Human Gene HS3ST6 (ENST00000454677.3_8) from GENCODE V47lift37

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Description: heparan sulfate-glucosamine 3-sulfotransferase 6 (from RefSeq NM_001009606.4)
Gencode Transcript: ENST00000454677.3_8
Gencode Gene: ENSG00000162040.7_9
Transcript (Including UTRs)
Position: hg19 chr16:1,961,476-1,968,416 Size: 6,941 Total Exon Count: 2 Strand: -
Coding Region
Position: hg19 chr16:1,961,591-1,968,324 Size: 6,734 Coding Exon Count: 2

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr16:1,961,476-1,968,416)			mRNA (may differ from genome)		Protein (342 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
Malacards	MGI	PubMed	Reactome	UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: HS3S6_HUMAN DESCRIPTION: RecName: Full=Heparan sulfate glucosamine 3-O-sulfotransferase 6; EC=2.8.2.23; AltName: Full=Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 6; Short=3-OST-6; Short=Heparan sulfate 3-O-sulfotransferase 6; Short=h3-OST-6; FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to heparan sulfate. The substrate-specific O-sulfation generates an enzyme-modified heparan sulfate which acts as a binding receptor to Herpes Simplex Virus-1 (HSV-1) and permits its entry. Unlike 3- OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate. CATALYTIC ACTIVITY: 3'-phosphoadenylyl sulfate + [heparan sulfate]-glucosamine = adenosine 3',5'-bisphosphate + [heparan sulfate]-glucosamine 3-sulfate. SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (Probable). SIMILARITY: Belongs to the sulfotransferase 1 family. SEQUENCE CAUTION: Sequence=AAK61299.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAC42157.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/";

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: HS3ST6 Diseases sorted by gene-association score: mental retardation and microcephaly with pontine and cerebellar hypoplasia (2)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D002737 Chloroprene D002794 Choline D005492 Folic Acid D005839 Gentamicins D008715 Methionine C028007 nickel monoxide C428725 pyridaben

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 46.94 RPKM in Skin - Sun Exposed (Lower leg) Total median expression: 108.15 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-42.90	92	-0.466	Picture	PostScript	Text
3' UTR	-39.50	115	-0.343	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR000863 - Sulfotransferase_dom

Pfam Domains:
PF00685 - Sulfotransferase domain
PF13469 - Sulfotransferase family

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q96QI5


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0008146 sulfotransferase activity GO:0008467 [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity GO:0016740 transferase activity Biological Process: GO:0006024 glycosaminoglycan biosynthetic process Cellular Component: GO:0000139 Golgi membrane GO:0005794 Golgi apparatus GO:0016020 membrane GO:0016021 integral component of membrane

Descriptions from all associated GenBank mRNAs


	BC156438 - Synthetic construct Homo sapiens clone IMAGE:100063024, MGC:190666 heparan sulfate (glucosamine) 3-O-sulfotransferase 6 (HS3ST6) mRNA, encodes complete protein. BC172540 - Synthetic construct Homo sapiens clone IMAGE:100069234, MGC:199245 heparan sulfate (glucosamine) 3-O-sulfotransferase 6 (HS3ST6) mRNA, encodes complete protein.

Biochemical and Signaling Pathways


	BioCyc Knowledge Library PWY-6558 - heparan sulfate biosynthesis (late stages) PWY-6564 - heparan sulfate biosynthesis Reactome (by CSHL, EBI, and GO) Protein Q96QI5 (Reactome details) participates in the following event(s): R-HSA-2076611 HS3STs sulfate GlcN at C3 in heparan sulfate R-HSA-2022928 HS-GAG biosynthesis R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism R-HSA-1630316 Glycosaminoglycan metabolism R-HSA-71387 Metabolism of carbohydrates R-HSA-1430728 Metabolism

Other Names for This Gene


	Alternate Gene Symbols: ENST00000454677.1, ENST00000454677.2, HS3S6_HUMAN, HS3ST5, NM_001009606, Q96QI5, Q96RX7, uc320vum.1, uc320vum.2 UCSC ID: ENST00000454677.3_8 RefSeq Accession: NM_001009606.4 Protein: Q96QI5 (aka HS3S6_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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