St6gal1 (ST6 beta-galactoside alpha-2,6-sialyltransferase 1) - Rat Genome Database

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Gene: St6gal1 (ST6 beta-galactoside alpha-2,6-sialyltransferase 1) Rattus norvegicus
Analyze
Symbol: St6gal1
Name: ST6 beta-galactoside alpha-2,6-sialyltransferase 1
RGD ID: 3676
Description: Enables sialyltransferase activity. Involved in several processes, including negative regulation of macrophage apoptotic process; protein sialylation; and regulation of substrate adhesion-dependent cell spreading. Located in Golgi medial cisterna; Golgi trans cisterna; and endoplasmic reticulum. Used to study high grade glioma. Orthologous to human ST6GAL1 (ST6 beta-galactoside alpha-2,6-sialyltransferase 1); PARTICIPATES IN N-linked glycan biosynthetic pathway; O-linked glycan biosynthetic pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha 2,6-ST 1; beta galactoside alpha 2,6 sialyltransferase 1; beta-galactoside alpha-2,6-sialyltransferase 1; CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase 1; sialyltransferase 1; Sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase); Sialyltransferase 1 (beta-galactoside alpha-26-sialytransferase); Siat1; ST6 beta-galactosamide alpha-2,6-sialyltranferase 1; ST6Gal I; ST6GalI
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
mRatBN7.21177,526,837 - 77,653,474 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1177,526,837 - 77,653,310 (-)Ensembl
Rnor_6.01180,927,601 - 80,981,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1180,927,601 - 80,981,422 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01179,754,201 - 79,808,024 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41179,723,269 - 79,765,645 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11179,780,860 - 79,789,781 (-)NCBI
Celera1176,402,694 - 76,445,042 (-)NCBICelera
Cytogenetic Map11q23NCBI
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
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,4-dinitrotoluene  (EXP)
2-amino-2-deoxy-D-glucopyranose  (ISO)
2-butoxyethanol  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-dichloroaniline  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
aflatoxin B1  (ISO)
aldehydo-D-glucosamine  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (ISO)
atrazine  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
beta-D-glucosamine  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
butanal  (ISO)
C60 fullerene  (EXP)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
choline  (ISO)
cisplatin  (ISO)
clofibrate  (EXP)
clofibric acid  (EXP)
copper(II) chloride  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
endosulfan  (EXP)
ethyl methanesulfonate  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
furan  (EXP)
gentamycin  (EXP)
L-ethionine  (EXP)
L-methionine  (ISO)
lithocholic acid  (ISO)
manganese(II) chloride  (EXP)
methyl methanesulfonate  (ISO)
N-nitrosodiethylamine  (EXP)
nefazodone  (EXP)
nickel dichloride  (ISO)
nicotinic acid  (EXP)
nimesulide  (EXP)
O-methyleugenol  (ISO)
omeprazole  (EXP)
oxaliplatin  (EXP)
oxazepam  (ISO)
p-toluidine  (EXP)
paracetamol  (ISO)
parathion  (ISO)
PCB138  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
quercetin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
tamoxifen  (ISO)
terbufos  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
topotecan  (EXP)
triclosan  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vancomycin  (ISO)
vorinostat  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:1983783   PMID:2249992   PMID:2793863   PMID:8889548   PMID:11278697   PMID:12068010   PMID:12473667   PMID:12966079   PMID:15364953   PMID:17897958   PMID:19150807   PMID:20378551  
PMID:21081508   PMID:21098517   PMID:22039275   PMID:23376485   PMID:23999306   PMID:24155237  


Genomics

Comparative Map Data
St6gal1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21177,526,837 - 77,653,474 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1177,526,837 - 77,653,310 (-)Ensembl
Rnor_6.01180,927,601 - 80,981,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1180,927,601 - 80,981,422 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01179,754,201 - 79,808,024 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41179,723,269 - 79,765,645 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11179,780,860 - 79,789,781 (-)NCBI
Celera1176,402,694 - 76,445,042 (-)NCBICelera
Cytogenetic Map11q23NCBI
ST6GAL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3186,930,325 - 187,078,553 (+)EnsemblGRCh38hg38GRCh38
GRCh383186,930,526 - 187,078,553 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373186,648,315 - 186,796,341 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363188,131,210 - 188,279,035 (+)NCBINCBI36hg18NCBI36
Celera3185,080,508 - 185,228,493 (+)NCBI
Cytogenetic Map3q27.3NCBI
HuRef3184,053,004 - 184,200,845 (+)NCBIHuRef
CHM1_13186,611,743 - 186,760,043 (+)NCBICHM1_1
St6gal1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391623,043,478 - 23,179,100 (+)NCBIGRCm39mm39
GRCm39 Ensembl1623,043,490 - 23,179,100 (+)Ensembl
GRCm381623,224,729 - 23,360,350 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1623,224,740 - 23,360,350 (+)EnsemblGRCm38mm10GRCm38
MGSCv371623,224,835 - 23,360,421 (+)NCBIGRCm37mm9NCBIm37
MGSCv361623,140,096 - 23,275,682 (+)NCBImm8
Celera1623,783,051 - 23,918,950 (+)NCBICelera
Cytogenetic Map16B1NCBI
cM Map1614.03NCBI
St6gal1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542020,709,301 - 20,801,167 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542020,708,890 - 20,801,167 (-)NCBIChiLan1.0ChiLan1.0
ST6GAL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13192,421,036 - 192,569,970 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3192,488,087 - 192,569,970 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03183,955,462 - 184,104,537 (+)NCBIMhudiblu_PPA_v0panPan3
ST6GAL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13419,497,577 - 19,589,125 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3419,497,922 - 19,586,427 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3423,553,294 - 23,675,456 (+)NCBI
ROS_Cfam_1.03419,379,150 - 19,501,792 (+)NCBI
UMICH_Zoey_3.13419,410,367 - 19,531,590 (+)NCBI
UNSW_CanFamBas_1.03419,410,079 - 19,531,772 (+)NCBI
UU_Cfam_GSD_1.03419,643,504 - 19,764,764 (+)NCBI
St6gal1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602116,874,836 - 117,015,302 (-)NCBI
SpeTri2.0NW_0049365782,966,690 - 3,107,237 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ST6GAL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13124,700,133 - 124,837,843 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113124,699,622 - 124,837,847 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ST6GAL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11581,205,121 - 81,346,089 (+)NCBI
ChlSab1.1 Ensembl1581,239,631 - 81,349,173 (+)Ensembl
Vero_WHO_p1.0NW_02366604154,697,038 - 54,836,111 (+)NCBI
St6gal1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473069,746,207 - 69,871,020 (-)NCBI

Position Markers
D11Mgh7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21177,570,168 - 77,570,330 (+)MAPPERmRatBN7.2
Rnor_6.01180,982,388 - 80,982,549NCBIRnor6.0
Rnor_5.01179,753,076 - 79,753,237UniSTSRnor5.0
RGSC_v3.41179,766,610 - 79,766,772RGDRGSC3.4
RGSC_v3.41179,766,611 - 79,766,772UniSTSRGSC3.4
RGSC_v3.11179,824,199 - 79,824,361RGD
Celera1176,446,008 - 76,446,169UniSTS
RH 3.4 Map11641.7RGD
RH 3.4 Map11641.7UniSTS
Cytogenetic Map11q23UniSTS
D11Got72  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21177,570,225 - 77,570,369 (+)MAPPERmRatBN7.2
Rnor_6.01180,982,445 - 80,982,588NCBIRnor6.0
Rnor_5.01179,753,037 - 79,753,180UniSTSRnor5.0
RGSC_v3.41179,766,667 - 79,766,811RGDRGSC3.4
RGSC_v3.41179,766,668 - 79,766,811UniSTSRGSC3.4
RGSC_v3.11179,824,256 - 79,824,400RGD
Celera1176,446,065 - 76,446,208UniSTS
RH 3.4 Map11642.0RGD
RH 3.4 Map11642.0UniSTS
Cytogenetic Map11q23UniSTS
RH129723  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21177,526,913 - 77,527,133 (+)MAPPERmRatBN7.2
Rnor_6.01180,927,678 - 80,927,897NCBIRnor6.0
Rnor_5.01179,807,728 - 79,807,947UniSTSRnor5.0
RGSC_v3.41179,723,346 - 79,723,565UniSTSRGSC3.4
Celera1176,402,771 - 76,402,990UniSTS
RH 3.4 Map11641.7UniSTS
Cytogenetic Map11q23UniSTS
RH127455  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21177,527,065 - 77,527,258 (+)MAPPERmRatBN7.2
Rnor_6.01180,927,830 - 80,928,022NCBIRnor6.0
Rnor_5.01179,807,603 - 79,807,795UniSTSRnor5.0
RGSC_v3.41179,723,498 - 79,723,690UniSTSRGSC3.4
Celera1176,402,923 - 76,403,115UniSTS
RH 3.4 Map11641.9UniSTS
Cytogenetic Map11q23UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)117695713183051965Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2255
Count of miRNA genes:332
Interacting mature miRNAs:435
Transcripts:ENSRNOT00000002496, ENSRNOT00000002499, ENSRNOT00000044591
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 26 51 41 19 41 66 35 35 11
Low 1 17 6 8 11 8 6 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001113344 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_147205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248501 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768792 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087996 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087997 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BF418553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ210708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ222565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ224146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ226436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M18769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M54999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M73985 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M73987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M83142 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M83143 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002496   ⟹   ENSRNOP00000002496
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1177,526,842 - 77,653,310 (-)Ensembl
Rnor_6.0 Ensembl1180,927,612 - 80,981,422 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000002499   ⟹   ENSRNOP00000002499
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1180,927,601 - 80,981,415 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000044591   ⟹   ENSRNOP00000041089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1177,527,806 - 77,535,809 (-)Ensembl
Rnor_6.0 Ensembl1180,927,604 - 80,936,524 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099835   ⟹   ENSRNOP00000085188
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1177,526,837 - 77,535,809 (-)Ensembl
RefSeq Acc Id: NM_001113344   ⟹   NP_001106815
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,569,203 (-)NCBI
Rnor_6.01180,927,601 - 80,981,422 (-)NCBI
Rnor_5.01179,754,201 - 79,808,024 (+)NCBI
RGSC_v3.41179,723,269 - 79,765,645 (-)RGD
Celera1176,402,694 - 76,445,042 (-)RGD
Sequence:
RefSeq Acc Id: NM_147205   ⟹   NP_671738
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,535,760 (-)NCBI
Rnor_6.01180,927,601 - 80,936,524 (-)NCBI
Rnor_5.01179,754,201 - 79,808,024 (+)NCBI
RGSC_v3.41179,723,269 - 79,765,645 (-)RGD
Celera1176,402,694 - 76,411,617 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006248501   ⟹   XP_006248563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,653,305 (-)NCBI
Rnor_6.01180,927,601 - 80,981,424 (-)NCBI
Rnor_5.01179,754,201 - 79,808,024 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039087993   ⟹   XP_038943921
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,653,320 (-)NCBI
RefSeq Acc Id: XM_039087994   ⟹   XP_038943922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,652,181 (-)NCBI
RefSeq Acc Id: XM_039087995   ⟹   XP_038943923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,653,474 (-)NCBI
RefSeq Acc Id: XM_039087996   ⟹   XP_038943924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,653,410 (-)NCBI
RefSeq Acc Id: XM_039087997   ⟹   XP_038943925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21177,526,837 - 77,578,006 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_671738   ⟸   NM_147205
- Peptide Label: isoform 2
- UniProtKB: P13721 (UniProtKB/Swiss-Prot),   F2Z3S3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001106815   ⟸   NM_001113344
- Peptide Label: isoform 1
- UniProtKB: P13721 (UniProtKB/Swiss-Prot),   G3V680 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248563   ⟸   XM_006248501
- Peptide Label: isoform X1
- UniProtKB: G3V680 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002499   ⟸   ENSRNOT00000002499
RefSeq Acc Id: ENSRNOP00000002496   ⟸   ENSRNOT00000002496
RefSeq Acc Id: ENSRNOP00000041089   ⟸   ENSRNOT00000044591
RefSeq Acc Id: XP_038943923   ⟸   XM_039087995
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943924   ⟸   XM_039087996
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943921   ⟸   XM_039087993
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943922   ⟸   XM_039087994
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943925   ⟸   XM_039087997
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000085188   ⟸   ENSRNOT00000099835

Transcriptome

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

Promoters
RGD ID:13698248
Promoter ID:EPDNEW_R8768
Type:initiation region
Name:St6gal1_1
Description:ST6 beta-galactoside alpha-2,6-sialyltransferase 1
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_6.01180,981,433 - 80,981,493EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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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
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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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
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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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/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)
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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
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)
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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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
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:3676 AgrOrtholog
Ensembl Genes ENSRNOG00000001823 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002496 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000002499 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000041089 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002496 UniProtKB/Swiss-Prot
  ENSRNOT00000002499 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000044591 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.90.1480.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Glyco_trans_29 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GT29-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sialyl_trans UniProtKB/Swiss-Prot
KEGG Report rno:25197 UniProtKB/Swiss-Prot
NCBI Gene 25197 ENTREZGENE
Pfam Glyco_transf_29 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen St6gal1 PhenoGen
PIRSF Sialyl_trans UniProtKB/Swiss-Prot
UniProt F2Z3S3 ENTREZGENE, UniProtKB/TrEMBL
  G3V680 ENTREZGENE
  P13721 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D4ABR2 UniProtKB/Swiss-Prot
  G3V680 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 St6gal1  ST6 beta-galactoside alpha-2,6-sialyltransferase 1  St6gal1  ST6 beta-galactosamide alpha-2,6-sialyltranferase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 St6gal1  ST6 beta-galactosamide alpha-2,6-sialyltranferase 1  St6gal1  beta galactoside alpha 2,6 sialyltransferase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 St6gal1  beta galactoside alpha 2,6 sialyltransferase 1  Siat1  sialyltransferase 1  Symbol and Name updated 1299863 APPROVED
2002-06-10 Siat1  Sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA and protein levels are highest in liver 729777