Hmga1 (high mobility group AT-hook 1) - Rat Genome Database

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Gene: Hmga1 (high mobility group AT-hook 1) Rattus norvegicus
Analyze
Symbol: Hmga1
Name: high mobility group AT-hook 1
RGD ID: 628699
Description: Predicted to enable several functions, including DNA binding activity; DNA-binding transcription activator activity, RNA polymerase II-specific; and catalytic activity, acting on DNA. Predicted to be involved in several processes, including oncogene-induced cell senescence; positive regulation of cellular senescence; and regulation of transcription, DNA-templated. Predicted to act upstream of or within spermatogenesis. Predicted to be located in senescence-associated heterochromatin focus. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in type 2 diabetes mellitus. Orthologous to human HMGA1 (high mobility group AT-hook 1); PARTICIPATES IN interleukin-4 signaling pathway; INTERACTS WITH (+)-schisandrin B; 2-amino-2-deoxy-D-glucopyranose; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: high mobility group AT-hook protein 1; high mobility group protein A1; high mobility group protein HMG-I/HMG-Y; HMG-I(Y); Hmgi; Hmgiy; hypothetical protein LOC689053; LOC689053
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
mRatBN7.2205,611,088 - 5,618,755 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl205,611,694 - 5,618,752 (+)Ensembl
Rnor_6.0207,132,501 - 7,140,155 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl207,136,007 - 7,138,980 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0209,334,866 - 9,342,510 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,769,052 - 5,772,269 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1205,769,278 - 5,772,496 (+)NCBI
Celera207,177,471 - 7,180,533 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,3-dimethoxynaphthalene-1,4-dione  (ISO)
2,4-diaminotoluene  (ISO)
2-amino-2-deoxy-D-glucopyranose  (EXP)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-phenylbutyric acid  (ISO)
5-azacytidine  (ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (EXP)
alpha-pinene  (ISO)
alvocidib  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antimony(0)  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
Benzo[k]fluoranthene  (ISO)
beta-D-glucosamine  (EXP)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
cadmium dichloride  (EXP,ISO)
caffeine  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (EXP)
chromium atom  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cocaine  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (EXP,ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
dipotassium bis[mu-tartrato(4-)]diantimonate(2-) trihydrate  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
Ethylenethiourea  (EXP,ISO)
folic acid  (ISO)
formaldehyde  (ISO)
GW 4064  (ISO)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
methamphetamine  (EXP,ISO)
methyl methanesulfonate  (ISO)
mitomycin C  (ISO)
N-nitrosodimethylamine  (ISO)
nicotine  (ISO)
O-methyleugenol  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
PCB138  (ISO)
pepstatin A  (ISO)
perfluorooctanoic acid  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
quercetin  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
sunitinib  (ISO)
T-2 toxin  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP)
tetrahydropalmatine  (ISO)
thimerosal  (ISO)
topotecan  (ISO)
tributylstannane  (EXP)
trimellitic anhydride  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9253416   PMID:10428834   PMID:12032866   PMID:12653562   PMID:12874803   PMID:15192124   PMID:16157300   PMID:16641100   PMID:16791210   PMID:16901784   PMID:17005673   PMID:19389484  
PMID:19465398   PMID:21423176   PMID:24680881   PMID:25002582   PMID:25557289   PMID:29634420   PMID:30414623   PMID:30652345   PMID:30720182  


Genomics

Comparative Map Data
Hmga1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2205,611,088 - 5,618,755 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl205,611,694 - 5,618,752 (+)Ensembl
Rnor_6.0207,132,501 - 7,140,155 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl207,136,007 - 7,138,980 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0209,334,866 - 9,342,510 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4205,769,052 - 5,772,269 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1205,769,278 - 5,772,496 (+)NCBI
Celera207,177,471 - 7,180,533 (+)NCBICelera
Cytogenetic Map20p12NCBI
HMGA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl634,236,873 - 34,246,231 (+)EnsemblGRCh38hg38GRCh38
GRCh38634,236,873 - 34,246,231 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37634,204,650 - 34,214,008 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36634,312,628 - 34,321,986 (+)NCBINCBI36hg18NCBI36
Build 34634,314,545 - 34,321,986NCBI
Celera635,758,945 - 35,768,381 (+)NCBI
Cytogenetic Map6p21.31NCBI
HuRef633,927,318 - 33,936,673 (+)NCBIHuRef
CHM1_1634,207,231 - 34,216,597 (+)NCBICHM1_1
Hmga1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,775,548 - 27,782,646 (+)NCBIGRCm39mm39
GRCm39 Ensembl1727,775,471 - 27,782,648 (+)Ensembl
GRCm381727,556,574 - 27,563,672 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1727,556,497 - 27,563,674 (+)EnsemblGRCm38mm10GRCm38
GRCm38.p6 Ensembl11120,762,794 - 120,764,419 (+)EnsemblGRCm38mm10GRCm38
MGSCv371727,693,519 - 27,700,617 (+)NCBIGRCm37mm9NCBIm37
MGSCv361727,284,171 - 27,291,260 (+)NCBImm8
Celera1728,108,639 - 28,115,776 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1714.5NCBI
Hmga1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554372,478,414 - 2,486,809 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554372,478,414 - 2,486,809 (+)NCBIChiLan1.0ChiLan1.0
HMGA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1634,914,923 - 34,920,482 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0633,807,171 - 33,816,603 (+)NCBIMhudiblu_PPA_v0panPan3
HMGA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1123,528,818 - 3,538,533 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl123,533,102 - 3,538,533 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha123,544,725 - 3,554,094 (+)NCBI
ROS_Cfam_1.0123,865,251 - 3,874,712 (+)NCBI
UMICH_Zoey_3.1123,527,697 - 3,537,024 (+)NCBI
UNSW_CanFamBas_1.0123,609,068 - 3,618,412 (+)NCBI
UU_Cfam_GSD_1.0123,707,513 - 3,716,880 (+)NCBI
Hmga1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494639,156,880 - 39,164,376 (+)NCBI
SpeTri2.0NW_00493647624,795,854 - 24,803,138 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMGA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl730,320,454 - 30,329,409 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1730,320,090 - 30,329,413 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,981,570 - 34,990,089 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap7q11NCBI
HMGA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11737,848,110 - 37,857,835 (-)NCBI
ChlSab1.1 Ensembl1737,849,412 - 37,853,880 (-)Ensembl
Vero_WHO_p1.0NW_02366604434,150,889 - 34,160,977 (+)NCBI
Hmga1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475422,888,052 - 22,900,685 (-)NCBI

Position Markers
RH128050  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X31,610,924 - 31,611,116 (+)MAPPERmRatBN7.2
mRatBN7.2205,618,454 - 5,618,649 (+)MAPPERmRatBN7.2
Rnor_6.0207,139,855 - 7,140,049NCBIRnor6.0
Rnor_6.0X33,348,165 - 33,348,356NCBIRnor6.0
Rnor_5.0209,342,210 - 9,342,404UniSTSRnor5.0
Rnor_5.0X33,695,628 - 33,695,819UniSTSRnor5.0
RGSC_v3.4X52,351,648 - 52,351,839UniSTSRGSC3.4
RGSC_v3.4205,773,144 - 5,773,338UniSTSRGSC3.4
Celera207,181,408 - 7,181,602UniSTS
CeleraX31,924,692 - 31,924,883UniSTS
RH 3.4 Map2076.95UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036216499243559Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362164910078919Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2046066076691706Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:100
Count of miRNA genes:80
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000000580
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 4 4 4 6 2
Medium 3 39 31 23 19 23 3 68 29 38 11
Low 4 22 14 14 8 8 6 1 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_139327 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006256164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC095263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF507966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF511040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ225551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ227331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000324 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X62875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000000580   ⟹   ENSRNOP00000000580
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,611,694 - 5,618,622 (+)Ensembl
Rnor_6.0 Ensembl207,136,007 - 7,138,980 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099939   ⟹   ENSRNOP00000082413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,611,697 - 5,618,752 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113836   ⟹   ENSRNOP00000086846
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,614,569 - 5,618,737 (+)Ensembl
RefSeq Acc Id: NM_139327   ⟹   NP_647543
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,614,605 - 5,617,580 (+)NCBI
Rnor_6.0207,136,007 - 7,138,980 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
RGSC_v3.4205,769,052 - 5,772,269 (+)RGD
Celera207,177,471 - 7,180,533 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256156   ⟹   XP_006256218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,598 - 5,618,755 (+)NCBI
Rnor_6.0207,133,039 - 7,140,155 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256157   ⟹   XP_006256219
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,604 - 5,618,755 (+)NCBI
Rnor_6.0207,133,038 - 7,140,155 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256158   ⟹   XP_006256220
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,088 - 5,618,755 (+)NCBI
Rnor_6.0207,132,501 - 7,140,155 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256162   ⟹   XP_006256224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,089 - 5,618,755 (+)NCBI
Rnor_6.0207,132,503 - 7,140,155 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256163   ⟹   XP_006256225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,612,372 - 5,618,755 (+)NCBI
Rnor_6.0207,133,946 - 7,140,155 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256164   ⟹   XP_006256226
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,598 - 5,617,614 (+)NCBI
Rnor_6.0207,133,023 - 7,140,153 (+)NCBI
Rnor_5.0209,334,866 - 9,342,510 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601532   ⟹   XP_017457021
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,611,626 - 5,618,755 (+)NCBI
Rnor_6.0207,133,039 - 7,140,155 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098388   ⟹   XP_038954316
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,612,372 - 5,618,755 (+)NCBI
RefSeq Acc Id: XM_039098389   ⟹   XP_038954317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2205,613,077 - 5,618,755 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_647543   ⟸   NM_139327
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256220   ⟸   XM_006256158
- Peptide Label: isoform X1
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256224   ⟸   XM_006256162
- Peptide Label: isoform X2
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256226   ⟸   XM_006256164
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006256219   ⟸   XM_006256157
- Peptide Label: isoform X1
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256218   ⟸   XM_006256156
- Peptide Label: isoform X1
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256225   ⟸   XM_006256163
- Peptide Label: isoform X2
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017457021   ⟸   XM_017601532
- Peptide Label: isoform X2
- UniProtKB: Q8K585 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000000580   ⟸   ENSRNOT00000000580
RefSeq Acc Id: XP_038954316   ⟸   XM_039098388
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038954317   ⟸   XM_039098389
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000082413   ⟸   ENSRNOT00000099939
RefSeq Acc Id: ENSRNOP00000086846   ⟸   ENSRNOT00000113836

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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)
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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)
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)
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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)
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)
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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)
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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)
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)
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)
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: 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)
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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:628699 AgrOrtholog
Ensembl Genes ENSRNOG00000000488 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000000580 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000000580 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro AT_hook_DNA-bd_motif UniProtKB/Swiss-Prot
  HMGA UniProtKB/Swiss-Prot
  HMGA1_mammal UniProtKB/Swiss-Prot
  HMGI/Y_DNA-bd_CS UniProtKB/Swiss-Prot
KEGG Report rno:117062 UniProtKB/Swiss-Prot
NCBI Gene 117062 ENTREZGENE
PANTHER PTHR23341:SF6 UniProtKB/Swiss-Prot
Pfam AT_hook UniProtKB/Swiss-Prot
PhenoGen Hmga1 PhenoGen
PRINTS ATHOOK UniProtKB/Swiss-Prot
  HIGHMOBLTYIY UniProtKB/Swiss-Prot
PROSITE HMGI_Y UniProtKB/Swiss-Prot
SMART AT_hook UniProtKB/Swiss-Prot
UniProt HMGA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q8K1F5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Hmga1  high mobility group AT-hook 1  LOC689053  hypothetical protein LOC689053  Data Merged 737654 PROVISIONAL
2006-11-20 LOC689053  hypothetical protein LOC689053      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-09-10 Hmga1  high mobility group AT-hook 1      Symbol and Name status set to approved 1299863 APPROVED
2003-02-27 Hmga1  high mobility group AT-hook 1      Symbol and Name status set to provisional 70820 PROVISIONAL