Human Gene ST8SIA4 (uc003knk.3)
  Description: Homo sapiens ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 (ST8SIA4), transcript variant 1, mRNA.
RefSeq Summary (NM_005668): The protein encoded by this gene catalyzes the polycondensation of alpha-2,8-linked sialic acid required for the synthesis of polysialic acid, a modulator of the adhesive properties of neural cell adhesion molecule (NCAM1). The encoded protein, which is a member of glycosyltransferase family 29, is a type II membrane protein that may be present in the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr5:100,142,639-100,238,987 Size: 96,349 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr5:100,147,551-100,238,659 Size: 91,109 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:100,142,639-100,238,987)mRNA (may differ from genome)Protein (359 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIA8D_HUMAN
DESCRIPTION: RecName: Full=CMP-N-acetylneuraminate-poly-alpha-2,8-sialyltransferase; EC=2.4.99.-; AltName: Full=Alpha-2,8-sialyltransferase 8D; AltName: Full=Polysialyltransferase-1; AltName: Full=Sialyltransferase 8D; Short=SIAT8-D; AltName: Full=Sialytransferase St8Sia IV; Short=ST8SiaIV;
FUNCTION: Catalyzes the polycondensation of alpha-2,8-linked sialic acid required for the synthesis of polysialic acid (PSA), which is present on the embryonic neural cell adhesion molecule (N-CAM), necessary for plasticity of neural cells.
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein (Potential).
TISSUE SPECIFICITY: Highly expressed in fetal brain, lung and kidney and in adult heart, spleen and thymus. Present to a lesser extent in adult brain, placenta, lung, large and small intestine and peripheral blood leukocytes.
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=ST8SIA4";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=ST8Sia IV; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_639";

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ST8SIA4
CDC HuGE Published Literature: ST8SIA4
Positive Disease Associations: Albuminuria , Blood Pressure , Body Mass Index , Body Weight , Carotid Arteries , Cholesterol, HDL , Conduct Disorder , Creatinine , Echocardiography , Erythrocyte Indices , Fibrinogen , Glomerular Filtration Rate , Inflammatory Bowel Diseases , Lipoproteins, VLDL
Related Studies:
  1. Albuminuria
    Shih-Jen Hwang et al. BMC medical genetics 2007, A genome-wide association for kidney function and endocrine-related traits in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903292]
    Kidney function traits and TSH are associated with SNPs on the Affymetrix GeneChip Human Mapping 100K SNP set. These data will serve as a valuable resource for replication as more SNPs associated with kidney function and endocrine traits are identified.
  2. Blood Pressure
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  3. Blood Pressure
    Christopher J O'Donnell et al. BMC medical genetics 2007, Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study., BMC medical genetics. [PubMed 17903303]
    The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: ST8SIA4
Diseases sorted by gene-association score: granuloma inguinale (2)

-  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: 7.79 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 51.04 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 -125.30328-0.382 Picture PostScript Text
3' UTR -1252.304912-0.255 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
IPR012163 - Sialyl_trans

Pfam Domains:
PF00777 - Glycosyltransferase family 29 (sialyltransferase)

ModBase Predicted Comparative 3D Structure on Q92187
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003828 alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity
GO:0008373 sialyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0033691 sialic acid binding

Biological Process:
GO:0001574 ganglioside biosynthetic process
GO:0006464 cellular protein modification process
GO:0006486 protein glycosylation
GO:0006491 N-glycan processing
GO:0007399 nervous system development
GO:0009311 oligosaccharide metabolic process
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
  BC040671 - Homo sapiens ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4, mRNA (cDNA clone IMAGE:4816784).
DL492306 - Novel nucleic acids.
DL490801 - Novel nucleic acids.
JD362513 - Sequence 343537 from Patent EP1572962.
JD381327 - Sequence 362351 from Patent EP1572962.
JD069997 - Sequence 51021 from Patent EP1572962.
BC053657 - Homo sapiens ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4, mRNA (cDNA clone MGC:61459 IMAGE:5752337), complete cds.
L41680 - Homo sapiens alpha-2,8-polysialyltransferase (PST) gene, complete cds.
JD514805 - Sequence 495829 from Patent EP1572962.
JD324147 - Sequence 305171 from Patent EP1572962.
JD314567 - Sequence 295591 from Patent EP1572962.
JD546743 - Sequence 527767 from Patent EP1572962.
JD171259 - Sequence 152283 from Patent EP1572962.
AK292872 - Homo sapiens cDNA FLJ75830 complete cds, highly similar to Homo sapiens ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 (ST8SIA4), transcript variant 1, mRNA.
JD168079 - Sequence 149103 from Patent EP1572962.
JD111322 - Sequence 92346 from Patent EP1572962.
AB529101 - Synthetic construct DNA, clone: pF1KB4480, Homo sapiens ST8SIA4 gene for ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4, without stop codon, in Flexi system.
BC027866 - Homo sapiens ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4, mRNA (cDNA clone IMAGE:5203343), complete cds.
CU693302 - Synthetic construct Homo sapiens gateway clone IMAGE:100017952 5' read ST8SIA4 mRNA.
HQ448744 - Synthetic construct Homo sapiens clone IMAGE:100072190; CCSB008773_01 ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 (ST8SIA4) gene, encodes complete protein.
KJ897792 - Synthetic construct Homo sapiens clone ccsbBroadEn_07186 ST8SIA4 gene, encodes complete protein.
JD426146 - Sequence 407170 from Patent EP1572962.
JD513719 - Sequence 494743 from Patent EP1572962.
JD184346 - Sequence 165370 from Patent EP1572962.
JD106554 - Sequence 87578 from Patent EP1572962.
JD360442 - Sequence 341466 from Patent EP1572962.
JD362423 - Sequence 343447 from Patent EP1572962.
JD048835 - Sequence 29859 from Patent EP1572962.
JD199937 - Sequence 180961 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00604 - Glycosphingolipid biosynthesis - ganglio series

BioCarta from NCI Cancer Genome Anatomy Project
h_aMANpathway - Steps in the Glycosylation of Mammalian N-linked Oligosaccarides

Reactome (by CSHL, EBI, and GO)

Protein Q92187 (Reactome details) participates in the following event(s):

R-HSA-422454 Polysialylation of NCAM1
R-HSA-4084978 ST8SIA1-6 transfer Neu5Ac to terminal Neu5Ac residues
R-HSA-419037 NCAM1 interactions
R-HSA-4085001 Sialic acid metabolism
R-HSA-375165 NCAM signaling for neurite out-growth
R-HSA-446219 Synthesis of substrates in N-glycan biosythesis
R-HSA-422475 Axon guidance
R-HSA-446193 Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-1266738 Developmental Biology
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8KA07, NM_005668, NP_005659, PST, PST1, Q92187, Q92693, SIA8D_HUMAN, SIAT8D
UCSC ID: uc003knk.3
RefSeq Accession: NM_005668
Protein: Q92187 (aka SIA8D_HUMAN or SI8D_HUMAN)
CCDS: CCDS4091.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005668.4
exon count: 5CDS single in 3' UTR: no RNA size: 6330
ORF size: 1080CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2286.50frame shift in genome: no % Coverage: 99.84
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.