CHSY1 (chondroitin sulfate synthase 1) - Rat Genome Database

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Gene: CHSY1 (chondroitin sulfate synthase 1) Canis lupus familiaris
Analyze
Symbol: CHSY1
Name: chondroitin sulfate synthase 1
RGD ID: 12056061
Description: ENCODES a protein that exhibits acetylgalactosaminyltransferase activity (inferred); glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (inferred); glycosyltransferase activity (inferred); INVOLVED IN bone morphogenesis (ortholog); cartilage development (ortholog); chondrocyte development (ortholog); ASSOCIATED WITH chromosome 15q26-qter deletion syndrome (ortholog); Experimental Liver Cirrhosis (ortholog); genetic disease (ortholog); FOUND IN Golgi apparatus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: carbohydrate (chondroitin) synthase 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0340,234,309 - 40,307,861 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl340,235,605 - 40,306,490 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1339,767,324 - 39,840,760 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0340,004,150 - 40,077,669 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0340,207,051 - 40,279,606 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0340,234,309 - 40,307,861 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl340,235,605 - 40,306,490 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1339,767,324 - 39,840,760 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0340,004,150 - 40,077,669 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0340,207,051 - 40,279,606 (+)NCBIUU_Cfam_GSD_1.0
CHSY1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3815101,175,727 - 101,252,048 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl15101,175,727 - 101,252,048 (-)EnsemblGRCh38hg38GRCh38
GRCh3715101,715,932 - 101,792,253 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361599,533,455 - 99,609,649 (-)NCBINCBI36Build 36hg18NCBI36
Build 341599,533,455 - 99,609,649NCBI
Celera1578,129,035 - 78,204,977 (-)NCBICelera
Cytogenetic Map15q26.3NCBI
HuRef1577,838,413 - 77,914,374 (-)NCBIHuRef
CHM1_115101,556,975 - 101,633,122 (-)NCBICHM1_1
T2T-CHM13v2.01598,930,755 - 99,007,076 (-)NCBIT2T-CHM13v2.0
Chsy1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39765,759,240 - 65,823,546 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl765,759,263 - 65,823,546 (+)EnsemblGRCm39 Ensembl
GRCm38766,109,492 - 66,173,798 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl766,109,515 - 66,173,798 (+)EnsemblGRCm38mm10GRCm38
MGSCv37773,254,401 - 73,318,684 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36765,988,465 - 66,052,748 (+)NCBIMGSCv36mm8
Celera763,545,296 - 63,619,383 (+)NCBICelera
Cytogenetic Map7CNCBI
Chsy1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81129,100,088 - 129,161,167 (+)NCBIGRCr8
mRatBN7.21119,689,626 - 119,750,711 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1119,686,350 - 119,750,601 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1127,682,577 - 127,743,312 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01134,854,019 - 134,914,754 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01127,663,508 - 127,724,487 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01127,010,587 - 127,071,570 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1127,010,588 - 127,071,570 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01128,095,353 - 128,156,041 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41120,539,002 - 120,600,102 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v21690,765,804 - 90,841,828 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11594,466,529 - 94,543,052 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01579,901,340 - 79,976,067 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11599,186,705 - 99,259,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1599,186,705 - 99,260,591 (-)Ensemblpanpan1.1panPan2
Chsy1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640143,648,412 - 143,720,663 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364832,613,820 - 2,686,276 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
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 - 139,804,657 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12919,633,335 - 19,707,547 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2919,632,026 - 19,707,425 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605926,833,395 - 26,907,460 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chsy1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247683,567,770 - 3,628,360 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CHSY1
626 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 15 6 2 9 10
Low 5 5 7 6 6 4 6 3 8 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000016812   ⟹   ENSCAFP00000015558
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl339,844,195 - 39,915,113 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000089826   ⟹   ENSCAFP00000048074
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl339,844,195 - 40,021,573 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845001524   ⟹   ENSCAFP00845001199
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl340,235,605 - 40,306,490 (+)Ensembl
RefSeq Acc Id: XM_038471714   ⟹   XP_038327642
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1339,768,676 - 39,840,760 (+)NCBI
RefSeq Acc Id: XM_038471715   ⟹   XP_038327643
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1339,767,324 - 39,840,760 (+)NCBI
RefSeq Acc Id: XM_038473220   ⟹   XP_038329148
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha342,532,031 - 42,605,585 (+)NCBI
RefSeq Acc Id: XM_038532637   ⟹   XP_038388565
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0340,207,051 - 40,279,606 (+)NCBI
RefSeq Acc Id: XM_038596941   ⟹   XP_038452869
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0340,005,491 - 40,077,669 (+)NCBI
RefSeq Acc Id: XM_038596942   ⟹   XP_038452870
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0340,004,150 - 40,077,669 (+)NCBI
RefSeq Acc Id: XM_038661151   ⟹   XP_038517079
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0340,235,686 - 40,307,861 (+)NCBI
RefSeq Acc Id: XM_038661152   ⟹   XP_038517080
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0340,234,309 - 40,307,861 (+)NCBI
RefSeq Acc Id: XM_545821   ⟹   XP_545821
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1339,844,227 - 39,916,484 (+)NCBI
Dog10K_Boxer_Tasha342,533,364 - 42,605,585 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_545821   ⟸   XM_545821
- Peptide Label: isoform X1
- UniProtKB: A0A8C0M2I7 (UniProtKB/TrEMBL),   A0A8C0R4R3 (UniProtKB/TrEMBL),   A0A8I3MD46 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000048074   ⟸   ENSCAFT00000089826
RefSeq Acc Id: ENSCAFP00000015558   ⟸   ENSCAFT00000016812
RefSeq Acc Id: XP_038327643   ⟸   XM_038471715
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038327642   ⟸   XM_038471714
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038452870   ⟸   XM_038596942
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038452869   ⟸   XM_038596941
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038517080   ⟸   XM_038661152
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038517079   ⟸   XM_038661151
- Peptide Label: isoform X1
- UniProtKB: A0A8C0M2I7 (UniProtKB/TrEMBL),   A0A8C0R4R3 (UniProtKB/TrEMBL),   A0A8I3MD46 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038329148   ⟸   XM_038473220
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038388565   ⟸   XM_038532637
- Peptide Label: isoform X1
- UniProtKB: A0A8C0M2I7 (UniProtKB/TrEMBL),   A0A8C0R4R3 (UniProtKB/TrEMBL),   A0A8I3MD46 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845001199   ⟸   ENSCAFT00845001524

Promoters
RGD ID:13682727
Promoter ID:EPDNEW_C795
Type:multiple initiation site
Name:CHSY1_1
Description:chondroitin sulfate synthase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1339,844,228 - 39,844,288EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000010579 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030001980 UniProtKB/TrEMBL
  ENSCAFG00040022932 UniProtKB/TrEMBL
  ENSCAFG00845000910 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000016812.6 UniProtKB/TrEMBL
  ENSCAFT00030003575.1 UniProtKB/TrEMBL
  ENSCAFT00040042636.1 UniProtKB/TrEMBL
  ENSCAFT00845001524 ENTREZGENE
  ENSCAFT00845001524.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.550.50 UniProtKB/TrEMBL
InterPro Chond_GalNAc UniProtKB/TrEMBL
  Nucleotide-diphossugar_trans UniProtKB/TrEMBL
NCBI Gene CHSY1 ENTREZGENE
PANTHER CHONDROITIN SULFATE SYNTHASE 1 UniProtKB/TrEMBL
  CHONDROITIN SYNTHASE UniProtKB/TrEMBL
Pfam CHGN UniProtKB/TrEMBL
Superfamily-SCOP SSF53448 UniProtKB/TrEMBL
UniProt A0A8C0M2I7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0R4R3 ENTREZGENE
  A0A8I3MD46 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:39259 ENTREZGENE