Csgalnact1 (chondroitin sulfate N-acetylgalactosaminyltransferase 1) - Rat Genome Database
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Gene: Csgalnact1 (chondroitin sulfate N-acetylgalactosaminyltransferase 1) Rattus norvegicus
Analyze
Symbol: Csgalnact1
Name: chondroitin sulfate N-acetylgalactosaminyltransferase 1
RGD ID: 1307618
Description: Predicted to have transferase activity, transferring hexosyl groups. Predicted to be involved in several processes, including chondroitin sulfate proteoglycan biosynthetic process; nucleotide-sugar metabolic process; and skeletal system development. Predicted to localize to Golgi cisterna membrane and integral component of membrane. Orthologous to human CSGALNACT1 (chondroitin sulfate N-acetylgalactosaminyltransferase 1); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; INTERACTS WITH 3,3',5,5'-tetrabromobisphenol A; acetamide; benzo[a]pyrene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Chgn; chondroitin beta1,4 N-acetylgalactosaminyltransferase; LOC306375; RGD1307618; similar to chondroitin beta1,4 N-acetylgalactosaminyltransferase
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
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Rnor_6.0 Ensembl1622,979,444 - 23,074,798 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01622,704,318 - 23,075,071 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01622,733,680 - 22,963,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41622,852,516 - 22,947,139 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11622,852,484 - 22,946,543 (+)NCBI
Celera1621,395,359 - 21,488,688 (+)NCBICelera
Cytogenetic Map16p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11514575   PMID:12163485   PMID:12477932   PMID:20812917   PMID:21148564  


Genomics

Comparative Map Data
Csgalnact1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Rnor_6.0 Ensembl1622,979,444 - 23,074,798 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01622,704,318 - 23,075,071 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01622,733,680 - 22,963,531 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41622,852,516 - 22,947,139 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11622,852,484 - 22,946,543 (+)NCBI
Celera1621,395,359 - 21,488,688 (+)NCBICelera
Cytogenetic Map16p14NCBI
CSGALNACT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl819,404,161 - 19,758,029 (-)EnsemblGRCh38hg38GRCh38
GRCh38819,404,161 - 19,757,908 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37819,261,672 - 19,615,419 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37819,261,672 - 19,540,261 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36819,305,952 - 19,584,374 (-)NCBINCBI36hg18NCBI36
Celera818,225,010 - 18,503,692 (-)NCBI
Cytogenetic Map8p21.3NCBI
HuRef817,801,989 - 18,080,455 (-)NCBIHuRef
CHM1_1819,463,117 - 19,741,804 (-)NCBICHM1_1
Csgalnact1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39868,809,433 - 69,188,270 (-)NCBIGRCm39mm39
GRCm38868,356,781 - 68,735,621 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl868,356,781 - 68,735,146 (-)EnsemblGRCm38mm10GRCm38
MGSCv37870,880,682 - 71,259,041 (-)NCBIGRCm37mm9NCBIm37
MGSCv36871,285,783 - 71,664,123 (-)NCBImm8
Celera870,901,764 - 71,270,170 (-)NCBICelera
Cytogenetic Map8B3.3NCBI
Csgalnact1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540343,178,520 - 43,478,885 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540343,178,520 - 43,347,121 (-)NCBIChiLan1.0ChiLan1.0
CSGALNACT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1815,576,416 - 15,929,342 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl815,576,416 - 15,904,123 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0818,626,998 - 18,980,416 (-)NCBIMhudiblu_PPA_v0panPan3
CSGALNACT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1622,219,861 - 22,392,937 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11622,219,324 - 22,546,501 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Csgalnact1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365553,639,459 - 3,807,483 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSGALNACT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11712,145,141 - 12,498,777 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21710,059,885 - 10,154,331 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CSGALNACT1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1817,494,312 - 17,851,497 (-)NCBI
ChlSab1.1 Ensembl817,494,187 - 17,695,037 (-)Ensembl
Csgalnact1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475815,200,726 - 15,517,146 (-)NCBI

Position Markers
D16Rat120  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01622,848,249 - 22,848,479NCBIRnor6.0
Rnor_5.01622,737,302 - 22,737,532UniSTSRnor5.0
RGSC_v3.41622,742,152 - 22,742,383RGDRGSC3.4
RGSC_v3.41622,742,153 - 22,742,383UniSTSRGSC3.4
RGSC_v3.11622,741,905 - 22,742,400RGD
Celera1621,264,603 - 21,264,833UniSTS
SHRSP x BN Map169.04UniSTS
SHRSP x BN Map169.04RGD
Cytogenetic Map16p14UniSTS
D16Got23  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01622,948,046 - 22,948,273NCBIRnor6.0
Rnor_5.01622,836,759 - 22,836,986UniSTSRnor5.0
RGSC_v3.41622,820,199 - 22,820,427RGDRGSC3.4
RGSC_v3.41622,820,200 - 22,820,427UniSTSRGSC3.4
RGSC_v3.11622,820,198 - 22,820,425RGD
Celera1621,363,702 - 21,363,929UniSTS
RH 3.4 Map16257.1RGD
RH 3.4 Map16257.1UniSTS
RH 2.0 Map16298.2RGD
Cytogenetic Map16p14UniSTS
RH129371  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01623,074,843 - 23,075,025NCBIRnor6.0
Rnor_5.01622,963,303 - 22,963,485UniSTSRnor5.0
RGSC_v3.41622,947,901 - 22,948,083UniSTSRGSC3.4
Celera1621,489,450 - 21,489,632UniSTS
RH 3.4 Map16256.66UniSTS
Cytogenetic Map16p14UniSTS
BQ190966  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01623,067,443 - 23,067,634NCBIRnor6.0
Rnor_5.01622,955,903 - 22,956,094UniSTSRnor5.0
RGSC_v3.41622,939,631 - 22,939,822UniSTSRGSC3.4
Celera1621,481,966 - 21,482,157UniSTS
RH 3.4 Map16254.77UniSTS
Cytogenetic Map16p14UniSTS
UniSTS:532267  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01623,057,358 - 23,057,522NCBIRnor6.0
Rnor_5.01622,945,976 - 22,946,140UniSTSRnor5.0
Celera1621,471,806 - 21,471,970UniSTS
Cytogenetic Map16p14UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
631517Scl9Serum cholesterol level QTL 93.3blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)161730939622744540Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161939818770590230Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)162075555680316424Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:180
Count of miRNA genes:126
Interacting mature miRNAs:158
Transcripts:ENSRNOT00000017822
Prediction methods:Miranda, 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 11 4 16 4 31 6 6 11
Low 3 43 46 37 3 37 8 10 43 29 34 8
Below cutoff 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017822   ⟹   ENSRNOP00000017822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1622,979,444 - 23,074,798 (+)Ensembl
RefSeq Acc Id: NM_001107309   ⟹   NP_001100779
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21621,236,008 - 21,329,602 (+)NCBI
Rnor_6.01622,979,668 - 23,074,078 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
RGSC_v3.41622,852,516 - 22,947,139 (+)RGD
Celera1621,395,359 - 21,488,688 (+)RGD
Sequence:
RefSeq Acc Id: XM_006253026   ⟹   XP_006253088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,852,738 - 23,075,071 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253027   ⟹   XP_006253089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21621,148,032 - 21,330,586 (+)NCBI
Rnor_6.01622,891,174 - 23,075,071 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253028   ⟹   XP_006253090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21621,100,081 - 21,330,586 (+)NCBI
Rnor_6.01622,842,529 - 23,075,071 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253029   ⟹   XP_006253091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21621,147,975 - 21,330,586 (+)NCBI
Rnor_6.01622,890,798 - 23,075,071 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006253031   ⟹   XP_006253093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,938,385 - 23,075,071 (+)NCBI
Rnor_5.01622,733,680 - 22,963,531 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771114   ⟹   XP_008769336
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Rnor_6.01622,704,318 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771116   ⟹   XP_008769338
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21621,147,277 - 21,330,586 (+)NCBI
Rnor_6.01622,890,257 - 23,075,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600092   ⟹   XP_017455581
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,704,319 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600093   ⟹   XP_017455582
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,704,319 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600094   ⟹   XP_017455583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,713,586 - 23,075,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600095   ⟹   XP_017455584
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Rnor_6.01622,704,319 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600096   ⟹   XP_017455585
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Rnor_6.01622,704,319 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600097   ⟹   XP_017455586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,715,083 - 23,075,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600098   ⟹   XP_017455587
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,716,871 - 23,075,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600099   ⟹   XP_017455588
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,704,319 - 23,075,058 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017600100   ⟹   XP_017455589
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01622,741,334 - 23,075,071 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039094494   ⟹   XP_038950422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
RefSeq Acc Id: XM_039094495   ⟹   XP_038950423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21620,995,210 - 21,330,586 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100779   ⟸   NM_001107309
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253090   ⟸   XM_006253028
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253088   ⟸   XM_006253026
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006253091   ⟸   XM_006253029
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253089   ⟸   XM_006253027
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253093   ⟸   XM_006253031
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008769336   ⟸   XM_008771114
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008769338   ⟸   XM_008771116
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455581   ⟸   XM_017600092
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455582   ⟸   XM_017600093
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455584   ⟸   XM_017600095
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455588   ⟸   XM_017600099
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455585   ⟸   XM_017600096
- Peptide Label: isoform X1
- UniProtKB: B5DEY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455583   ⟸   XM_017600094
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455586   ⟸   XM_017600097
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455587   ⟸   XM_017600098
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017455589   ⟸   XM_017600100
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000017822   ⟸   ENSRNOT00000017822
RefSeq Acc Id: XP_038950422   ⟸   XM_039094494
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038950423   ⟸   XM_039094495
- Peptide Label: isoform X1

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (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)
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
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307618 AgrOrtholog
Ensembl Genes ENSRNOG00000013024 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000017822 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017822 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.90.550.10 UniProtKB/TrEMBL
InterPro Chond_GalNAc UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/TrEMBL
KEGG Report rno:306375 UniProtKB/TrEMBL
NCBI Gene 306375 ENTREZGENE
Pfam CHGN UniProtKB/TrEMBL
PhenoGen Csgalnact1 PhenoGen
Superfamily-SCOP SSF53448 UniProtKB/TrEMBL
UniProt B5DEY9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-19 Csgalnact1  chondroitin sulfate N-acetylgalactosaminyltransferase 1  Chgn  chondroitin beta1,4 N-acetylgalactosaminyltransferase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Chgn  chondroitin beta1,4 N-acetylgalactosaminyltransferase  RGD1307618_predicted  similar to chondroitin beta1,4 N-acetylgalactosaminyltransferase (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307618_predicted  similar to chondroitin beta1,4 N-acetylgalactosaminyltransferase (predicted)  LOC306375_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC306375_predicted  similar to chondroitin beta1,4 N-acetylgalactosaminyltransferase (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL