Galnt6 (polypeptide N-acetylgalactosaminyltransferase 6) - Rat Genome Database

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Gene: Galnt6 (polypeptide N-acetylgalactosaminyltransferase 6) Rattus norvegicus
Analyze
Symbol: Galnt6
Name: polypeptide N-acetylgalactosaminyltransferase 6
RGD ID: 2319726
Description: Predicted to have polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in protein glycosylation and protein phosphopantetheinylation. Predicted to localize to Golgi apparatus and perinuclear region of cytoplasm. Orthologous to human GALNT6 (polypeptide N-acetylgalactosaminyltransferase 6); PARTICIPATES IN O-linked glycan biosynthetic pathway; INTERACTS WITH 1,3-dinitrobenzene; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: LOC100361647; LOC683264; polypeptide N-acetylgalactosaminyltransferase 6-like; UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6; UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)
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
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Rnor_6.0 Ensembl7142,322,172 - 142,352,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07142,322,172 - 142,364,281 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07140,126,996 - 140,169,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,457,808 - 139,481,964 (-)NCBIRGSC3.4rn4RGSC3.4
Celera7128,266,012 - 128,291,542 (-)NCBICelera
Cytogenetic Map7q36NCBI
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:10464263   PMID:12506059  


Genomics

Comparative Map Data
Galnt6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Rnor_6.0 Ensembl7142,322,172 - 142,352,382 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.07142,322,172 - 142,364,281 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.07140,126,996 - 140,169,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47139,457,808 - 139,481,964 (-)NCBIRGSC3.4rn4RGSC3.4
Celera7128,266,012 - 128,291,542 (-)NCBICelera
Cytogenetic Map7q36NCBI
GALNT6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1251,351,247 - 51,392,867 (-)EnsemblGRCh38hg38GRCh38
GRCh381251,351,252 - 51,391,955 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371251,745,036 - 51,785,190 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361250,032,100 - 50,071,467 (-)NCBINCBI36hg18NCBI36
Build 341250,033,431 - 50,059,832NCBI
Celera1250,547,314 - 50,586,667 (-)NCBI
Cytogenetic Map12q13.13NCBI
HuRef1248,778,778 - 48,818,157 (-)NCBIHuRef
CHM1_11251,712,388 - 51,751,734 (-)NCBICHM1_1
Galnt6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915100,587,796 - 100,627,257 (-)NCBIGRCm39mm39
GRCm39 Ensembl15100,589,694 - 100,627,257 (-)Ensembl
GRCm3815100,689,915 - 100,729,376 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15100,691,813 - 100,729,376 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715100,520,346 - 100,559,807 (-)NCBIGRCm37mm9NCBIm37
MGSCv3615100,519,848 - 100,557,410 (-)NCBImm8
Celera15102,843,144 - 102,873,752 (-)NCBICelera
Cytogenetic Map15F1NCBI
Galnt6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555471,825,716 - 1,859,325 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555471,828,767 - 1,859,327 (-)NCBIChiLan1.0ChiLan1.0
GALNT6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11238,246,778 - 38,287,184 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1238,247,129 - 38,286,570 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01237,361,418 - 37,401,927 (+)NCBIMhudiblu_PPA_v0panPan3
GALNT6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,507,314 - 3,539,263 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,507,333 - 3,537,480 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2742,718,762 - 42,754,668 (-)NCBI
ROS_Cfam_1.0273,497,184 - 3,533,094 (+)NCBI
UMICH_Zoey_3.1273,515,887 - 3,551,740 (+)NCBI
UNSW_CanFamBas_1.0273,502,424 - 3,538,258 (+)NCBI
UU_Cfam_GSD_1.02743,116,201 - 43,152,083 (-)NCBI
Galnt6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494564,196,707 - 64,233,491 (+)NCBI
SpeTri2.0NW_0049365128,932,129 - 8,960,494 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GALNT6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.2517,455,646 - 17,463,899 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GALNT6
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11147,549,775 - 47,589,696 (-)NCBI
ChlSab1.1 Ensembl1147,548,801 - 47,577,605 (-)Ensembl
Galnt6
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624816860,124 - 899,679 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7120746024145692398Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7121654760145729302Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7121986439143965591Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7122421276143965415Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7129412003145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:76
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000048488
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 3 2 8 18 7 6 4
Low 32 27 19 1 19 20 31 34 7
Below cutoff 9 22 22 22 8 10 45 4 1 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000048488   ⟹   ENSRNOP00000042281
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7142,323,622 - 142,352,382 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078848   ⟹   ENSRNOP00000070003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7142,322,172 - 142,348,232 (-)Ensembl
RefSeq Acc Id: NM_001172063   ⟹   NP_001165534
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,789,836 - 131,815,505 (-)NCBI
Rnor_6.07142,322,172 - 142,348,232 (-)NCBI
Rnor_5.07140,126,996 - 140,169,063 (-)NCBI
Celera7128,266,012 - 128,291,542 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242294   ⟹   XP_006242356
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07142,323,626 - 142,360,473 (-)NCBI
Rnor_5.07140,126,996 - 140,169,063 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242295   ⟹   XP_006242357
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Rnor_6.07142,323,626 - 142,361,912 (-)NCBI
Rnor_5.07140,126,996 - 140,169,063 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006242296   ⟹   XP_006242358
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Rnor_6.07142,323,626 - 142,361,912 (-)NCBI
Rnor_5.07140,126,996 - 140,169,063 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765651   ⟹   XP_008763873
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Rnor_6.07142,323,626 - 142,361,912 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594563   ⟹   XP_017450052
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07142,323,626 - 142,364,281 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039078233   ⟹   XP_038934161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27131,789,836 - 131,828,077 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001165534   ⟸   NM_001172063
- UniProtKB: D4A864 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242357   ⟸   XM_006242295
- Peptide Label: isoform X1
- UniProtKB: D4A864 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242358   ⟸   XM_006242296
- Peptide Label: isoform X1
- UniProtKB: D4A864 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006242356   ⟸   XM_006242294
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008763873   ⟸   XM_008765651
- Peptide Label: isoform X1
- UniProtKB: D4A864 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450052   ⟸   XM_017594563
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000042281   ⟸   ENSRNOT00000048488
RefSeq Acc Id: ENSRNOP00000070003   ⟸   ENSRNOT00000078848
RefSeq Acc Id: XP_038934161   ⟸   XM_039078233
- Peptide Label: isoform X1
Protein Domains
Ricin B-type lectin

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)
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)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (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)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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 (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (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
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
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:2319726 AgrOrtholog
Ensembl Genes ENSRNOG00000033059 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042281 UniProtKB/TrEMBL
  ENSRNOP00000070003 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048488 UniProtKB/TrEMBL
  ENSRNOT00000078848 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.90.550.10 UniProtKB/TrEMBL
InterPro Glyco_trans_2 UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/TrEMBL
  Ricin_B-like_lectins UniProtKB/TrEMBL
  Ricin_B_lectin UniProtKB/TrEMBL
KEGG Report rno:100361647 UniProtKB/TrEMBL
NCBI Gene 100361647 ENTREZGENE
Pfam Glycos_transf_2 UniProtKB/TrEMBL
  Ricin_B_lectin UniProtKB/TrEMBL
PhenoGen Galnt6 PhenoGen
PROSITE RICIN_B_LECTIN UniProtKB/TrEMBL
SMART RICIN UniProtKB/TrEMBL
Superfamily-SCOP RicinB_like UniProtKB/TrEMBL
  SSF53448 UniProtKB/TrEMBL
UniProt D4A864 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-03-21 Galnt6  polypeptide N-acetylgalactosaminyltransferase 6  Galnt6  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-03 Galnt6  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)  Galnt6  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-03 LOC100361647  polypeptide N-acetylgalactosaminyltransferase 6-like  LOC683264  similar to Polypeptide N-acetylgalactosaminyltransferase 6 (Protein-UDP acetylgalactosaminyltransferase 6) (UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6) (Polypeptide GalNAc transferase 6) (GalNAc-T6) (pp-GaNTase 6)  Data Merged 737654 APPROVED
2012-01-03 Galnt6  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6  LOC100361647  polypeptide N-acetylgalactosaminyltransferase 6-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361647  polypeptide N-acetylgalactosaminyltransferase 6-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC683264  similar to Polypeptide N-acetylgalactosaminyltransferase 6 (Protein-UDP acetylgalactosaminyltransferase 6) (UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6) (Polypeptide GalNAc transferase 6) (GalNAc-T6) (pp-GaNTase 6)      Symbol and Name status set to provisional 70820 PROVISIONAL