Chst3 (carbohydrate sulfotransferase 3) - Rat Genome Database

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Gene: Chst3 (carbohydrate sulfotransferase 3) Rattus norvegicus
Analyze
Symbol: Chst3
Name: carbohydrate sulfotransferase 3
RGD ID: 620355
Description: Enables proteoglycan sulfotransferase activity. Involved in chondroitin sulfate biosynthetic process and peripheral nervous system axon regeneration. Predicted to be located in Golgi membrane. Predicted to be active in trans-Golgi network. Human ortholog(s) of this gene implicated in osteochondrodysplasia and spondyloepiphyseal dysplasia with congenital joint dislocations. Orthologous to human CHST3 (carbohydrate sulfotransferase 3); PARTICIPATES IN chondroitin sulfate biosynthetic pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C6ST-1; carbohydrate (chondroitin 6) sulfotransferase 3; carbohydrate (chondroitin 6/keratan) sulfotransferase 3; chondroitin 6-O-sulfotransferase 1; chondroitin 6-sulfotransferase 3; galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 0; GST-0; LOC102554900; uncharacterized LOC102554900
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82028,657,308 - 28,694,976 (-)NCBIGRCr8
mRatBN7.22028,114,386 - 28,152,046 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2028,114,404 - 28,121,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2029,133,379 - 29,135,921 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02028,519,672 - 28,522,214 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02029,262,146 - 29,264,688 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02029,731,828 - 29,768,656 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2029,731,816 - 29,738,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02031,532,769 - 31,569,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42027,480,448 - 27,482,990 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12027,494,247 - 27,496,790 (-)NCBI
Celera2029,558,419 - 29,560,961 (-)NCBICelera
Cytogenetic Map20q11NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Upregulation of chondroitin 6-sulphotransferase-1 facilitates Schwann cell migration during axonal growth. Liu J, etal., J Cell Sci. 2006 Mar 1;119(Pt 5):933-42.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. GOA pipeline RGD automated data pipeline
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Loss of chondroitin 6-O-sulfotransferase-1 function results in severe human chondrodysplasia with progressive spinal involvement. Thiele H, etal., Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10155-60. Epub 2004 Jun 23.
12. Chondroitin 4-sulphotransferase-1 and chondroitin 6-sulphotransferase-1 are affected differently by uronic acid residues neighbouring the acceptor GalNAc residues. Yamada T, etal., Biochem J 2004 Dec 15;384(Pt 3):567-75.
Additional References at PubMed
PMID:9597547   PMID:9883891   PMID:11696535  


Genomics

Comparative Map Data
Chst3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82028,657,308 - 28,694,976 (-)NCBIGRCr8
mRatBN7.22028,114,386 - 28,152,046 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2028,114,404 - 28,121,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2029,133,379 - 29,135,921 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02028,519,672 - 28,522,214 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02029,262,146 - 29,264,688 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02029,731,828 - 29,768,656 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2029,731,816 - 29,738,506 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02031,532,769 - 31,569,063 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42027,480,448 - 27,482,990 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12027,494,247 - 27,496,790 (-)NCBI
Celera2029,558,419 - 29,560,961 (-)NCBICelera
Cytogenetic Map20q11NCBI
CHST3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381071,964,395 - 72,013,558 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1071,964,395 - 72,013,558 (+)EnsemblGRCh38hg38GRCh38
GRCh371073,724,153 - 73,773,316 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361073,394,126 - 73,443,318 (+)NCBINCBI36Build 36hg18NCBI36
Build 341073,394,125 - 73,443,318NCBI
Celera1067,007,692 - 67,056,893 (+)NCBICelera
Cytogenetic Map10q22.1NCBI
HuRef1067,718,863 - 67,768,083 (+)NCBIHuRef
CHM1_11074,006,249 - 74,055,464 (+)NCBICHM1_1
T2T-CHM13v2.01072,835,220 - 72,884,391 (+)NCBIT2T-CHM13v2.0
Chst3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391060,017,349 - 60,057,936 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1060,017,354 - 60,055,082 (-)EnsemblGRCm39 Ensembl
GRCm381060,181,527 - 60,222,114 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1060,181,532 - 60,219,260 (-)EnsemblGRCm38mm10GRCm38
MGSCv371059,644,275 - 59,682,008 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361059,576,891 - 59,584,064 (-)NCBIMGSCv36mm8
Celera1061,277,814 - 61,316,112 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1029.7NCBI
Chst3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543719,563,088 - 19,569,889 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543719,563,645 - 19,605,747 (-)NCBIChiLan1.0ChiLan1.0
CHST3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2884,107,391 - 84,156,788 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11084,112,712 - 84,162,115 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01068,427,305 - 68,476,512 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11070,951,211 - 71,000,022 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1070,951,190 - 70,994,936 (+)Ensemblpanpan1.1panPan2
CHST3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1422,668,430 - 22,699,157 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl422,691,336 - 22,694,254 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha422,801,236 - 22,835,722 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0422,946,343 - 22,980,845 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl422,973,213 - 22,975,930 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1422,846,108 - 22,880,565 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0423,046,351 - 23,080,822 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0423,400,019 - 23,434,552 (+)NCBIUU_Cfam_GSD_1.0
Chst3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721358,371,731 - 58,407,387 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365216,863,642 - 6,900,041 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365216,864,456 - 6,900,122 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHST3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1474,850,931 - 74,891,520 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11474,850,931 - 74,891,527 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21480,739,187 - 80,779,620 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHST3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1959,292,705 - 59,295,821 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl959,293,158 - 59,300,866 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604819,934,549 - 19,979,113 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chst3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247545,829,546 - 5,831,941 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247545,800,240 - 5,832,290 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Chst3
173 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:50
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000000697
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat


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 2 8 5 20 4 18 1
Low 1 40 26 18 14 18 7 10 54 31 21 10 7
Below cutoff 3 23 23 23 1 1 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000697   ⟹   ENSRNOP00000000697
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2028,114,404 - 28,121,807 (-)Ensembl
Rnor_6.0 Ensembl2029,731,816 - 29,738,506 (-)Ensembl
RefSeq Acc Id: NM_053408   ⟹   NP_445860
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82028,657,308 - 28,694,526 (-)NCBI
mRatBN7.22028,114,386 - 28,151,602 (-)NCBI
Rnor_6.02029,735,866 - 29,738,408 (-)NCBI
Rnor_5.02031,532,769 - 31,569,063 (-)NCBI
RGSC_v3.42027,480,448 - 27,482,990 (-)RGD
Celera2029,558,419 - 29,560,961 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099127   ⟹   XP_038955055
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82028,657,309 - 28,694,976 (-)NCBI
mRatBN7.22028,114,387 - 28,152,046 (-)NCBI
Protein Sequences
Protein RefSeqs NP_445860 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955055 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD54386 (Get FASTA)   NCBI Sequence Viewer  
  EDL93054 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000000697
  ENSRNOP00000000697.2
GenBank Protein Q9QZL2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_445860   ⟸   NM_053408
- Sequence:
RefSeq Acc Id: ENSRNOP00000000697   ⟸   ENSRNOT00000000697
RefSeq Acc Id: XP_038955055   ⟸   XM_039099127
- Peptide Label: isoform X1
- UniProtKB: Q9QZL2 (UniProtKB/Swiss-Prot),   F1LN90 (UniProtKB/TrEMBL),   A6K3W8 (UniProtKB/TrEMBL)
Protein Domains
Sulfotransferase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9QZL2-F1-model_v2 AlphaFold Q9QZL2 1-474 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620355 AgrOrtholog
BioCyc Gene G2FUF-3745 BioCyc
BioCyc Pathway PWY-6567 [chondroitin sulfate biosynthesis] BioCyc
BioCyc Pathway Image PWY-6567 BioCyc
Ensembl Genes ENSRNOG00000000572 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000697.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Carbohydrate_sulfotransferase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sulfotransferase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84468 UniProtKB/Swiss-Prot
NCBI Gene 84468 ENTREZGENE
PANTHER CARBOHYDRATE SULFOTRANSFERASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CARBOHYDRATE SULFOTRANSFERASE 3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Sulfotransfer_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Chst3 PhenoGen
PIRSF Carbohydrate_sulfotransferase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000572 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6K3W8 ENTREZGENE, UniProtKB/TrEMBL
  CHST3_RAT UniProtKB/Swiss-Prot
  F1LN90 ENTREZGENE, UniProtKB/TrEMBL
  Q9QZL2 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-18 Chst3  carbohydrate sulfotransferase 3  Chst3  carbohydrate (chondroitin 6) sulfotransferase 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Chst3  carbohydrate (chondroitin 6) sulfotransferase 3  LOC102554900  uncharacterized LOC102554900  Data merged from RGD:7635649 737654 PROVISIONAL
2013-12-18 LOC102554900  uncharacterized LOC102554900      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-02-04 Chst3  carbohydrate (chondroitin 6) sulfotransferase 3  Chst3  carbohydrate sulfotransferase 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Chst3  carbohydrate sulfotransferase 3  Chst3  carbohydrate (chondroitin 6/keratan) sulfotransferase 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Chst3  carbohydrate (chondroitin 6/keratan) sulfotransferase 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Chst3  carbohydrate (chondroitin 6/keratan) sulfotransferase 3      Symbol and Name status set to provisional 70820 PROVISIONAL