CHST13 (carbohydrate sulfotransferase 13) - Rat Genome Database

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Gene: CHST13 (carbohydrate sulfotransferase 13) Homo sapiens
Analyze
Symbol: CHST13
Name: carbohydrate sulfotransferase 13
RGD ID: 1347829
HGNC Page HGNC
Description: Exhibits N-acetylgalactosamine 4-O-sulfotransferase activity and chondroitin 4-sulfotransferase activity. Involved in chondroitin sulfate biosynthetic process. Predicted to localize to Golgi membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: C4ST-3; C4ST3; carbohydrate (chondroitin 4) sulfotransferase 13; chondroitin 4-O-sulfotransferase 3; chondroitin 4-sulfotransferase 3; MGC119278; MGC119279; MGC119281
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3126,524,155 - 126,543,291 (+)EnsemblGRCh38hg38GRCh38
GRCh383126,524,155 - 126,543,291 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373126,242,998 - 126,262,134 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363127,725,866 - 127,744,824 (+)NCBINCBI36hg18NCBI36
Build 343127,725,873 - 127,744,831NCBI
Celera3124,668,006 - 124,686,803 (+)NCBI
Cytogenetic Map3q21.3NCBI
HuRef3123,622,746 - 123,642,308 (+)NCBIHuRef
CHM1_13126,206,151 - 126,225,141 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (HEP)

Gene-Chemical Interaction 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

Additional References at PubMed
PMID:10781601   PMID:12080076   PMID:12477932   PMID:18976975   PMID:20580388   PMID:21873635   PMID:26993826   PMID:30118797   PMID:30948266   PMID:31845005   PMID:32296183  


Genomics

Comparative Map Data
CHST13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3126,524,155 - 126,543,291 (+)EnsemblGRCh38hg38GRCh38
GRCh383126,524,155 - 126,543,291 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373126,242,998 - 126,262,134 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363127,725,866 - 127,744,824 (+)NCBINCBI36hg18NCBI36
Build 343127,725,873 - 127,744,831NCBI
Celera3124,668,006 - 124,686,803 (+)NCBI
Cytogenetic Map3q21.3NCBI
HuRef3123,622,746 - 123,642,308 (+)NCBIHuRef
CHM1_13126,206,151 - 126,225,141 (+)NCBICHM1_1
Chst13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39690,285,333 - 90,302,167 (-)NCBIGRCm39mm39
GRCm39 Ensembl690,285,331 - 90,302,167 (-)Ensembl
GRCm38690,308,351 - 90,325,185 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl690,308,349 - 90,325,185 (-)EnsemblGRCm38mm10GRCm38
MGSCv37690,258,345 - 90,275,179 (-)NCBIGRCm37mm9NCBIm37
MGSCv36690,273,854 - 90,290,666 (-)NCBImm8
Celera692,202,178 - 92,218,890 (-)NCBICelera
Cytogenetic Map6D1NCBI
Chst13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24122,824,712 - 122,837,935 (-)NCBI
Rnor_6.0 Ensembl4122,224,535 - 122,237,754 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04122,223,846 - 122,244,848 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04186,765,215 - 186,786,132 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44124,571,623 - 124,584,842 (-)NCBIRGSC3.4rn4RGSC3.4
Celera4111,749,499 - 111,762,718 (-)NCBICelera
Cytogenetic Map4q34NCBI
Chst13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542121,770,083 - 21,787,563 (+)NCBIChiLan1.0ChiLan1.0
CHST13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13130,901,424 - 130,908,466 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3130,889,157 - 130,907,762 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03123,569,493 - 123,592,816 (+)NCBIMhudiblu_PPA_v0panPan3
CHST13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.120723,380 - 746,935 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha20773,922 - 781,049 (+)NCBI
ROS_Cfam_1.020751,286 - 758,416 (+)NCBI
UMICH_Zoey_3.120479,194 - 486,324 (+)NCBI
UNSW_CanFamBas_1.020808,930 - 815,289 (+)NCBI
UU_Cfam_GSD_1.020767,055 - 774,182 (+)NCBI
CHST13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1373,350,671 - 73,366,086 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11373,350,670 - 73,366,374 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21380,925,716 - 80,943,006 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CHST13
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12254,471,165 - 54,491,436 (-)NCBI
ChlSab1.1 Ensembl2254,471,879 - 54,490,342 (-)Ensembl
Vero_WHO_p1.0NW_023666041111,802,094 - 111,820,440 (+)NCBI
Chst13
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477344,189 - 68,630 (-)NCBI

Position Markers
RH99101  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373126,261,781 - 126,261,964UniSTSGRCh37
Build 363127,744,471 - 127,744,654RGDNCBI36
Celera3124,686,450 - 124,686,633RGD
Cytogenetic Map3q21.3UniSTS
HuRef3123,641,955 - 123,642,138UniSTS
GeneMap99-GB4 RH Map3449.27UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:440
Count of miRNA genes:369
Interacting mature miRNAs:397
Transcripts:ENST00000319340
Prediction methods:Miranda, Rnahybrid
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


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 36 214 424 424 255 424 28 4 75 371 11
Low 690 903 232 52 925 28 1060 215 911 252 297 620 29 531 541
Below cutoff 1506 1638 902 126 229 9 2624 1597 2450 79 633 791 120 630 1777 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000319340   ⟹   ENSP00000317404
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3126,524,155 - 126,543,291 (+)Ensembl
RefSeq Acc Id: ENST00000615522   ⟹   ENSP00000478416
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3126,524,333 - 126,542,879 (+)Ensembl
RefSeq Acc Id: NM_152889   ⟹   NP_690849
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383126,524,155 - 126,543,291 (+)NCBI
GRCh373126,243,131 - 126,262,134 (+)NCBI
Build 363127,725,866 - 127,744,824 (+)NCBI Archive
Celera3124,668,006 - 124,686,803 (+)RGD
HuRef3123,622,746 - 123,642,308 (+)NCBI
CHM1_13126,206,151 - 126,225,141 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_690849   ⟸   NM_152889
- Peptide Label: precursor
- UniProtKB: Q8NET6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000478416   ⟸   ENST00000615522
RefSeq Acc Id: ENSP00000317404   ⟸   ENST00000319340

Promoters
RGD ID:6865548
Promoter ID:EPDNEW_H5939
Type:initiation region
Name:CHST13_1
Description:carbohydrate sulfotransferase 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh383126,524,309 - 126,524,369EPDNEW
RGD ID:6800964
Promoter ID:HG_KWN:46083
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   NB4
Transcripts:ENST00000383575,   NM_152889
Position:
Human AssemblyChrPosition (strand)Source
Build 363127,725,639 - 127,726,139 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q21.3(chr3:126167799-126819908)x3 copy number gain See cases [RCV000051531] Chr3:126167799..126819908 [GRCh38]
Chr3:125886642..126538751 [GRCh37]
Chr3:127369332..128021441 [NCBI36]
Chr3:3q21.3
uncertain significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29
pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3
pathogenic
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 copy number loss See cases [RCV000140814] Chr3:121925147..126782249 [GRCh38]
Chr3:121643994..126501092 [GRCh37]
Chr3:123126684..127983782 [NCBI36]
Chr3:3q13.33-21.3
pathogenic
GRCh38/hg38 3q21.3-23(chr3:126106779-140918089)x3 copy number gain See cases [RCV000142010] Chr3:126106779..140918089 [GRCh38]
Chr3:125825622..140636931 [GRCh37]
Chr3:127308312..142119621 [NCBI36]
Chr3:3q21.3-23
uncertain significance
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24
pathogenic
GRCh38/hg38 3q13.32-21.3(chr3:118673898-126540730)x1 copy number loss See cases [RCV000143695] Chr3:118673898..126540730 [GRCh38]
Chr3:118392745..126259573 [GRCh37]
Chr3:119875435..127742263 [NCBI36]
Chr3:3q13.32-21.3
pathogenic
GRCh37/hg19 3q21.2-21.3(chr3:124806350-126567150)x4 copy number gain See cases [RCV000448957] Chr3:124806350..126567150 [GRCh37]
Chr3:3q21.2-21.3
uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3q21.2-21.3(chr3:124369671-126423192) copy number loss not provided [RCV000767706] Chr3:124369671..126423192 [GRCh37]
Chr3:3q21.2-21.3
likely pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:21755 AgrOrtholog
COSMIC CHST13 COSMIC
Ensembl Genes ENSG00000180767 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000317404 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000478416 UniProtKB/TrEMBL
Ensembl Transcript ENST00000319340 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000615522 UniProtKB/TrEMBL
GTEx ENSG00000180767 GTEx
HGNC ID HGNC:21755 ENTREZGENE
Human Proteome Map CHST13 Human Proteome Map
InterPro Carb_sulfotrans_8-10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sulfotransferase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:166012 UniProtKB/Swiss-Prot
NCBI Gene 166012 ENTREZGENE
OMIM 610124 OMIM
PANTHER PTHR12137 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Sulfotransfer_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134976803 PharmGKB
UniProt A0A087WU70_HUMAN UniProtKB/TrEMBL
  CHSTD_HUMAN UniProtKB/Swiss-Prot
  Q3ZCR4_HUMAN UniProtKB/TrEMBL
  Q3ZCU8_HUMAN UniProtKB/TrEMBL
  Q8NET6 ENTREZGENE
UniProt Secondary Q3SYA3 UniProtKB/Swiss-Prot
  Q3SYA5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-17 CHST13  carbohydrate sulfotransferase 13  CHST13  carbohydrate (chondroitin 4) sulfotransferase 13  Symbol and/or name change 5135510 APPROVED