Chsy3 (chondroitin sulfate synthase 3) - Rat Genome Database

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Gene: Chsy3 (chondroitin sulfate synthase 3) Mus musculus
Analyze
Symbol: Chsy3
Name: chondroitin sulfate synthase 3
RGD ID: 1616679
MGI Page MGI
Description: Enables N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity and glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Involved in chondroitin sulfate biosynthetic process. Is active in Golgi apparatus. Is expressed in articular cartilage; cartilage; cerebral cortex; and humerus. Orthologous to human CHSY3 (chondroitin sulfate synthase 3).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 4833446K15Rik; AI662215; carbohydrate synthase 2; chondroitin glucuronyltransferase 3; chondroitin synthase 2; chSy-2; glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase II; N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase 3; N-acetylgalactosaminyltransferase 3
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391859,308,412 - 59,544,408 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1859,308,473 - 59,669,071 (+)EnsemblGRCm39 Ensembl
GRCm381859,175,340 - 59,411,336 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1859,175,401 - 59,535,999 (+)EnsemblGRCm38mm10GRCm38
MGSCv371859,334,994 - 59,570,990 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361859,300,709 - 59,536,705 (+)NCBIMGSCv36mm8
Celera1860,481,285 - 60,714,414 (+)NCBICelera
Cytogenetic Map18D3NCBI
cM Map1833.93NCBI
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

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:6781479   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14681479   PMID:16141072   PMID:16141073   PMID:17145758   PMID:17253960  
PMID:21267068   PMID:21873635   PMID:29287114   PMID:30228991   PMID:33903225   PMID:33905568   PMID:36047655   PMID:38355793  


Genomics

Comparative Map Data
Chsy3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391859,308,412 - 59,544,408 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1859,308,473 - 59,669,071 (+)EnsemblGRCm39 Ensembl
GRCm381859,175,340 - 59,411,336 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1859,175,401 - 59,535,999 (+)EnsemblGRCm38mm10GRCm38
MGSCv371859,334,994 - 59,570,990 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361859,300,709 - 59,536,705 (+)NCBIMGSCv36mm8
Celera1860,481,285 - 60,714,414 (+)NCBICelera
Cytogenetic Map18D3NCBI
cM Map1833.93NCBI
CHSY3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385129,903,979 - 130,186,634 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5129,904,465 - 130,186,634 (+)EnsemblGRCh38hg38GRCh38
GRCh375129,240,158 - 129,522,327 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365129,268,422 - 129,550,226 (+)NCBINCBI36Build 36hg18NCBI36
Celera5125,370,892 - 125,652,732 (+)NCBICelera
Cytogenetic Map5q23.3NCBI
HuRef5124,432,045 - 124,713,660 (+)NCBIHuRef
CHM1_15128,673,143 - 128,955,624 (+)NCBICHM1_1
T2T-CHM13v2.05130,422,787 - 130,705,475 (+)NCBIT2T-CHM13v2.0
Chsy3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81854,842,260 - 55,096,008 (+)NCBIGRCr8
mRatBN7.21852,644,356 - 52,901,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1852,644,461 - 52,898,098 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01854,243,626 - 54,497,475 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1854,243,949 - 54,496,585 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01853,477,339 - 53,731,655 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41854,963,517 - 55,273,226 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1850,748,557 - 51,001,455 (+)NCBICelera
Cytogenetic Map18q12.1NCBI
Chsy3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554152,748,777 - 2,991,782 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554152,748,776 - 2,994,041 (+)NCBIChiLan1.0ChiLan1.0
CHSY3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24125,214,859 - 125,496,222 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan15123,354,421 - 123,641,132 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v05125,319,738 - 125,601,102 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.15131,491,059 - 131,772,060 (+)NCBIpanpan1.1PanPan1.1panPan2
CHSY3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11118,621,196 - 18,855,018 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1118,620,781 - 18,854,177 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1117,420,827 - 17,654,322 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01119,375,694 - 19,642,226 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1119,375,694 - 19,641,379 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11118,100,068 - 18,370,955 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01117,935,119 - 18,202,405 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01118,549,166 - 18,816,845 (+)NCBIUU_Cfam_GSD_1.0
Chsy3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213141,374,905 - 141,626,875 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365042,949,014 - 3,200,006 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365042,948,878 - 2,952,518 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHSY3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl2132,535,984 - 132,802,188 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.12132,536,085 - 132,803,476 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22137,866,436 - 138,011,589 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHSY3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12332,803,714 - 33,088,720 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603444,921,259 - 45,206,662 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chsy3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477411,174,047 - 11,466,657 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477411,173,221 - 11,466,657 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chsy3
8980 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:43
Count of miRNA genes:42
Interacting mature miRNAs:42
Transcripts:ENSMUST00000080721
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302163Bmd16_mbone mineral density 16 (mouse)Not determined182966791463668060Mouse
1302099Hdlq30_mHDL QTL 30 (mouse)Not determined185166830085668468Mouse
11252137Modvl5_mmodifier of vacuolated lens 5 (mouse)185105215685052311Mouse
12910791Pwgrq8_mpre-weaning growth rate QTL 8 (mouse)185802139969349142Mouse
4141431Msmr2_mMSM lymphoma resistance 2 (mouse)Not determined5497587361238870Mouse
10412183Sstapa2_mSuseptibility to Staphylococus aureus infection 2 (mouse)Not determined185679463066952485Mouse
10412244Par5_mpulmonary adenoma resistance 5 (mouse)Not determined185166830085668468Mouse
1301400Lmr13_mleishmaniasis resistance 13 (mouse)Not determined182810938062109518Mouse
1301215Thcr_mT helper cell response (mouse)Not determined184513060468778777Mouse
1301853Heal9_mwound healing/regeneration 9 (mouse)Not determined185280527686805416Mouse
25823173Hrsq12_mhost response to SARS QTL 12, hemorrhage (mouse)182489588178339555Mouse
1357639Obsty4_mobesity 4 (mouse)Not determined183961991484638778Mouse
4142443Pgis1_mproteoglycan induced spondylitis 1 (mouse)Not determined185329102276914293Mouse
4140971Mbmq1_mmale body mass QTL 1 (mouse)Not determined5799028190720763Mouse
1558849W3q15_mweight 3 weeks QTL 15 (mouse)Not determined18504111961272643Mouse
12880412V125Dq12_mvitamin D active form serum level QTL 12 (mouse)183023306764233067Mouse
1301771Pcyts6_mplasmacytoma susceptibility 6 (mouse)Not determined183565863269658851Mouse
1301902Hrtfm4_mheart failure modifier 4 (mouse)Not determined184331112077311343Mouse
4141857Mhysq5_mmale hybrid sterility QTL 5 (mouse)Not determined2813060462130739Mouse
1300685Scc5_mcolon tumor susceptibility 5 (mouse)Not determined183198848065988629Mouse
12880410V125Dq13_mvitamin D active form serum level QTL 13 (mouse)185643307190433071Mouse
4142366Chlq10_mcirculating hormone level QTL 10 (mouse)Not determined183629102270291180Mouse
12050070Nabq2_mnasal bone morphology QTL 2 (mouse)183910367773103793Mouse
12880428V125Dq14_mvitamin D active form serum level QTL 14 (mouse)185743307190720763Mouse
1357630Tgq1_mtriglyceride QTL 1 (mouse)Not determined185105215685052311Mouse
12880430Fgf23lq4_mFGF23 serum level QTL 4 (mouse)185643307190433071Mouse
11039492Ltpr8a_mLeishmania tropica response 8a (mouse)185918009290720763Mouse
12904745Carcdq2_mcardiac collagen deposition QTL 2 (mouse)184642328780423287Mouse
11039493Ltpr8d_mLeishmania tropica response 8d (mouse)184687490380875042Mouse
1357690Vtbt19_mvertebral trabecular bone trait 19 (mouse)Not determined183309104367091221Mouse
11039494Ltpr8b_mLeishmania tropica response 8b (mouse)184687490380875042Mouse
1301500Szs4_mseizure susceptibility 4 (mouse)Not determined185497587385514143Mouse
11039495Ltpr8c_mLeishmania tropica response 8c (mouse)185918009290720763Mouse
15039381Ltgq8_mliver triglyceride QTL 8 (mouse)183820656972206569Mouse
1302050Radpf4_mradiation pulmonary fibrosis 4 (mouse)Not determined185296615668778777Mouse
12904950Smmq3_msoleus muscle mass QTL 3 (mouse)182605687560056875Mouse
15039383Mvlq5_mmicrovesicular liver lesion QTL 5 (mouse)183820656972206569Mouse
4141132Eae18_mexperimental allergic encephalomyelitis susceptibility 18 (mouse)Not determined5759055982604728Mouse
11049564Lmr29_mleishmaniasis resistance 29 (mouse)185918009290720763Mouse
1357603Mom3_mmodifier of Min 3 (mouse)Not determined181403002367098962Mouse
1301353Lbw6_mlupus NZB x NZW 6 (mouse)Not determined185756233890720763Mouse
27226723Tibw9_mtibia width 9, proximal, 16 week (mouse)18320000060933072Mouse
15039384Liviq1_mliver inflammation QTL 1 (mouse)183820656972206569Mouse
15039386Mvlq4_mmacrovesicular liver lesion QTL 4 (mouse)183820656972206569Mouse
27226720Tibw5_mtibia width 5, proximal, 10 week (mouse)185043306762633071Mouse

Markers in Region
RH133228  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381859,411,061 - 59,411,240UniSTSGRCm38
MGSCv371859,570,715 - 59,570,894UniSTSGRCm37
Celera1860,714,139 - 60,714,318UniSTS
Cytogenetic Map18D3UniSTS
AI662215  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381859,411,063 - 59,411,154UniSTSGRCm38
MGSCv371859,570,717 - 59,570,808UniSTSGRCm37
Celera1860,714,141 - 60,714,232UniSTS
Cytogenetic Map18D3UniSTS
Whitehead/MRC_RH18771.95UniSTS
UniSTS:224960  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381859,222,070 - 59,222,260UniSTSGRCm38
MGSCv371859,381,724 - 59,381,914UniSTSGRCm37
Celera1860,528,149 - 60,528,339UniSTS
Cytogenetic Map18D3UniSTS
Chsy3  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map18D3UniSTS
cM Map1833.93UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000080721   ⟹   ENSMUSP00000079546
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1859,308,722 - 59,544,408 (+)Ensembl
GRCm38.p6 Ensembl1859,175,650 - 59,411,336 (+)Ensembl
Ensembl Acc Id: ENSMUST00000237594
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1859,308,473 - 59,315,093 (+)Ensembl
GRCm38.p6 Ensembl1859,175,401 - 59,182,021 (+)Ensembl
Ensembl Acc Id: ENSMUST00000238155   ⟹   ENSMUSP00000158180
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1859,308,525 - 59,669,071 (+)Ensembl
GRCm38.p6 Ensembl1859,175,453 - 59,535,999 (+)Ensembl
RefSeq Acc Id: NM_001081328   ⟹   NP_001074797
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391859,308,412 - 59,544,408 (+)NCBI
GRCm381859,175,340 - 59,411,336 (+)ENTREZGENE
MGSCv371859,334,994 - 59,570,990 (+)RGD
Celera1860,481,285 - 60,714,414 (+)RGD
cM Map18 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_001074797   ⟸   NM_001081328
- UniProtKB: B2RXU7 (UniProtKB/Swiss-Prot),   Q5DTK1 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000158180   ⟸   ENSMUST00000238155
Ensembl Acc Id: ENSMUSP00000079546   ⟸   ENSMUST00000080721

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5DTK1-F1-model_v2 AlphaFold Q5DTK1 1-884 view protein structure

Promoters
RGD ID:13677874
Promoter ID:EPDNEW_M23086
Type:initiation region
Name:Chsy3_1
Description:Mus musculus chondroitin sulfate synthase 3 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381859,175,397 - 59,175,457EPDNEW
RGD ID:6829145
Promoter ID:MM_KWN:25371
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   Kidney,   Liver,   Lung
Transcripts:NM_001081328
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361859,334,566 - 59,335,227 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1926173 AgrOrtholog
Ensembl Genes ENSMUSG00000058152 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000080721 ENTREZGENE
  ENSMUST00000080721.6 UniProtKB/Swiss-Prot
  ENSMUST00000238155.2 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.550.50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Chond_GalNAc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CS_glycosyltransferase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:78923 UniProtKB/Swiss-Prot
MGD MGI:1926173 ENTREZGENE
NCBI Gene 78923 ENTREZGENE
PANTHER CHONDROITIN SULFATE SYNTHASE 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHONDROITIN SYNTHASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CHGN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chsy3 PhenoGen
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2RXU7 ENTREZGENE
  CHSS3_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q8BRJ2_MOUSE UniProtKB/TrEMBL
  Q8BRQ5_MOUSE UniProtKB/TrEMBL
  Q8CEL5_MOUSE UniProtKB/TrEMBL
UniProt Secondary B2RXU7 UniProtKB/Swiss-Prot