Human Gene ST3GAL1 (uc003yuk.2)
  Description: Homo sapiens ST3 beta-galactoside alpha-2,3-sialyltransferase 1 (ST3GAL1), transcript variant 2, mRNA.
RefSeq Summary (NM_173344): The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi but can be proteolytically processed to a soluble form. Correct glycosylation of the encoded protein may be critical to its sialyltransferase activity. This protein, which is a member of glycosyltransferase family 29, can use the same acceptor substrates as does sialyltransferase 4B. Two transcript variants encoding the same protein have been found for this gene. Other transcript variants may exist, but have not been fully characterized yet. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr8:134,467,091-134,584,183 Size: 117,093 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr8:134,472,007-134,488,267 Size: 16,261 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:134,467,091-134,584,183)mRNA (may differ from genome)Protein (340 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SIA4A_HUMAN
DESCRIPTION: RecName: Full=CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1; Short=Alpha 2,3-ST 1; Short=Beta-galactoside alpha-2,3-sialyltransferase 1; EC=2.4.99.4; AltName: Full=Gal-NAc6S; AltName: Full=Gal-beta-1,3-GalNAc-alpha-2,3-sialyltransferase; AltName: Full=SIATFL; AltName: Full=ST3Gal I; Short=ST3GalI; AltName: Full=ST3GalA.1; AltName: Full=ST3O; AltName: Full=Sialyltransferase 4A; Short=SIAT4-A;
FUNCTION: It may be responsible for the synthesis of the sequence NeuAc-alpha-2,3-Gal-beta-1,3-GalNAc- found on sugar chains O- linked to Thr or Ser and also as a terminal sequence on certain gangliosides. SIAT4A and SIAT4B sialylate the same acceptor substrates but exhibit different Km values.
CATALYTIC ACTIVITY: CMP-N-acetylneuraminate + beta-D-galactosyl- 1,3-N-acetyl-alpha-D-galactosaminyl-R = CMP + alpha-N- acetylneuraminyl-2,3-beta-D-galactosyl-1,3-N-acetyl-alpha-D- galactosaminyl-R.
PATHWAY: Protein modification; protein glycosylation.
SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane; Single-pass type II membrane protein. Secreted. Note=Membrane- bound form in trans cisternae of Golgi. Secreted into the body fluid.
TISSUE SPECIFICITY: Expressed in several tissues. Highest expression in lung, liver, skeletal muscle, kidney, pancreas, spleen and placenta.
PTM: The soluble form derives from the membrane form by proteolytic processing.
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=ST3GAL1";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=ST3Gal I; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_622";

-  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): ST3GAL1
CDC HuGE Published Literature: ST3GAL1
Positive Disease Associations: Albuminuria , Alzheimer Disease , Blood Pressure , Calcium , Cardiomegaly , Carotid Artery Diseases , Cholesterol, LDL , Echocardiography , Heart Failure , Heart Rate , Hip , Lipoproteins, LDL , Lipoproteins, VLDL , Phosphorus , Sleep , Stroke
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. Alzheimer Disease
    , , . [PubMed 0]
  3. Alzheimer Disease
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 38.56 RPKM in Thyroid
Total median expression: 411.15 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 -275.20829-0.332 Picture PostScript Text
3' UTR -1855.384916-0.377 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 Q11201
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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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003836 beta-galactoside (CMP) alpha-2,3-sialyltransferase activity
GO:0008373 sialyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups

Biological Process:
GO:0006054 N-acetylneuraminate metabolic process
GO:0006464 cellular protein modification process
GO:0006486 protein glycosylation
GO:0006487 protein N-linked glycosylation
GO:0009311 oligosaccharide metabolic process
GO:0016266 O-glycan processing
GO:0018146 keratan sulfate biosynthetic process
GO:0018279 protein N-linked glycosylation via asparagine
GO:0097503 sialylation

Cellular Component:
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005794 Golgi apparatus
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032580 Golgi cisterna membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AF059321 - Homo sapiens alpha-2,3-sialyltransferase (SIATFL) mRNA, complete cds.
BC018357 - Homo sapiens ST3 beta-galactoside alpha-2,3-sialyltransferase 1, mRNA (cDNA clone MGC:9183 IMAGE:3925036), complete cds.
BX648001 - Homo sapiens mRNA; cDNA DKFZp686E1559 (from clone DKFZp686E1559).
L13972 - Homo sapiens beta-galactoside alpha-2,3-sialyltransferase (SIAT4A) mRNA, complete cds.
L29555 - Human (clone hST3O-1) sialyltransferase mRNA, complete cds.
KJ897555 - Synthetic construct Homo sapiens clone ccsbBroadEn_06949 ST3GAL1 gene, encodes complete protein.
DQ891156 - Synthetic construct clone IMAGE:100003786; FLH169822.01X; RZPDo839G0696D ST3 beta-galactoside alpha-2,3-sialyltransferase 1 (ST3GAL1) gene, encodes complete protein.
DQ894335 - Synthetic construct Homo sapiens clone IMAGE:100008795; FLH169818.01L; RZPDo839G0695D ST3 beta-galactoside alpha-2,3-sialyltransferase 1 (ST3GAL1) gene, encodes complete protein.
CU676236 - Synthetic construct Homo sapiens gateway clone IMAGE:100018147 5' read ST3GAL1 mRNA.
AK024824 - Homo sapiens cDNA: FLJ21171 fis, clone CAS10962.
BC063665 - Homo sapiens hypothetical protein LOC286167, mRNA (cDNA clone IMAGE:3846489), partial cds.
AL833743 - Homo sapiens mRNA; cDNA DKFZp666E036 (from clone DKFZp666E036).
BX537506 - Homo sapiens mRNA; cDNA DKFZp779K2051 (from clone DKFZp779K2051).
JD522145 - Sequence 503169 from Patent EP1572962.
JD090178 - Sequence 71202 from Patent EP1572962.
JD234822 - Sequence 215846 from Patent EP1572962.
JD419888 - Sequence 400912 from Patent EP1572962.
JD162816 - Sequence 143840 from Patent EP1572962.
JD523728 - Sequence 504752 from Patent EP1572962.
JD351802 - Sequence 332826 from Patent EP1572962.
JD490268 - Sequence 471292 from Patent EP1572962.
JD108689 - Sequence 89713 from Patent EP1572962.
JD043622 - Sequence 24646 from Patent EP1572962.
JD435879 - Sequence 416903 from Patent EP1572962.
JD061527 - Sequence 42551 from Patent EP1572962.
JD433866 - Sequence 414890 from Patent EP1572962.
JD433983 - Sequence 415007 from Patent EP1572962.
BC048803 - Homo sapiens, clone IMAGE:4401795, mRNA.
AK093867 - Homo sapiens cDNA FLJ36548 fis, clone TRACH2007816.
JD499326 - Sequence 480350 from Patent EP1572962.
JD117962 - Sequence 98986 from Patent EP1572962.
JD482189 - Sequence 463213 from Patent EP1572962.
JD260733 - Sequence 241757 from Patent EP1572962.
JD186647 - Sequence 167671 from Patent EP1572962.
JD472861 - Sequence 453885 from Patent EP1572962.
JD404117 - Sequence 385141 from Patent EP1572962.
JD452051 - Sequence 433075 from Patent EP1572962.
JD534598 - Sequence 515622 from Patent EP1572962.
JD470848 - Sequence 451872 from Patent EP1572962.
JD453227 - Sequence 434251 from Patent EP1572962.
JD556106 - Sequence 537130 from Patent EP1572962.
JD383375 - Sequence 364399 from Patent EP1572962.
JD147578 - Sequence 128602 from Patent EP1572962.
JD427385 - Sequence 408409 from Patent EP1572962.
JD205453 - Sequence 186477 from Patent EP1572962.
JD063284 - Sequence 44308 from Patent EP1572962.
JD086162 - Sequence 67186 from Patent EP1572962.
JD252007 - Sequence 233031 from Patent EP1572962.
JD143940 - Sequence 124964 from Patent EP1572962.
JD338241 - Sequence 319265 from Patent EP1572962.
JD444284 - Sequence 425308 from Patent EP1572962.
JD546253 - Sequence 527277 from Patent EP1572962.
JD202067 - Sequence 183091 from Patent EP1572962.
JD260320 - Sequence 241344 from Patent EP1572962.
JD460972 - Sequence 441996 from Patent EP1572962.
JD336392 - Sequence 317416 from Patent EP1572962.
JD054504 - Sequence 35528 from Patent EP1572962.
JD094561 - Sequence 75585 from Patent EP1572962.
JD492896 - Sequence 473920 from Patent EP1572962.
JD361111 - Sequence 342135 from Patent EP1572962.
JD433075 - Sequence 414099 from Patent EP1572962.
JD350098 - Sequence 331122 from Patent EP1572962.
JD392407 - Sequence 373431 from Patent EP1572962.
JD098680 - Sequence 79704 from Patent EP1572962.
JD356144 - Sequence 337168 from Patent EP1572962.
JD273886 - Sequence 254910 from Patent EP1572962.
JD279018 - Sequence 260042 from Patent EP1572962.
JD265643 - Sequence 246667 from Patent EP1572962.
JD223732 - Sequence 204756 from Patent EP1572962.
JD272668 - Sequence 253692 from Patent EP1572962.
JD307297 - Sequence 288321 from Patent EP1572962.
JD095416 - Sequence 76440 from Patent EP1572962.
JD547377 - Sequence 528401 from Patent EP1572962.
JD172062 - Sequence 153086 from Patent EP1572962.
JD206014 - Sequence 187038 from Patent EP1572962.
JD459826 - Sequence 440850 from Patent EP1572962.
JD238730 - Sequence 219754 from Patent EP1572962.
JD543628 - Sequence 524652 from Patent EP1572962.
JD145194 - Sequence 126218 from Patent EP1572962.
JD097284 - Sequence 78308 from Patent EP1572962.
JD503702 - Sequence 484726 from Patent EP1572962.
JD428031 - Sequence 409055 from Patent EP1572962.
JD525011 - Sequence 506035 from Patent EP1572962.
JD319688 - Sequence 300712 from Patent EP1572962.
JD054582 - Sequence 35606 from Patent EP1572962.
JD278558 - Sequence 259582 from Patent EP1572962.
JD230569 - Sequence 211593 from Patent EP1572962.
JD561502 - Sequence 542526 from Patent EP1572962.
JD166053 - Sequence 147077 from Patent EP1572962.
JD262434 - Sequence 243458 from Patent EP1572962.
JD532930 - Sequence 513954 from Patent EP1572962.
JD323853 - Sequence 304877 from Patent EP1572962.
JD508298 - Sequence 489322 from Patent EP1572962.
JD050447 - Sequence 31471 from Patent EP1572962.
JD450772 - Sequence 431796 from Patent EP1572962.
JD117126 - Sequence 98150 from Patent EP1572962.
JD412836 - Sequence 393860 from Patent EP1572962.
JD197831 - Sequence 178855 from Patent EP1572962.
JD396852 - Sequence 377876 from Patent EP1572962.
JD512813 - Sequence 493837 from Patent EP1572962.
JD384629 - Sequence 365653 from Patent EP1572962.
JD114108 - Sequence 95132 from Patent EP1572962.
JD086860 - Sequence 67884 from Patent EP1572962.
JD542280 - Sequence 523304 from Patent EP1572962.
JD422315 - Sequence 403339 from Patent EP1572962.
JD132300 - Sequence 113324 from Patent EP1572962.
JD347023 - Sequence 328047 from Patent EP1572962.
JD291887 - Sequence 272911 from Patent EP1572962.
JD509988 - Sequence 491012 from Patent EP1572962.
JD300918 - Sequence 281942 from Patent EP1572962.
JD090260 - Sequence 71284 from Patent EP1572962.
JD333953 - Sequence 314977 from Patent EP1572962.
JD260835 - Sequence 241859 from Patent EP1572962.
JD247240 - Sequence 228264 from Patent EP1572962.
JD365433 - Sequence 346457 from Patent EP1572962.
JD269201 - Sequence 250225 from Patent EP1572962.
JD133019 - Sequence 114043 from Patent EP1572962.
JD057006 - Sequence 38030 from Patent EP1572962.
JD514811 - Sequence 495835 from Patent EP1572962.
AK311319 - Homo sapiens cDNA, FLJ18361.
JD445574 - Sequence 426598 from Patent EP1572962.
JD341480 - Sequence 322504 from Patent EP1572962.
JD533436 - Sequence 514460 from Patent EP1572962.
JD057654 - Sequence 38678 from Patent EP1572962.
JD328262 - Sequence 309286 from Patent EP1572962.
JD316698 - Sequence 297722 from Patent EP1572962.
JD448950 - Sequence 429974 from Patent EP1572962.
JD168447 - Sequence 149471 from Patent EP1572962.
JD184365 - Sequence 165389 from Patent EP1572962.
JD437716 - Sequence 418740 from Patent EP1572962.
JD443958 - Sequence 424982 from Patent EP1572962.
JD436342 - Sequence 417366 from Patent EP1572962.
JD062265 - Sequence 43289 from Patent EP1572962.
JD480978 - Sequence 462002 from Patent EP1572962.
JD472815 - Sequence 453839 from Patent EP1572962.
JD172736 - Sequence 153760 from Patent EP1572962.
JD329486 - Sequence 310510 from Patent EP1572962.
JD149246 - Sequence 130270 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00512 - O-Glycan biosynthesis
hsa00533 - Glycosaminoglycan biosynthesis - keratan sulfate
hsa00603 - Glycosphingolipid biosynthesis - globo series
hsa00604 - Glycosphingolipid biosynthesis - ganglio series
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q11201 (Reactome details) participates in the following event(s):

R-HSA-981497 ST3GAL1-4 can add a sialic acid to the T antigen at the alpha 3 position
R-HSA-2046285 The keratan chain can be capped by N-acetylneuraminic acid
R-HSA-4084984 ST3GAL1-6 transfer Neu5Ac to terminal Gal (alpha-2,3 link)
R-HSA-977068 Termination of O-glycan biosynthesis
R-HSA-2022854 Keratan sulfate biosynthesis
R-HSA-4085001 Sialic acid metabolism
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-1638074 Keratan sulfate/keratin metabolism
R-HSA-446219 Synthesis of substrates in N-glycan biosythesis
R-HSA-5173105 O-linked glycosylation
R-HSA-1630316 Glycosaminoglycan metabolism
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-71387 Metabolism of carbohydrates
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-392499 Metabolism of proteins
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: NM_173344, NP_775479, O60677, Q11201, Q9UN51, SIA4A_HUMAN, SIAT4, SIAT4A
UCSC ID: uc003yuk.2
RefSeq Accession: NM_173344
Protein: Q11201 (aka SIA4A_HUMAN or SI4A_HUMAN)
CCDS: CCDS6373.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_173344.2
exon count: 10CDS single in 3' UTR: no RNA size: 6768
ORF size: 1023CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1936.00frame shift in genome: no % Coverage: 100.00
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.