Chsy1 (chondroitin sulfate synthase 1) - Rat Genome Database

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Gene: Chsy1 (chondroitin sulfate synthase 1) Mus musculus
Analyze
Symbol: Chsy1
Name: chondroitin sulfate synthase 1
RGD ID: 1323607
MGI Page MGI
Description: Exhibits transferase activity, transferring glycosyl groups. Involved in several processes, including chondroitin sulfate biosynthetic process; positive regulation of smoothened signaling pathway; and skeletal system development. Predicted to localize to extracellular region. Is expressed in several structures, including alimentary system; brain; cranium; ear; and respiratory system. Human ortholog(s) of this gene implicated in temtamy preaxial brachydactyly syndrome. Orthologous to human CHSY1 (chondroitin sulfate synthase 1); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; INTERACTS WITH 1,2-dichloroethane; 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: carbohydrate (chondroitin) synthase 1; chondroitin glucuronyltransferase 1; chondroitin synthase 1; chSy-1; glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase 1; KIAA0990; mKIAA0990; N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase 1; N-acetylgalactosaminyltransferase 1; skt
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39765,759,240 - 65,823,546 (+)NCBIGRCm39mm39
GRCm39 Ensembl765,759,263 - 65,823,546 (+)Ensembl
GRCm38766,109,492 - 66,173,798 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl766,109,515 - 66,173,798 (+)EnsemblGRCm38mm10GRCm38
MGSCv37773,254,401 - 73,318,684 (+)NCBIGRCm37mm9NCBIm37
MGSCv36765,988,465 - 66,052,748 (+)NCBImm8
Celera763,545,296 - 63,619,383 (+)NCBICelera
Cytogenetic Map7CNCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Mammalian Phenotype
abnormal axial skeleton morphology  (IAGP)
abnormal bone mineral content  (IAGP)
abnormal bone structure  (IAGP)
abnormal carpal bone morphology  (IAGP)
abnormal craniofacial bone morphology  (IAGP)
abnormal extracellular matrix morphology  (IAGP)
abnormal limb bone morphology  (IAGP)
abnormal long bone hypertrophic chondrocyte zone  (IAGP)
abnormal metacarpal bone morphology  (IAGP)
abnormal metatarsal bone morphology  (IAGP)
abnormal phalanx morphology  (IAGP)
abnormal photoreceptor outer segment morphology  (IAGP)
abnormal retina morphology  (IAGP)
abnormal retinal outer nuclear layer morphology  (IAGP)
abnormal rib morphology  (IAGP)
abnormal rod electrophysiology  (IAGP)
arthritis  (IEA)
brachypodia  (IAGP)
chondrodystrophy  (IAGP)
decreased a-wave amplitude  (IAGP)
decreased b-wave amplitude  (IAGP)
decreased body size  (IAGP)
decreased bone mineral content  (IEA)
decreased bone trabecula number  (IEA)
decreased macrophage cell number  (IAGP)
decreased neutrophil cell number  (IAGP)
decreased red blood cell distribution width  (IEA)
decreased trabecular bone connectivity density  (IEA)
decreased trabecular bone thickness  (IEA)
decreased trabecular bone volume  (IEA)
decreased volumetric bone mineral density  (IEA)
delayed chondrocyte differentiation  (IAGP)
disorganized photoreceptor outer segment  (IAGP)
hippocampal neuron degeneration  (IAGP)
hunched posture  (IAGP)
increased mean corpuscular hemoglobin  (IEA)
kidney inflammation  (IAGP)
kinked tail  (IAGP)
microgliosis  (IAGP)
neurodegeneration  (IAGP)
photoreceptor outer segment degeneration  (IAGP)
premature death  (IAGP)
premature hair loss  (IAGP)
proportional dwarf  (IEA)
retinal degeneration  (IEA)
retinal outer nuclear layer degeneration  (IAGP)
retinal photoreceptor degeneration  (IAGP)
short limbs  (IAGP)
short ribs  (IAGP)
thin retinal outer nuclear layer  (IAGP)
thin ribs  (IAGP)
weakness  (IEA)
References

Additional References at PubMed
PMID:8889548   PMID:12477932   PMID:14681479   PMID:17145758   PMID:18799693   PMID:20562862   PMID:21069351   PMID:21873635   PMID:22280990   PMID:22952769   PMID:25568321   PMID:27507650  
PMID:28378742   PMID:28706196   PMID:30228991   PMID:31138677   PMID:31754016   PMID:32098917   PMID:32201365  


Genomics

Comparative Map Data
Chsy1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39765,759,240 - 65,823,546 (+)NCBIGRCm39mm39
GRCm39 Ensembl765,759,263 - 65,823,546 (+)Ensembl
GRCm38766,109,492 - 66,173,798 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl766,109,515 - 66,173,798 (+)EnsemblGRCm38mm10GRCm38
MGSCv37773,254,401 - 73,318,684 (+)NCBIGRCm37mm9NCBIm37
MGSCv36765,988,465 - 66,052,748 (+)NCBImm8
Celera763,545,296 - 63,619,383 (+)NCBICelera
Cytogenetic Map7CNCBI
CHSY1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl15101,175,727 - 101,252,048 (-)EnsemblGRCh38hg38GRCh38
GRCh3815101,175,727 - 101,252,048 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3715101,715,932 - 101,792,253 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361599,533,455 - 99,609,649 (-)NCBINCBI36hg18NCBI36
Build 341599,533,455 - 99,609,649NCBI
Celera1578,129,035 - 78,204,977 (-)NCBI
Cytogenetic Map15q26.3NCBI
HuRef1577,838,413 - 77,914,374 (-)NCBIHuRef
CHM1_115101,556,975 - 101,633,122 (-)NCBICHM1_1
Chsy1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21119,689,626 - 119,750,711 (+)NCBI
Rnor_6.0 Ensembl1127,010,588 - 127,071,570 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01127,010,587 - 127,071,570 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01128,095,353 - 128,156,041 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41120,539,002 - 120,600,102 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11120,616,912 - 120,677,080 (+)NCBI
Celera1111,901,152 - 111,961,962 (+)NCBICelera
Cytogenetic Map1q22NCBI
Chsy1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541628,070,710 - 28,135,590 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541628,070,981 - 28,136,848 (-)NCBIChiLan1.0ChiLan1.0
CHSY1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11599,186,705 - 99,259,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1599,186,705 - 99,260,591 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01579,901,340 - 79,976,067 (-)NCBIMhudiblu_PPA_v0panPan3
CHSY1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1339,844,227 - 39,916,484 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl339,844,195 - 40,021,573 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha342,532,031 - 42,605,585 (+)NCBI
ROS_Cfam_1.0340,234,309 - 40,307,861 (+)NCBI
UMICH_Zoey_3.1339,767,324 - 39,840,760 (+)NCBI
UNSW_CanFamBas_1.0340,004,150 - 40,077,669 (+)NCBI
UU_Cfam_GSD_1.0340,207,051 - 40,279,606 (+)NCBI
Chsy1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640143,648,412 - 143,720,663 (-)NCBI
SpeTri2.0NW_0049364832,613,820 - 2,685,986 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHSY1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1139,730,721 - 139,804,583 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11139,730,703 - 139,804,458 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21155,960,054 - 156,033,821 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHSY1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12919,633,335 - 19,707,547 (-)NCBI
ChlSab1.1 Ensembl2919,632,026 - 19,707,425 (-)Ensembl
Chsy1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247683,567,770 - 3,628,360 (+)NCBI

Position Markers
RH135931  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38766,130,104 - 66,130,282UniSTSGRCm38
MGSCv37773,274,990 - 73,275,168UniSTSGRCm37
Celera763,565,989 - 63,566,166UniSTS
Cytogenetic Map7CUniSTS
UniSTS:235684  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38766,173,113 - 66,173,312UniSTSGRCm38
MGSCv37773,317,999 - 73,318,198UniSTSGRCm37
Celera763,618,698 - 63,618,897UniSTS
Cytogenetic Map7CUniSTS
Chsy1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7CUniSTS
cM Map735.5UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7346321287493512Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360000072900000Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76500000133900000Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718994869119886157Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719413473142366067Mouse
4141805Sle19_msystematic lupus erythematosus susceptibility 19 (mouse)Not determined3033306081485905Mouse
26884404Huml1_mhumerus length 1, 5 week (mouse)730500000109400000Mouse
1300996Aorls2_maortic lesion size 2 (mouse)Not determined73274478466744933Mouse
1559000Ossc1_mosteosarcoma susceptibility 1 (mouse)Not determined73440327768403475Mouse
10045622Heal20_mwound healing/regeneration 20 (mouse)Not determined73466713968667295Mouse
1357586Mdmsc3_mmodifier of muscularity 3 (mouse)Not determined73479812168798270Mouse
1301514Rigs1_mradiation induced gastroschisis 1 (mouse)Not determined73658059092745138Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736580590116817642Mouse
25314301Vmm3_mvariable multisystem mineralization 3, lung (mouse)73760000072400000Mouse
25314303Vmm4_mvariable multisystem mineralization 4, kidney (mouse)73760000087400000Mouse
1300878Skts1_mskin tumor susceptibility 1 (mouse)Not determined73824163872241834Mouse
10402488Dipa2_mdrug induced psychomotor activation 2 (mouse)Not determined73877180072771936Mouse
1300791Abbp3_mA/J and C57BL/6 blood pressure 3 (mouse)Not determined740024463103860803Mouse
4141929Chlq18_mcirculating hormone level QTL 18 (mouse)Not determined74149907275499217Mouse
11252140Fdr1_mfat response to dietary restriction 1 (mouse)74149907275499217Mouse
10043926Bw1n_mbody weight 1 in NSY (mouse)Not determined745512542119094307Mouse
12880417V125Dq5_mvitamin D active form serum level QTL 5 (mouse)74560000079600000Mouse
25314302Vmm2_mvariable multisystem mineralization 2, heart (mouse)74750000074500000Mouse
1302141Fcsa6_mfemoral cross-sectional area 6 (mouse)Not determined74873471382734859Mouse
11532741Tbrs5_mtuberculosis resistance 5 (mouse)74950947983586207Mouse
1357752Tabw_mtally ho asscoiated body weight (mouse)Not determined74954353083543642Mouse
10054064Bwq11_mbody weight QTL 11 (mouse)Not determined75147520685475345Mouse
10053685Eae43_mexperimental allergic encephalomyelitis susceptibility 43 (mouse)Not determined75147520685475345Mouse
13208555Lgth10_mbody length 10 (mouse)752000000126000000Mouse
12880418V125Dq6_mvitamin D active form serum level QTL 6 (mouse)75250000086500000Mouse
27226751Femd5_mfemur midshaft diameter 5, 10 week (mouse)753600000143600000Mouse
25823170Hrsq7_mhost response to SARS QTL 7, log titer (mouse)755169841117223580Mouse
11565101Tsve1_mvariable short tail (Tsv) enhancer 1 (mouse)75623976087493512Mouse
27226778Femd11_mfemur midshaft diameter 11, 16 week (mouse)757300000134400000Mouse
1300952Hcs1_mhepatocarcinogenesis susceptibility 1 (mouse)Not determined75767637391676604Mouse
1301465Egrm3_mearly growth rate (mouse)Not determined75767637391676604Mouse
1301663Skull9_mskull morphology 9 (mouse)Not determined75767637391676604Mouse
26884408Bzwq13_mbi-zygomatic width QTL 13, 16 week (mouse)762100000121800000Mouse
27095916Scvln15_msacral vertebrae length 2, 16 week (mouse)762100000124100000Mouse
25314305Vmm6_mvariable multisystem mineralization 6, eye (mouse)762200000103100000Mouse
13506761Tbthq1_mtrabecular bone thickness QTL 1 (mouse)76270000068100000Mouse
1301383Aem2_manti-erythrocyte autoantibody modifier 2 (mouse)Not determined76448567698485905Mouse
26884381Bzwq2_mbi-zygomatic width QTL 2, 5 week (mouse)76560000097300000Mouse
26884440Sklq4_mskull length QTL 4, 5 week (mouse)765600000126900000Mouse
13506750Tbthq2_mtrabecular bone thickness QTL 2 (mouse)76601000077900000Mouse
11553865Stmm1c_mskin tumor modifier of MSM 1c (mouse)766139778100139778Mouse
11553866Stmm1d_mskin tumor modifier of MSM 1d (mouse)766139778100139778Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:434
Count of miRNA genes:315
Interacting mature miRNAs:361
Transcripts:ENSMUST00000036372
Prediction methods: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


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000036372   ⟹   ENSMUSP00000047487
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl766,109,515 - 66,173,798 (+)Ensembl
RefSeq Acc Id: NM_001081163   ⟹   NP_001074632
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39765,759,240 - 65,823,546 (+)NCBI
GRCm38766,109,492 - 66,173,798 (+)NCBI
MGSCv37773,254,401 - 73,318,684 (+)RGD
Celera763,545,296 - 63,619,383 (+)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006540910   ⟹   XP_006540973
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39765,763,448 - 65,823,537 (+)NCBI
GRCm38766,113,694 - 66,173,789 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001074632   ⟸   NM_001081163
- Peptide Label: precursor
- UniProtKB: Q6ZQ11 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006540973   ⟸   XM_006540910
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000047487   ⟸   ENSMUST00000036372

Promoters
RGD ID:8664379
Promoter ID:EPDNEW_M10220
Type:multiple initiation site
Name:Chsy1_1
Description:Mus musculus chondroitin sulfate synthase 1 , 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
GRCm38766,109,492 - 66,109,552EPDNEW
RGD ID:6840836
Promoter ID:MM_KWN:50949
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_001081163
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36773,254,171 - 73,254,912 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2681120 AgrOrtholog
Ensembl Genes ENSMUSG00000032640 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000047487 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000036372 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.550.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Chond_GalNAc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:269941 UniProtKB/Swiss-Prot
MGD MGI:2681120 ENTREZGENE
NCBI Gene 269941 ENTREZGENE
Pfam CHGN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chsy1 PhenoGen
Superfamily-SCOP SSF53448 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A2VCT7_MOUSE UniProtKB/TrEMBL
  A8E635_MOUSE UniProtKB/TrEMBL
  A8E636_MOUSE UniProtKB/TrEMBL
  CHSS1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE