Chst6 (carbohydrate sulfotransferase 6) - Rat Genome Database

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Gene: Chst6 (carbohydrate sulfotransferase 6) Rattus norvegicus
Analyze
Symbol: Chst6 (Ensembl: Chst5)
Name: carbohydrate sulfotransferase 6 (Ensembl:carbohydrate sulfotransferase 5)
RGD ID: 1561144
Description: Predicted to enable N-acetylglucosamine 6-O-sulfotransferase activity and keratan sulfotransferase activity. Predicted to be involved in N-acetylglucosamine metabolic process; keratan sulfate proteoglycan biosynthetic process; and sulfur compound metabolic process. Predicted to be located in Golgi membrane. Predicted to be active in trans-Golgi network. Human ortholog(s) of this gene implicated in macular corneal dystrophy. Orthologous to several human genes including CHST6 (carbohydrate sulfotransferase 6); PARTICIPATES IN keratan sulfate biosynthetic pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5; carbohydrate sulfotransferase 5; Chst5; LOC307859; RGD1561144; similar to N-acetylglucosamine 6-O-sulfotransferase
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,769,991 - 56,790,276 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1956,769,967 - 56,790,306 (-)EnsemblGRCr8
mRatBN7.21939,860,729 - 39,881,019 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,860,501 - 39,881,064 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1946,719,098 - 46,744,874 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,372,429 - 47,398,208 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,617,795 - 49,643,612 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,115,065 - 44,136,092 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,115,120 - 44,135,387 (-)Ensemblrn6Rnor6.0
Rnor_5.01954,922,189 - 54,942,505 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41941,830,419 - 41,850,686 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1939,220,192 - 39,241,612 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:11278593   PMID:11352640   PMID:12218059  


Genomics

Comparative Map Data
Chst6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81956,769,991 - 56,790,276 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1956,769,967 - 56,790,306 (-)EnsemblGRCr8
mRatBN7.21939,860,729 - 39,881,019 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1939,860,501 - 39,881,064 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1946,719,098 - 46,744,874 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01947,372,429 - 47,398,208 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01949,617,795 - 49,643,612 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,115,065 - 44,136,092 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,115,120 - 44,135,387 (-)Ensemblrn6Rnor6.0
Rnor_5.01954,922,189 - 54,942,505 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41941,830,419 - 41,850,686 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1939,220,192 - 39,241,612 (-)NCBICelera
Cytogenetic Map19q12NCBI
CHST6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381675,472,042 - 75,495,441 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1675,472,052 - 75,495,458 (-)Ensemblhg38GRCh38
GRCh371675,505,940 - 75,529,339 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361674,064,523 - 74,086,427 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341674,064,525 - 74,086,427NCBI
Celera1659,801,332 - 59,823,234 (-)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1661,258,395 - 61,267,163 (-)NCBIHuRef
CHM1_11676,919,368 - 76,941,254 (-)NCBICHM1_1
T2T-CHM13v2.01681,520,232 - 81,543,637 (-)NCBIT2T-CHM13v2.0
Chst5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398112,615,767 - 112,636,831 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8112,615,768 - 112,637,079 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388111,889,135 - 111,910,199 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8111,889,136 - 111,910,447 (-)Ensemblmm10GRCm38
MGSCv378114,413,035 - 114,434,099 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368114,775,809 - 114,815,449 (-)NCBIMGSCv36mm8
Celera8116,117,689 - 116,138,892 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map858.11NCBI
CHST6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21885,190,118 - 85,210,987 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11691,112,794 - 91,133,660 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01656,041,518 - 56,062,463 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11675,389,610 - 75,410,263 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1675,394,187 - 75,395,374 (-)EnsemblpanPan2panpan1.1
LOC489707
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1575,266,932 - 75,280,790 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha575,243,924 - 75,257,918 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0575,580,429 - 75,594,782 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1575,516,316 - 75,530,593 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0575,351,643 - 75,365,789 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0575,842,944 - 75,856,924 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC100522551
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1612,166,178 - 12,188,165 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2612,006,544 - 12,029,057 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHST6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1560,962,903 - 60,979,834 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604715,080,448 - 15,098,439 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chst6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474611,429,970 - 11,444,277 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Chst6
29 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:197
Count of miRNA genes:152
Interacting mature miRNAs:164
Transcripts:ENSRNOT00000026262
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)191922068964220689Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)192010930665109306Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat

Markers in Region
RH141146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21939,860,731 - 39,860,932 (+)MAPPERmRatBN7.2
Rnor_6.01944,115,120 - 44,115,320NCBIRnor6.0
Rnor_5.01954,922,209 - 54,922,409UniSTSRnor5.0
RGSC_v3.41941,830,419 - 41,830,619UniSTSRGSC3.4
Celera1939,220,192 - 39,220,392UniSTS
RH 3.4 Map19516.2UniSTS
Cytogenetic Map19q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
14 11 29 129 74 81 52 24 52 6 219 75 11 114 70 87 29 11 11

Sequence


Ensembl Acc Id: ENSRNOT00000026262   ⟹   ENSRNOP00000026262
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1956,769,992 - 56,790,306 (-)Ensembl
mRatBN7.2 Ensembl1939,860,720 - 39,881,052 (-)Ensembl
Rnor_6.0 Ensembl1944,115,120 - 44,135,387 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000109790   ⟹   ENSRNOP00000088767
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1956,769,967 - 56,773,239 (-)Ensembl
mRatBN7.2 Ensembl1939,860,724 - 39,865,153 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116386   ⟹   ENSRNOP00000077730
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1956,769,995 - 56,779,803 (-)Ensembl
mRatBN7.2 Ensembl1939,860,501 - 39,881,064 (-)Ensembl
RefSeq Acc Id: NM_001107431   ⟹   NP_001100901
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,770,004 - 56,790,272 (-)NCBI
mRatBN7.21939,860,732 - 39,881,018 (-)NCBI
Rnor_6.01944,115,120 - 44,135,387 (-)NCBI
Rnor_5.01954,922,189 - 54,942,505 (-)NCBI
RGSC_v3.41941,830,419 - 41,850,686 (-)RGD
Celera1939,220,192 - 39,241,612 (-)RGD
Sequence:
RefSeq Acc Id: XM_006255632   ⟹   XP_006255694
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,769,991 - 56,790,276 (-)NCBI
mRatBN7.21939,860,729 - 39,881,007 (-)NCBI
Rnor_6.01944,115,130 - 44,136,092 (-)NCBI
Rnor_5.01954,922,189 - 54,942,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006255633   ⟹   XP_006255695
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81956,769,991 - 56,790,276 (-)NCBI
mRatBN7.21939,860,729 - 39,881,019 (-)NCBI
Rnor_6.01944,115,065 - 44,136,092 (-)NCBI
Rnor_5.01954,922,189 - 54,942,505 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001100901   ⟸   NM_001107431
- UniProtKB: D4A9P8 (UniProtKB/TrEMBL),   A6IZB3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255695   ⟸   XM_006255633
- Peptide Label: isoform X1
- UniProtKB: A0A8I6GGK1 (UniProtKB/TrEMBL),   A6IZB4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255694   ⟸   XM_006255632
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000026262   ⟸   ENSRNOT00000026262
Ensembl Acc Id: ENSRNOP00000088767   ⟸   ENSRNOT00000109790
Ensembl Acc Id: ENSRNOP00000077730   ⟸   ENSRNOT00000116386
Protein Domains
Sulfotransferase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9P8-F1-model_v2 AlphaFold D4A9P8 1-418 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:1561144 AgrOrtholog
BioCyc Gene G2FUF-5638 BioCyc
Ensembl Genes ENSRNOG00000021521 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026262 ENTREZGENE
  ENSRNOT00000026262.7 UniProtKB/TrEMBL
  ENSRNOT00000109790 ENTREZGENE
  ENSRNOT00000109790.2 UniProtKB/TrEMBL
  ENSRNOT00000116386.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro Carbohydrate_sulfotransferase UniProtKB/TrEMBL
  Gal/GlcNAc/GalNAc_ST UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Sulfotransferase_dom UniProtKB/TrEMBL
KEGG Report rno:307859 UniProtKB/TrEMBL
NCBI Gene 307859 ENTREZGENE
PANTHER CARBOHYDRATE SULFOTRANSFERASE UniProtKB/TrEMBL
  CARBOHYDRATE SULFOTRANSFERASE 6 UniProtKB/TrEMBL
Pfam Sulfotransfer_1 UniProtKB/TrEMBL
PhenoGen Chst6 PhenoGen
PIRSF Carbohydrate_sulfotransferase UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021521 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8I6GGK1 ENTREZGENE, UniProtKB/TrEMBL
  A6IZB3 ENTREZGENE, UniProtKB/TrEMBL
  A6IZB4 ENTREZGENE, UniProtKB/TrEMBL
  D4A9P8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2025-02-03 Chst6  carbohydrate sulfotransferase 6  Chst5  carbohydrate sulfotransferase 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2017-07-17 Chst5  carbohydrate sulfotransferase 5  Chst5  carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Chst5  carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5  RGD1561144_predicted  similar to N-acetylglucosamine 6-O-sulfotransferase (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561144_predicted  similar to N-acetylglucosamine 6-O-sulfotransferase (predicted)  LOC307859  similar to N-acetylglucosamine 6-O-sulfotransferase  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC307859  similar to N-acetylglucosamine 6-O-sulfotransferase      Symbol and Name status set to provisional 70820 PROVISIONAL