smooth muscle growth 628455
gene_regulation mRNA and protein expression increased by growth factors which stimulate binding and transcription and expression blocked by neutralizing antibodies against fibroblast growth factors 628455