Human Gene ST6GALNAC4 (ENST00000335791.10_7) from GENCODE V47lift37
  Description: ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4, transcript variant 1 (from RefSeq NM_175039.4)
Gencode Transcript: ENST00000335791.10_7
Gencode Gene: ENSG00000136840.19_10
Transcript (Including UTRs)
   Position: hg19 chr9:130,670,165-130,679,320 Size: 9,156 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr9:130,670,671-130,678,698 Size: 8,028 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:130,670,165-130,679,320)mRNA (may differ from genome)Protein (302 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIA7D_HUMAN
DESCRIPTION: RecName: Full=Alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3-N-acetyl-galactosaminide alpha-2,6-sialyltransferase; EC=2.4.99.7; AltName: Full=NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc-alpha-2,6-sialyltransferase; AltName: Full=ST6GalNAc IV; Short=ST6GalNAcIV; AltName: Full=Sialyltransferase 3C; Short=SIAT3-C; AltName: Full=Sialyltransferase 7D; Short=SIAT7-D;
FUNCTION: Involved in the biosynthesis of ganglioside GD1A from GM1B. Transfers CMP-NeuAc with an alpha-2,6-linkage to GalNAc residue on NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc of glycoproteins and glycolipids. Prefers glycoproteins to glycolipids (By similarity).
CATALYTIC ACTIVITY: CMP-N-acetylneuraminate + N-acetyl-alpha- neuraminyl-(2->3)-beta-D-galactosyl-(1->3)-N-acetyl-D- galactosaminyl-R = CMP + N-acetyl-alpha-neuraminyl-(2->3)-beta-D- galactosyl-(1->3)-(N-acetyl-alpha-neuraminyl-(2->6))-N-acetyl-D- galactosaminyl-R.
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (By similarity).
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the glycosyltransferase 29 family.
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/Homolog?cat=symbol&symbol=ST6GALNAC4";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=ST6GalNAc IV; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_633";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.73 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 431.74 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -115.00291-0.395 Picture PostScript Text
3' UTR -212.30506-0.420 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
IPR001675 - Glyco_trans_29

Pfam Domains:
PF00777 - Glycosyltransferase family 29 (sialyltransferase)

ModBase Predicted Comparative 3D Structure on Q9H4F1
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001665 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity
GO:0008373 sialyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0047290 (alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha-sialyltransferase activity

Biological Process:
GO:0006486 protein glycosylation
GO:0006664 glycolipid metabolic process
GO:0009311 oligosaccharide metabolic process
GO:0016266 O-glycan processing
GO:0018279 protein N-linked glycosylation via asparagine
GO:0097503 sialylation

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
  AK292049 - Homo sapiens cDNA FLJ77235 complete cds, highly similar to Homo sapiens ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1, 3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 (ST6GALNAC4), transcript variant 3, mRNA.
BC036705 - Homo sapiens ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1, 3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4, mRNA (cDNA clone MGC:12606 IMAGE:4309208), complete cds.
AK000600 - Homo sapiens cDNA FLJ20593 fis, clone KAT08984.
AJ271734 - Homo sapiens mRNA for alpha2,6-sialyltransferase (ST6GalNAc IV gene).
JD484842 - Sequence 465866 from Patent EP1572962.
JD210249 - Sequence 191273 from Patent EP1572962.
JD566134 - Sequence 547158 from Patent EP1572962.
AF127142 - Homo sapiens NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc-alpha-2,6-sialyltransferase alpha2,6-sialyltransferase mRNA, complete cds.
JD123359 - Sequence 104383 from Patent EP1572962.
JD288517 - Sequence 269541 from Patent EP1572962.
JD252069 - Sequence 233093 from Patent EP1572962.
JD058333 - Sequence 39357 from Patent EP1572962.
JD511270 - Sequence 492294 from Patent EP1572962.
JD114581 - Sequence 95605 from Patent EP1572962.
JD366138 - Sequence 347162 from Patent EP1572962.
AB035172 - Homo sapiens ST6GalNAc4 mRNA for N-acetylgalactosaminide alpha2,6-sialyltransferase, complete cds.
KJ893599 - Synthetic construct Homo sapiens clone ccsbBroadEn_02993 ST6GALNAC4 gene, encodes complete protein.
JD379894 - Sequence 360918 from Patent EP1572962.
JD188596 - Sequence 169620 from Patent EP1572962.
JD394862 - Sequence 375886 from Patent EP1572962.
JD464599 - Sequence 445623 from Patent EP1572962.
JD336246 - Sequence 317270 from Patent EP1572962.
JD099781 - Sequence 80805 from Patent EP1572962.
JD157364 - Sequence 138388 from Patent EP1572962.
JD219700 - Sequence 200724 from Patent EP1572962.
JD402254 - Sequence 383278 from Patent EP1572962.
JD121757 - Sequence 102781 from Patent EP1572962.
JD157478 - Sequence 138502 from Patent EP1572962.
JD211527 - Sequence 192551 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H4F1 (Reactome details) participates in the following event(s):

R-HSA-981809 ST6GALNAC3/4 can add a sialic acid to the sialyl T antigen to form the disialyl T antigen
R-HSA-4084980 ST6GALNAC1-6 transfer Neu5Ac to terminal GalNAc (alpha-2,6 link)
R-HSA-977068 Termination of O-glycan biosynthesis
R-HSA-4085001 Sialic acid metabolism
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-446219 Synthesis of substrates in N-glycan biosythesis
R-HSA-5173105 O-linked glycosylation
R-HSA-446193 Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-597592 Post-translational protein modification
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000335791.1, ENST00000335791.2, ENST00000335791.3, ENST00000335791.4, ENST00000335791.5, ENST00000335791.6, ENST00000335791.7, ENST00000335791.8, ENST00000335791.9, NM_175039, Q5T9D0, Q9H4F1, Q9NWU6, Q9UKU1, Q9ULB9, Q9Y3G3, Q9Y3G4, SIA7D_HUMAN, SIAT3C, SIAT7D, uc317uji.1, uc317uji.2
UCSC ID: ENST00000335791.10_7
RefSeq Accession: NM_175039.4
Protein: Q9H4F1 (aka SIA7D_HUMAN or SI7D_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.