Galnt9 (polypeptide N-acetylgalactosaminyltransferase 9) - Rat Genome Database

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Gene: Galnt9 (polypeptide N-acetylgalactosaminyltransferase 9) Rattus norvegicus
Analyze
Symbol: Galnt9
Name: polypeptide N-acetylgalactosaminyltransferase 9
RGD ID: 1311523
Description: Predicted to have carbohydrate binding activity; metal ion binding activity; and polypeptide N-acetylgalactosaminyltransferase activity. Predicted to be involved in protein glycosylation and protein phosphopantetheinylation. Predicted to localize to Golgi apparatus. Orthologous to human GALNT9 (polypeptide N-acetylgalactosaminyltransferase 9); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; flavonoids.
Type: protein-coding
RefSeq Status: INFERRED
Also known as: LOC304571; UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9
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
mRatBN7.21246,050,395 - 46,128,626 (-)NCBI
Rnor_6.0 Ensembl1252,106,506 - 52,187,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01252,106,506 - 52,187,205 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01253,844,763 - 53,922,179 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41246,195,007 - 46,273,810 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11246,059,177 - 46,139,571 (-)NCBI
Celera1247,609,184 - 47,686,598 (-)NCBICelera
Cytogenetic Map12q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References


Genomics

Comparative Map Data
Galnt9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21246,050,395 - 46,128,626 (-)NCBI
Rnor_6.0 Ensembl1252,106,506 - 52,187,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01252,106,506 - 52,187,205 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01253,844,763 - 53,922,179 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41246,195,007 - 46,273,810 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11246,059,177 - 46,139,571 (-)NCBI
Celera1247,609,184 - 47,686,598 (-)NCBICelera
Cytogenetic Map12q16NCBI
GALNT9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl12132,196,372 - 132,329,589 (-)EnsemblGRCh38hg38GRCh38
GRCh3812132,196,372 - 132,329,589 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3712132,680,917 - 132,906,175 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3612131,246,870 - 131,256,526 (-)NCBINCBI36hg18NCBI36
Build 3412131,347,147 - 131,356,803NCBI
Celera12132,299,988 - 132,366,500 (-)NCBI
Cytogenetic Map12q24.33NCBI
HuRef12129,611,816 - 129,690,426 (-)NCBIHuRef
HuRef12129,565,322 - 129,574,999 (-)NCBIHuRef
CHM1_112132,501,248 - 132,723,926 (-)NCBICHM1_1
Galnt9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395110,692,176 - 110,769,249 (+)NCBIGRCm39mm39
GRCm39 Ensembl5110,692,221 - 110,769,246 (+)Ensembl
GRCm385110,544,032 - 110,621,383 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5110,544,355 - 110,621,380 (+)EnsemblGRCm38mm10GRCm38
MGSCv375110,973,364 - 111,050,401 (+)NCBIGRCm37mm9NCBIm37
MGSCv365110,855,787 - 110,861,684 (+)NCBImm8
Celera5107,675,872 - 107,752,903 (+)NCBICelera
Cytogenetic Map5FNCBI
Galnt9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955482564,913 - 616,123 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955482564,234 - 614,630 (+)NCBIChiLan1.0ChiLan1.0
LOC100993574
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112134,273,671 - 134,398,185 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12134,273,671 - 134,398,185 (-)Ensemblpanpan1.1panPan2
GALNT9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.126702,187 - 781,243 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl26702,057 - 777,942 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha26746,058 - 825,851 (+)NCBI
ROS_Cfam_1.026762,830 - 842,633 (+)NCBI
UMICH_Zoey_3.126701,756 - 781,520 (+)NCBI
UNSW_CanFamBas_1.026790,414 - 870,160 (+)NCBI
UU_Cfam_GSD_1.026721,524 - 801,303 (+)NCBI
Galnt9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118122,325,276 - 122,391,089 (+)NCBI
SpeTri2.0NW_0049366602,331,318 - 2,395,803 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GALNT9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1423,105,728 - 23,229,481 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11423,118,148 - 23,228,530 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21424,538,381 - 24,613,201 (+)NCBISscrofa10.2Sscrofa10.2susScr3
GALNT9
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.111127,577,969 - 127,698,902 (-)NCBI
ChlSab1.1 Ensembl11127,577,861 - 127,698,883 (-)Ensembl
Vero_WHO_p1.0NW_023666037117,178,639 - 117,366,842 (+)NCBI
Galnt9
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474727,832,331 - 27,879,470 (-)NCBI

Position Markers
RH133669  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,050,489 - 46,050,670 (+)MAPPER
Rnor_6.01252,106,583 - 52,106,763NCBIRnor6.0
Rnor_5.01253,844,840 - 53,845,020UniSTSRnor5.0
RGSC_v3.41246,195,084 - 46,195,264UniSTSRGSC3.4
Celera1247,609,261 - 47,609,441UniSTS
RH 3.4 Map12798.7UniSTS
Cytogenetic Map12q16UniSTS
AU046633  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,120,563 - 46,120,767 (+)MAPPER
Rnor_6.01252,179,162 - 52,179,365NCBIRnor6.0
Rnor_5.01253,914,123 - 53,914,326UniSTSRnor5.0
RGSC_v3.41246,265,808 - 46,266,011UniSTSRGSC3.4
Celera1247,678,503 - 47,678,700UniSTS
Cytogenetic Map12q16UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411547Bw129Body weight QTL 1290.001body mass (VT:0001259)body weight gain (CMO:0000420)6922362652716770Rat
7411588Foco6Food consumption QTL 60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411597Foco10Food consumption QTL 100.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
7411641Foco19Food consumption QTL 1927.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)12922362652716770Rat
8552918Pigfal7Plasma insulin-like growth factor 1 level QTL 7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552964Pigfal17Plasma insulin-like growth factor 1 level QTL 173.5blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922362652716770Rat
8552912Pigfal6Plasma insulin-like growth factor 1 level QTL 65blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)12922363052716770Rat
10059594Kidm46Kidney mass QTL 463.790.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)12978983452716770Rat
61404Bw120Body weight QTL 1205.1body mass (VT:0001259)body mass index (BMI) (CMO:0000105)121441977552716770Rat
1549829Scl48Serum cholesterol level QTL 485blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)121502198652716770Rat
2300186Bmd59Bone mineral density QTL 597.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)121590890052716770Rat
2293699Bss49Bone structure and strength QTL 495.610.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)121590890052716770Rat
1641928Alcrsp5Alcohol response QTL 5response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)121834247752716770Rat
2303569Gluco44Glucose level QTL 442blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)121834247752716770Rat
2302060Pia37Pristane induced arthritis QTL 376.10.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)121872904352716770Rat
1549902Bp269Blood pressure QTL 269arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)121875259352716770Rat
1549912Bp268Blood pressure QTL 268arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)101875259352716770Rat
61324Eae5Experimental allergic encephalomyelitis QTL 514nervous system integrity trait (VT:0010566)percentage of study population developing relapsing-remitting experimental autoimmune encephalomyelitis during a period of time (CMO:0001402)122265070252716770Rat
631560Apr1Acute phase response QTL 16.1orosomucoid 1 amount (VT:0010541)plasma orosomucoid 1 level (CMO:0001467)122490659052716770Rat
7411643Foco20Food consumption QTL 200.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)122609884552716770Rat
1600386Calcic2Intracellular calcium level QTL 20.001platelet physiology trait (VT:0005464)platelet intracellular calcium level (CMO:0000922)123172356552716770Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:91
Count of miRNA genes:73
Interacting mature miRNAs:78
Transcripts:ENSRNOT00000056722
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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 52
Low 1 22 19
Below cutoff 2 8 15 11 2 11 6 9 10 19 3 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000056722   ⟹   ENSRNOP00000053563
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1252,106,506 - 52,187,164 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088839   ⟹   ENSRNOP00000073030
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1252,106,506 - 52,124,779 (-)Ensembl
RefSeq Acc Id: NM_001107151   ⟹   NP_001100621
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,050,413 - 46,068,066 (-)NCBI
Rnor_6.01252,106,506 - 52,124,779 (-)NCBI
Rnor_5.01253,844,763 - 53,922,179 (-)NCBI
RGSC_v3.41246,195,007 - 46,273,810 (-)RGD
Celera1247,609,184 - 47,626,040 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001122644   ⟹   NP_001116116
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,050,413 - 46,128,578 (-)NCBI
Rnor_6.01252,106,506 - 52,187,164 (-)NCBI
Rnor_5.01253,844,763 - 53,922,179 (-)NCBI
RGSC_v3.41246,195,007 - 46,273,810 (-)RGD
Celera1247,609,184 - 47,686,598 (-)RGD
Sequence:
RefSeq Acc Id: XM_008769333   ⟹   XP_008767555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,050,409 - 46,128,626 (-)NCBI
Rnor_6.01252,106,506 - 52,187,205 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769334   ⟹   XP_008767556
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01252,106,506 - 52,169,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039089515   ⟹   XP_038945443
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21246,050,395 - 46,128,157 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100621 (Get FASTA)   NCBI Sequence Viewer  
  NP_001116116 (Get FASTA)   NCBI Sequence Viewer  
  XP_008767555 (Get FASTA)   NCBI Sequence Viewer  
  XP_038945443 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM14039 (Get FASTA)   NCBI Sequence Viewer  
  EDM14040 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001116116   ⟸   NM_001122644
- Peptide Label: isoform A
- UniProtKB: D3ZQA1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001100621   ⟸   NM_001107151
- Peptide Label: isoform B
- UniProtKB: A0A0G2K4G1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008767555   ⟸   XM_008769333
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008767556   ⟸   XM_008769334
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000053563   ⟸   ENSRNOT00000056722
RefSeq Acc Id: ENSRNOP00000073030   ⟸   ENSRNOT00000088839
RefSeq Acc Id: XP_038945443   ⟸   XM_039089515
- Peptide Label: isoform X2
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)
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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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 53921716 53921717 G A snv SBH/Ygl (KNAW), SBH/Ygl (MCW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 52186701 52186702 G A snv SBH/Ygl (RGD), SBH/Ygl (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
12 46273347 46273348 G A snv SBH/Ygl (ICL)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311523 AgrOrtholog
Ensembl Genes ENSRNOG00000037476 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053563 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000073030 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000056722 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000088839 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:304571 UniProtKB/TrEMBL
NCBI Gene 304571 ENTREZGENE
Pfam Glycos_transf_2 UniProtKB/TrEMBL
  Ricin_B_lectin UniProtKB/TrEMBL
PhenoGen Galnt9 PhenoGen
PROSITE RICIN_B_LECTIN UniProtKB/TrEMBL
SMART RICIN UniProtKB/TrEMBL
Superfamily-SCOP RicinB_like UniProtKB/TrEMBL
  SSF53448 UniProtKB/TrEMBL
UniProt A0A0G2K4G1 ENTREZGENE, UniProtKB/TrEMBL
  D3ZQA1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-02-25 Galnt9  polypeptide N-acetylgalactosaminyltransferase 9  Galnt9  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Galnt9  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9   Galnt9_predicted  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Galnt9_predicted  UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED