St6galnac1 (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1) - Rat Genome Database

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Gene: St6galnac1 (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1) Rattus norvegicus
Analyze
Symbol: St6galnac1
Name: ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1
RGD ID: 1562048
Description: Predicted to enable alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity. Predicted to be involved in protein glycosylation and sialylation. Predicted to act upstream of or within oligosaccharide biosynthetic process. Predicted to be located in Golgi apparatus. Predicted to be integral component of membrane. Orthologous to human ST6GALNAC1 (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1); PARTICIPATES IN O-linked glycan biosynthetic pathway; INTERACTS WITH bisphenol A; 1,2-dichloroethane (ortholog); 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: alpha-2,6-sialyltransferase ST6GalNAc I; alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1; sialyltransferase 7 ((alpha-N-acetylneuraminyl 2,3-beta-galactosyl-1,3)-N-acetyl galactosaminde alpha-2,6-sialyltransferase) A; Siat7A; ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1; ST6 GalNAc alpha-2,6-sialyltransferase 1; ST6GALNAC1, alpha-2,6-sialyltransferase 1
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
mRatBN7.210101,972,656 - 101,983,053 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10101,972,668 - 101,983,053 (-)Ensembl
Rnor_6.010105,713,305 - 105,723,700 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,713,317 - 105,723,700 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010105,374,445 - 105,384,844 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,837,311 - 106,881,619 (-)NCBIRGSC3.4rn4RGSC3.4
Celera10100,544,188 - 100,554,583 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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:10788794   PMID:15843597   PMID:30854566  


Genomics

Comparative Map Data
St6galnac1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.210101,972,656 - 101,983,053 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl10101,972,668 - 101,983,053 (-)Ensembl
Rnor_6.010105,713,305 - 105,723,700 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10105,713,317 - 105,723,700 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010105,374,445 - 105,384,844 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410106,837,311 - 106,881,619 (-)NCBIRGSC3.4rn4RGSC3.4
Celera10100,544,188 - 100,554,583 (-)NCBICelera
Cytogenetic Map10q32.2NCBI
ST6GALNAC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1776,624,761 - 76,643,786 (-)EnsemblGRCh38hg38GRCh38
GRCh381776,617,769 - 76,643,758 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371774,620,845 - 74,639,839 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,132,440 - 72,151,489 (-)NCBINCBI36hg18NCBI36
Build 341772,132,441 - 72,151,327NCBI
Celera1771,213,224 - 71,232,267 (-)NCBI
Cytogenetic Map17q25.1NCBI
HuRef1770,048,336 - 70,067,435 (-)NCBIHuRef
CHM1_11774,685,839 - 74,704,894 (-)NCBICHM1_1
St6galnac1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911116,655,851 - 116,666,333 (-)NCBIGRCm39mm39
GRCm39 Ensembl11116,655,851 - 116,666,333 (-)Ensembl
GRCm3811116,765,025 - 116,775,507 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11116,765,025 - 116,775,507 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711116,626,339 - 116,636,821 (-)NCBIGRCm37mm9NCBIm37
MGSCv3611116,581,115 - 116,591,597 (-)NCBImm8
Celera11128,478,824 - 128,520,872 (-)NCBICelera
Cytogenetic Map11E2NCBI
St6galnac1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555065,656,176 - 5,677,614 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555065,656,182 - 5,677,596 (+)NCBIChiLan1.0ChiLan1.0
LOC100990954
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11776,263,305 - 76,288,115 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1776,263,877 - 76,287,941 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01770,705,223 - 70,721,046 (-)NCBIMhudiblu_PPA_v0panPan3
ST6GALNAC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.194,098,881 - 4,124,417 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl94,101,050 - 4,123,896 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha94,782,442 - 4,805,244 (+)NCBI
ROS_Cfam_1.094,774,895 - 4,800,385 (+)NCBI
UMICH_Zoey_3.194,802,574 - 4,825,137 (+)NCBI
UNSW_CanFamBas_1.094,922,238 - 4,945,012 (+)NCBI
UU_Cfam_GSD_1.095,003,369 - 5,026,130 (+)NCBI
St6galnac1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056024,698,944 - 4,721,193 (+)NCBI
SpeTri2.0NW_0049365941,690,799 - 1,711,940 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ST6GALNAC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl124,890,406 - 4,909,351 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1124,889,852 - 4,909,345 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2124,742,080 - 4,760,387 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ST6GALNAC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11645,020,465 - 45,057,403 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1645,038,943 - 45,057,615 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607715,778,125 - 15,797,400 (+)NCBIVero_WHO_p1.0
St6galnac1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248016,478,153 - 6,500,047 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:77
Interacting mature miRNAs:81
Transcripts:ENSRNOT00000042321
Prediction methods: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 nervous system renal system reproductive system respiratory system
High
Medium 3
Low
Below cutoff 2 7 16 25 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000042321   ⟹   ENSRNOP00000042177
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10101,972,668 - 101,983,053 (-)Ensembl
Rnor_6.0 Ensembl10105,713,317 - 105,723,700 (-)Ensembl
RefSeq Acc Id: NM_001105859   ⟹   NP_001099329
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.210101,972,656 - 101,983,053 (-)NCBI
Rnor_6.010105,713,305 - 105,723,700 (-)NCBI
Rnor_5.010105,374,445 - 105,384,844 (-)NCBI
RGSC_v3.410106,837,311 - 106,881,619 (-)RGD
Celera10100,544,188 - 100,554,583 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099329 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAG25684 (Get FASTA)   NCBI Sequence Viewer  
  EDM06692 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001099329   ⟸   NM_001105859
- Peptide Label: precursor
- UniProtKB: G3V9C4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042177   ⟸   ENSRNOT00000042321

Transcriptome

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

Promoters
RGD ID:13697923
Promoter ID:EPDNEW_R8447
Type:single initiation site
Name:St6galnac1_1
Description:ST6 N-acetylgalactosaminide 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_6.010105,723,673 - 105,723,733EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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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)
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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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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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)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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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)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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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)
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 105375326 105375327 T C snv BDIX/NemOda (KyushuU), GH/OmrMcwi (MCW), NIG-III/Hok (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZF (KyushuU), ZFDM (KyushuU)
10 105375618 105375619 G T snv ZF (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), GH/OmrMcwi (MCW), BDIX/NemOda (KyushuU), NIG-III/Hok (KyushuU), ZFDM (KyushuU)
10 105376038 105376039 T A snv BDIX.Cg-Tal/NemOda (KyushuU), BDIX/NemOda (KyushuU), ZFDM (KyushuU), GH/OmrMcwi (MCW), ZF (KyushuU), NIG-III/Hok (KyushuU)
10 105376103 105376104 C A snv ZF (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZFDM (KyushuU), BDIX/NemOda (KyushuU)
10 105377300 105377301 G T snv BDIX.Cg-Tal/NemOda (KyushuU), NIG-III/Hok (KyushuU), BDIX/NemOda (KyushuU), ZFDM (KyushuU)
10 105377342 105377343 C T snv BDIX.Cg-Tal/NemOda (KyushuU), NIG-III/Hok (KyushuU), ZFDM (KyushuU), BDIX/NemOda (KyushuU), GH/OmrMcwi (MCW), ZF (KyushuU)
10 105377508 105377509 C T snv ZFDM (KyushuU), ZF (KyushuU), BDIX/NemOda (KyushuU), NIG-III/Hok (KyushuU), GH/OmrMcwi (MCW), BDIX.Cg-Tal/NemOda (KyushuU)
10 105378564 105378565 T G snv ZFDM (KyushuU), ZF (KyushuU), BDIX/NemOda (KyushuU), NIG-III/Hok (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), GH/OmrMcwi (MCW)
10 105384650 105384651 G T snv NIG-III/Hok (KyushuU), BDIX.Cg-Tal/NemOda (KyushuU), ZF (KyushuU), ZFDM (KyushuU)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 101973537 101973538 T C snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101973829 101973830 G T snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101974249 101974250 T A snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101974314 101974315 C A snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101975511 101975512 G T snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), HXB2/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB10/IpcvMcwi (2019), GK/FarMcwi (2019)
10 101975553 101975554 C T snv BXH2/CubMcwi (2020), SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), HXB2/IpcvMcwi (2019), WN/N (2020), HXB10/IpcvMcwi (2019), GK/FarMcwi (2019), BXH3/CubMcwi (2020), HXB20/IpcvMcwi (2020)
10 101975719 101975720 C T snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101976775 101976776 T G snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), WN/N (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), HXB20/IpcvMcwi (2020)
10 101976851 101976852 C A snv BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WN/N (2020)
10 101982859 101982860 G T snv SHR/OlalpcvMcwi (2019), SHRSP/A3NCrl (2019), HXB2/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), WN/N (2020), BXH2/CubMcwi (2020), HXB10/IpcvMcwi (2019)
10 101982934 101982935 G A snv WN/N (2020), SHR/OlalpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB10/IpcvMcwi (2019), BXH3/CubMcwi (2020), GK/FarMcwi (2019)
10 101982936 101982937 C T snv BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHR/OlalpcvMcwi (2019), WN/N (2020)
10 101982937 101982938 C T snv BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHR/OlalpcvMcwi (2019), WN/N (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 105714186 105714187 T C snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105714478 105714479 G T snv GH/OmrMcwi (MCW), BBDP/Wor (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), WN/N (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), BXH3/CubMcwi (2020)
10 105714898 105714899 T A snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105714963 105714964 C A snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105716160 105716161 G T snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105716202 105716203 C T snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105716351 105716352 C T snv F344/NCrl (RGD)
10 105716368 105716369 C T snv SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WN/N (2020), GH/OmrMcwi (MCW), BBDP/Wor (RGD)
10 105717299 105717300 G T snv BBDP/Wor (RGD)
10 105717424 105717425 T G snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), WN/N (2020), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), GK/FarMcwi (2019)
10 105717500 105717501 C A snv GH/OmrMcwi (MCW), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WKY/Gcrc (RGD), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHRSP/A3NCrl (2019), SHR/OlalpcvMcwi (2019), WN/N (2020)
10 105723506 105723507 G T snv GH/OmrMcwi (MCW), BXH2/CubMcwi (2020), BXH3/CubMcwi (2020), GK/FarMcwi (2019), SHRSP/A3NCrl (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), SHR/OlalpcvMcwi (2019), WN/N (2020), HXB10/IpcvMcwi (2019)
10 105723581 105723582 G A snv WN/N (2020), SHR/OlalpcvMcwi (2019), HXB2/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB10/IpcvMcwi (2019), GK/FarMcwi (2019), BXH3/CubMcwi (2020), GH/OmrMcwi (MCW)
10 105723583 105723584 C T snv BXH3/CubMcwi (2020), GK/FarMcwi (2019), HXB10/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB2/IpcvMcwi (2019), WN/N (2020), SHR/OlalpcvMcwi (2019)
10 105723584 105723585 C T snv HXB2/IpcvMcwi (2019), HXB20/IpcvMcwi (2020), HXB10/IpcvMcwi (2019), GK/FarMcwi (2019), BXH3/CubMcwi (2020), WN/N (2020), SHR/OlalpcvMcwi (2019)
10 105723589 105723590 C T snv GH/OmrMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
10 106872100 106872101 T C snv GH/OmrMcwi (MCW)
10 106872392 106872393 G T snv GH/OmrMcwi (MCW)
10 106872812 106872813 T A snv GH/OmrMcwi (MCW)
10 106874116 106874117 C T snv GH/OmrMcwi (MCW)
10 106874282 106874283 C T snv GH/OmrMcwi (MCW)
10 106875338 106875339 T G snv GH/OmrMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562048 AgrOrtholog
Ensembl Genes ENSRNOG00000000251 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042177 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000042321 UniProtKB/TrEMBL
Gene3D-CATH 3.90.1480.20 UniProtKB/TrEMBL
InterPro Glyco_trans_29 UniProtKB/TrEMBL
  GT29-like_sf UniProtKB/TrEMBL
KEGG Report rno:287920 UniProtKB/TrEMBL
NCBI Gene 287920 ENTREZGENE
Pfam Glyco_transf_29 UniProtKB/TrEMBL
PhenoGen St6galnac1 PhenoGen
UniProt G3V9C4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-04 St6galnac1  ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1  St6galnac1  ST6 GalNAc alpha-2,6-sialyltransferase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-27 St6galnac1  ST6 GalNAc alpha-2,6-sialyltransferase 1  St6galnac1  ST6GALNAC1, alpha-2,6-sialyltransferase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 St6galnac1  ST6GALNAC1, alpha-2,6-sialyltransferase 1  St6galnac1  ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 St6galnac1  ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1  Siat7A  sialyltransferase 7 ((alpha-N-acetylneuraminyl 2,3-beta-galactosyl-1,3)-N-acetyl galactosaminde alpha-2,6-sialyltransferase) A  Symbol and Name updated 1299863 APPROVED
2006-02-09 Siat7A  sialyltransferase 7 ((alpha-N-acetylneuraminyl 2,3-beta-galactosyl-1,3)-N-acetyl galactosaminde alpha-2,6-sialyltransferase) A      Symbol and Name status set to provisional 70820 PROVISIONAL