Chst4 (carbohydrate sulfotransferase 4) - Rat Genome Database

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Gene: Chst4 (carbohydrate sulfotransferase 4) Rattus norvegicus
Analyze
Symbol: Chst4
Name: carbohydrate sulfotransferase 4
RGD ID: 1310798
Description: Predicted to enable N-acetylglucosamine 6-O-sulfotransferase activity. Predicted to be involved in N-acetylglucosamine metabolic process; positive regulation of leukocyte tethering or rolling; and sulfur compound metabolic process. Predicted to act upstream of or within leukocyte tethering or rolling. Predicted to be located in Golgi membrane. Predicted to be active in trans-Golgi network. Orthologous to human CHST4 (carbohydrate sulfotransferase 4); PARTICIPATES IN keratan sulfate biosynthetic pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: carbohydrate (chondroitin 6/keratan) sulfotransferase 4; carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4; LOC307838
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81954,900,914 - 54,911,735 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1954,882,719 - 54,916,648 (-)EnsemblGRCr8
mRatBN7.21937,993,471 - 38,002,123 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,991,417 - 38,003,608 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1944,805,960 - 44,814,535 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01945,459,296 - 45,467,871 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01947,768,905 - 47,777,480 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01941,630,060 - 41,642,373 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1941,631,715 - 41,640,367 (+)Ensemblrn6Rnor6.0
Rnor_5.01952,453,925 - 52,465,993 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41939,900,812 - 39,909,464 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1937,396,998 - 37,405,591 (-)NCBICelera
RGSC_v3.11939,906,652 - 39,907,819 (-)NCBI
Cytogenetic Map19q12NCBI
JBrowse:




Disease 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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10330415   PMID:12855678   PMID:14597732  


Genomics

Comparative Map Data
Chst4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81954,900,914 - 54,911,735 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1954,882,719 - 54,916,648 (-)EnsemblGRCr8
mRatBN7.21937,993,471 - 38,002,123 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1937,991,417 - 38,003,608 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1944,805,960 - 44,814,535 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01945,459,296 - 45,467,871 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01947,768,905 - 47,777,480 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01941,630,060 - 41,642,373 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1941,631,715 - 41,640,367 (+)Ensemblrn6Rnor6.0
Rnor_5.01952,453,925 - 52,465,993 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41939,900,812 - 39,909,464 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1937,396,998 - 37,405,591 (-)NCBICelera
RGSC_v3.11939,906,652 - 39,907,819 (-)NCBI
Cytogenetic Map19q12NCBI
CHST4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381671,526,120 - 71,538,748 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1671,525,233 - 71,541,950 (+)Ensemblhg38GRCh38
GRCh371671,560,023 - 71,572,651 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361670,117,560 - 70,129,917 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341670,117,561 - 70,129,917NCBI
Celera1655,875,874 - 55,888,343 (+)NCBICelera
Cytogenetic Map16q22.2NCBI
HuRef1657,328,061 - 57,340,472 (+)NCBIHuRef
CHM1_11672,972,864 - 72,985,312 (+)NCBICHM1_1
T2T-CHM13v2.01677,343,320 - 77,355,947 (+)NCBIT2T-CHM13v2.0
Chst4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398110,755,776 - 110,766,033 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8110,755,785 - 110,766,372 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388110,029,075 - 110,039,401 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8110,029,153 - 110,039,740 (-)Ensemblmm10GRCm38
MGSCv378112,552,975 - 112,563,234 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368112,918,282 - 112,928,869 (-)NCBIMGSCv36mm8
Celera8114,251,169 - 114,261,515 (-)NCBICelera
Cytogenetic Map8D3NCBI
cM Map857.38NCBI
Chst4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554844,243,148 - 4,244,293 (+)Ensembl
ChiLan1.0NW_0049554844,234,677 - 4,245,092 (+)NCBIChiLan1.0ChiLan1.0
CHST4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21882,620,979 - 82,634,153 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11688,551,897 - 88,565,071 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01653,472,432 - 53,485,605 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11671,363,206 - 71,375,615 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1671,373,703 - 71,374,863 (+)EnsemblpanPan2panpan1.1
CHST4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1577,322,779 - 77,341,017 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl577,331,342 - 77,340,057 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha577,292,995 - 77,301,710 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0577,761,886 - 77,789,503 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl577,770,434 - 77,779,148 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1577,590,532 - 77,599,275 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0577,413,685 - 77,422,400 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0577,912,392 - 77,921,119 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Chst4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934937,360,087 - 37,362,145 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647522,227,835 - 22,229,022 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647522,227,702 - 22,229,022 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CHST4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl614,535,849 - 14,546,972 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1614,532,379 - 14,544,502 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2614,173,077 - 14,181,166 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CHST4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1554,650,418 - 54,663,195 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl554,661,280 - 54,662,446 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604717,469,725 - 17,471,726 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Chst4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474613,738,110 - 13,739,261 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474613,728,973 - 13,740,231 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Chst4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11729,730,011 - 29,741,173 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Chst4
21 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:116
Count of miRNA genes:89
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000022749
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 (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


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
16 10 60 90 81 80 50 26 50 6 217 107 1 70 36 88 30 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000022749   ⟹   ENSRNOP00000022749
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1954,894,429 - 54,911,610 (-)Ensembl
mRatBN7.2 Ensembl1937,991,417 - 38,002,234 (-)Ensembl
Rnor_6.0 Ensembl1941,631,715 - 41,640,367 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000118362   ⟹   ENSRNOP00000080768
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1937,991,417 - 38,003,608 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000160144   ⟹   ENSRNOP00000108802
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1954,882,719 - 54,916,648 (-)Ensembl
RefSeq Acc Id: NM_001107427   ⟹   NP_001100897
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,902,920 - 54,911,572 (-)NCBI
mRatBN7.21937,993,471 - 38,002,123 (-)NCBI
Rnor_6.01941,631,715 - 41,640,367 (+)NCBI
Rnor_5.01952,453,925 - 52,465,993 (+)NCBI
RGSC_v3.41939,900,812 - 39,909,464 (-)RGD
Celera1937,396,998 - 37,405,591 (-)RGD
Sequence:
RefSeq Acc Id: XM_063278054   ⟹   XP_063134124
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81954,900,914 - 54,911,735 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001100897 (Get FASTA)   NCBI Sequence Viewer  
  NP_001421366 (Get FASTA)   NCBI Sequence Viewer  
  XP_063134124 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92526 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022749
  ENSRNOP00000022749.2
  ENSRNOP00000108802.1
RefSeq Acc Id: NP_001100897   ⟸   NM_001107427
- UniProtKB: D3ZLS2 (UniProtKB/TrEMBL),   A6IZ48 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000022749   ⟸   ENSRNOT00000022749
Ensembl Acc Id: ENSRNOP00000080768   ⟸   ENSRNOT00000118362
RefSeq Acc Id: XP_063134124   ⟸   XM_063278054
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000108802   ⟸   ENSRNOT00000160144
Protein Domains
Sulfotransferase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZLS2-F1-model_v2 AlphaFold D3ZLS2 1-388 view protein structure

Transcriptome

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

Promoters
RGD ID:13701130
Promoter ID:EPDNEW_R11654
Type:multiple initiation site
Name:Chst4_1
Description:carbohydrate sulfotransferase 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01941,631,709 - 41,631,769EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310798 AgrOrtholog
BioCyc Gene G2FUF-5701 BioCyc
Ensembl Genes ENSRNOG00000016953 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022749 ENTREZGENE
  ENSRNOT00000022749.5 UniProtKB/TrEMBL
  ENSRNOT00000160144.1 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:307838 UniProtKB/TrEMBL
NCBI Gene 307838 ENTREZGENE
PANTHER CARBOHYDRATE SULFOTRANSFERASE UniProtKB/TrEMBL
  CARBOHYDRATE SULFOTRANSFERASE 4 UniProtKB/TrEMBL
Pfam Sulfotransfer_1 UniProtKB/TrEMBL
PhenoGen Chst4 PhenoGen
PIRSF Carbohydrate_sulfotransferase UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016953 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6IZ48 ENTREZGENE, UniProtKB/TrEMBL
  D3ZLS2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-29 Chst4  carbohydrate sulfotransferase 4  Chst4  carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-02-04 Chst4  carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4  Chst4  carbohydrate sulfotransferase 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Chst4  carbohydrate sulfotransferase 4  Chst4  carbohydrate (chondroitin 6/keratan) sulfotransferase 4   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Chst4  carbohydrate (chondroitin 6/keratan) sulfotransferase 4   Chst4_predicted  carbohydrate (chondroitin 6/keratan) sulfotransferase 4 (predicted)  'predicted' is removed 2292626 APPROVED