St3gal6 (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) - Rat Genome Database
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Gene: St3gal6 (ST3 beta-galactoside alpha-2,3-sialyltransferase 6) Rattus norvegicus
Analyze
Symbol: St3gal6
Name: ST3 beta-galactoside alpha-2,3-sialyltransferase 6
RGD ID: 1303279
Description: Predicted to have beta-galactoside alpha-2,3-sialyltransferase activity. Predicted to be involved in several processes, including cellular response to interleukin-6; glycolipid metabolic process; and oligosaccharide metabolic process. Predicted to localize to Golgi membrane and integral component of membrane. Orthologous to human ST3GAL6 (ST3 beta-galactoside alpha-2,3-sialyltransferase 6); PARTICIPATES IN lacto-series glycosphingolipid metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: CMP-NeuAc:beta-galactoside alpha-2,3-sialyltransferase VI; sialyltransferase 10 (alpha-2,3-sialyltransferase VI); Siat10; ST3Gal VI; ST3GalVI; type 2 lactosamine alpha-2,3-sialyltransferase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21142,061,282 - 42,121,801 (+)NCBI
Rnor_6.0 Ensembl1144,192,940 - 44,237,100 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01144,176,518 - 44,237,119 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01147,366,048 - 47,426,612 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41142,893,712 - 42,937,792 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11142,951,300 - 42,995,377 (+)NCBI
Celera1141,876,333 - 41,920,495 (+)NCBICelera
Cytogenetic Map11q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (EXP)
6-propyl-2-thiouracil  (EXP)
8-Br-cAMP  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
antirheumatic drug  (ISO)
atrazine  (ISO)
benzbromarone  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
clofibrate  (EXP)
cocaine  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
furan  (EXP)
L-ethionine  (EXP)
leflunomide  (ISO)
menadione  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
nickel sulfate  (ISO)
nimesulide  (EXP)
omeprazole  (EXP)
paracetamol  (ISO)
PD 0325901  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (ISO)
rimonabant  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
urethane  (ISO)
valproic acid  (ISO)
zebularine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10206952   PMID:12477932   PMID:15843597   PMID:17944600   PMID:19199708   PMID:23376485   PMID:23533145  


Genomics

Comparative Map Data
St3gal6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21142,061,282 - 42,121,801 (+)NCBI
Rnor_6.0 Ensembl1144,192,940 - 44,237,100 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01144,176,518 - 44,237,119 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01147,366,048 - 47,426,612 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41142,893,712 - 42,937,792 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11142,951,300 - 42,995,377 (+)NCBI
Celera1141,876,333 - 41,920,495 (+)NCBICelera
Cytogenetic Map11q12NCBI
ST3GAL6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl398,732,236 - 98,821,201 (+)EnsemblGRCh38hg38GRCh38
GRCh38398,732,262 - 98,795,852 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37398,451,106 - 98,514,696 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36399,934,262 - 99,995,927 (+)NCBINCBI36hg18NCBI36
Build 34399,934,261 - 99,995,924NCBI
Celera396,843,261 - 96,904,902 (+)NCBI
Cytogenetic Map3q12.1NCBI
HuRef395,823,269 - 95,886,702 (+)NCBIHuRef
CHM1_1398,414,233 - 98,477,819 (+)NCBICHM1_1
St3gal6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391658,290,105 - 58,344,616 (-)NCBIGRCm39mm39
GRCm39 Ensembl1658,288,488 - 58,344,606 (-)Ensembl
GRCm381658,469,742 - 58,524,260 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1658,468,125 - 58,524,243 (-)EnsemblGRCm38mm10GRCm38
MGSCv371658,470,654 - 58,523,425 (-)NCBIGRCm37mm9NCBIm37
MGSCv361658,413,084 - 58,465,855 (-)NCBImm8
Celera1658,755,151 - 58,808,030 (-)NCBICelera
Cytogenetic Map16C1.2NCBI
St3gal6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955427397,870 - 450,187 (+)NCBIChiLan1.0ChiLan1.0
ST3GAL6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13102,515,153 - 102,579,599 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3102,515,185 - 102,578,843 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0395,833,529 - 95,897,573 (+)NCBIMhudiblu_PPA_v0panPan3
ST3GAL6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl335,604,628 - 5,630,703 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1335,572,228 - 5,631,107 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
St3gal6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366304,226,539 - 4,281,064 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ST3GAL6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13160,158,242 - 160,224,821 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113160,158,238 - 160,225,355 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213170,305,811 - 170,328,056 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ST3GAL6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12282,059,441 - 82,126,508 (-)NCBI
ChlSab1.1 Ensembl2282,059,457 - 82,108,137 (-)Ensembl
St3gal6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478911,782,895 - 11,858,065 (+)NCBI

Position Markers
BF387674  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01144,210,598 - 44,210,781NCBIRnor6.0
Rnor_5.01147,400,091 - 47,400,274UniSTSRnor5.0
RGSC_v3.41142,911,370 - 42,911,553UniSTSRGSC3.4
Celera1141,893,991 - 41,894,174UniSTS
RH 3.4 Map11310.8UniSTS
Cytogenetic Map11q12UniSTS
RH140152  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01144,236,771 - 44,236,976NCBIRnor6.0
Rnor_5.01147,426,264 - 47,426,469UniSTSRnor5.0
RGSC_v3.41142,937,455 - 42,937,660UniSTSRGSC3.4
Celera1141,920,158 - 41,920,363UniSTS
RH 3.4 Map11312.9UniSTS
Cytogenetic Map11q12UniSTS
RH141458  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01144,236,132 - 44,236,348NCBIRnor6.0
Rnor_5.01147,425,625 - 47,425,841UniSTSRnor5.0
RGSC_v3.41142,936,816 - 42,937,032UniSTSRGSC3.4
Celera1141,919,519 - 41,919,735UniSTS
RH 3.4 Map11312.9UniSTS
Cytogenetic Map11q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
11528648Bss118Bone structure and strength QTL 1186.6580.00000022femur strength trait (VT:0010010)femur ultimate displacement (CMO:0002719)114278472545474665Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:330
Count of miRNA genes:215
Interacting mature miRNAs:255
Transcripts:ENSRNOT00000002255
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 43 45 37 19 37 8 11 33 35 29 11 8
Low 1 12 4 4 41 12
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002255   ⟹   ENSRNOP00000002255
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1144,192,940 - 44,237,100 (+)Ensembl
RefSeq Acc Id: NM_207602   ⟹   NP_997485
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,077,621 - 42,121,784 (+)NCBI
Rnor_6.01144,192,940 - 44,237,108 (+)NCBI
Rnor_5.01147,366,048 - 47,426,612 (+)NCBI
RGSC_v3.41142,893,712 - 42,937,792 (+)RGD
Celera1141,876,333 - 41,920,495 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248209   ⟹   XP_006248271
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,061,598 - 42,121,793 (+)NCBI
Rnor_6.01144,177,135 - 44,237,119 (+)NCBI
Rnor_5.01147,366,048 - 47,426,612 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006248210   ⟹   XP_006248272
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,061,282 - 42,121,793 (+)NCBI
Rnor_6.01144,176,518 - 44,237,119 (+)NCBI
Rnor_5.01147,366,048 - 47,426,612 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088384   ⟹   XP_038944312
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,086,817 - 42,121,801 (+)NCBI
RefSeq Acc Id: XM_039088385   ⟹   XP_038944313
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,086,817 - 42,121,801 (+)NCBI
RefSeq Acc Id: XM_039088386   ⟹   XP_038944314
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,086,817 - 42,121,801 (+)NCBI
RefSeq Acc Id: XM_039088387   ⟹   XP_038944315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,085,248 - 42,121,801 (+)NCBI
RefSeq Acc Id: XM_039088388   ⟹   XP_038944316
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,061,586 - 42,117,703 (+)NCBI
RefSeq Acc Id: XM_039088389   ⟹   XP_038944317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21142,061,583 - 42,106,058 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_997485   ⟸   NM_207602
- UniProtKB: Q569D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248272   ⟸   XM_006248210
- Peptide Label: isoform X1
- UniProtKB: Q569D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248271   ⟸   XM_006248209
- Peptide Label: isoform X1
- UniProtKB: Q569D2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002255   ⟸   ENSRNOT00000002255
RefSeq Acc Id: XP_038944317   ⟸   XM_039088389
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944316   ⟸   XM_039088388
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944315   ⟸   XM_039088387
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944312   ⟸   XM_039088384
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944313   ⟸   XM_039088385
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944314   ⟸   XM_039088386
- Peptide Label: isoform X1

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 (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 (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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)
Visual CSV TAB Printer
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)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
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
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/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
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 (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
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
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
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
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
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 (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
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
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 (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 (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
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 (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 (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 (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:1303279 AgrOrtholog
Ensembl Genes ENSRNOG00000001653 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002255 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002255 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.90.1480.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7308841 IMAGE-MGC_LOAD
InterPro Glyco_trans_29 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GT29-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sialyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:304023 UniProtKB/TrEMBL
MGC_CLONE MGC:108513 IMAGE-MGC_LOAD
NCBI Gene 304023 ENTREZGENE
Pfam Glyco_transf_29 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen St3gal6 PhenoGen
PIRSF Sialyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P61943 ENTREZGENE
  Q569D2 ENTREZGENE, UniProtKB/TrEMBL
  SIA10_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 St3gal6  ST3 beta-galactoside alpha-2,3-sialyltransferase 6  Siat10  sialyltransferase 10 (alpha-2,3-sialyltransferase VI)  Symbol and Name updated 1299863 APPROVED
2005-09-30 Siat10        Symbol and Name status set to provisional 70820 PROVISIONAL