Human Gene B4GALNT1 (ENST00000341156.9) from GENCODE V44
  Description: Homo sapiens beta-1,4-N-acetyl-galactosaminyltransferase 1 (B4GALNT1), transcript variant 1, mRNA. (from RefSeq NM_001478)
RefSeq Summary (NM_001478): GM2 and GD2 gangliosides are sialic acid-containing glycosphingolipids. GalNAc-T is the enzyme involved in the biosynthesis of G(M2) and G(D2) glycosphingolipids. GalNAc-T catalyzes the transfer of GalNAc into G(M3) and G(D3) by a beta-1,4 linkage, resulting in the synthesis of G(M2) and G(D2), respectively. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2013].
Gencode Transcript: ENST00000341156.9
Gencode Gene: ENSG00000135454.14
Transcript (Including UTRs)
   Position: hg38 chr12:57,623,409-57,633,201 Size: 9,793 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr12:57,626,744-57,632,132 Size: 5,389 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:57,623,409-57,633,201)mRNA (may differ from genome)Protein (533 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: B4GN1_HUMAN
DESCRIPTION: RecName: Full=Beta-1,4 N-acetylgalactosaminyltransferase 1; EC=2.4.1.92; AltName: Full=(N-acetylneuraminyl)-galactosylglucosylceramide; AltName: Full=GM2/GD2 synthase; AltName: Full=GalNAc-T;
FUNCTION: Involved in the biosynthesis of gangliosides GM2, GD2 and GA2.
CATALYTIC ACTIVITY: UDP-N-acetyl-D-galactosamine + 1-O-(O-(N- acetyl-alpha-neuraminosyl)-(2->3)-O-beta-D-galactopyranosyl- (1->4)-beta-D-glucopyranosyl)-ceramide = UDP + 1-O-(O-2- (acetylamino)-2-deoxy-beta-D-galactopyranosyl-(1->4)-O-(N-acetyl- alpha-neuraminosyl-(2->3))-O-beta-D-galactopyranosyl-(1->4)-beta- D-glucopyranosyl)-ceramide.
PATHWAY: Protein modification; protein glycosylation.
SUBUNIT: Homodimer; disulfide-linked.
SUBCELLULAR LOCATION: Golgi apparatus membrane; Single-pass type II membrane protein.
SIMILARITY: Belongs to the glycosyltransferase 2 family.
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/";
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=Beta-1,4 N-acetylgalactosaminyltransferase 1; URL="http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=gt_hum_480";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: B4GALNT1
Diseases sorted by gene-association score: spastic paraplegia 26, autosomal recessive* (1588), spastic paraplegia 26* (540), mucopolysaccharidosis iii (5)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 33.99 RPKM in Brain - Cerebellum
Total median expression: 202.45 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 -196.80431-0.457 Picture PostScript Text
3' UTR -1163.203335-0.349 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
IPR001173 - Glyco_trans_2
IPR011143 - GM2_synthase

Pfam Domains:
PF00535 - Glycosyl transferase family 2

ModBase Predicted Comparative 3D Structure on Q00973
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003947 (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity
GO:0008376 acetylgalactosaminyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0016758 transferase activity, transferring hexosyl groups

Biological Process:
GO:0001574 ganglioside biosynthetic process
GO:0005975 carbohydrate metabolic process
GO:0006629 lipid metabolic process
GO:0006665 sphingolipid metabolic process
GO:0006687 glycosphingolipid metabolic process
GO:0007283 spermatogenesis
GO:0019915 lipid storage
GO:0030259 lipid glycosylation

Cellular Component:
GO:0000139 Golgi membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030173 integral component of Golgi membrane


-  Descriptions from all associated GenBank mRNAs
  KY966298 - Homo sapiens cell line 94T778 B4GALNT1 isoform1/SLC28A3 fusion mRNA, partial sequence.
AB209460 - Homo sapiens mRNA for UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)- galactosylglucosylceramide N-acetylgalactosaminyltransferase variant protein.
BC015493 - Homo sapiens cDNA clone IMAGE:3903666.
LF208926 - JP 2014500723-A/16429: Polycomb-Associated Non-Coding RNAs.
MA444503 - JP 2018138019-A/16429: Polycomb-Associated Non-Coding RNAs.
M83651 - Human beta-1,4 N-acetylgalactosaminyltransferase mRNA, complete cds.
JD062246 - Sequence 43270 from Patent EP1572962.
JD444268 - Sequence 425292 from Patent EP1572962.
JD087300 - Sequence 68324 from Patent EP1572962.
JD216741 - Sequence 197765 from Patent EP1572962.
JD084736 - Sequence 65760 from Patent EP1572962.
JD045735 - Sequence 26759 from Patent EP1572962.
JD511985 - Sequence 493009 from Patent EP1572962.
JD409705 - Sequence 390729 from Patent EP1572962.
JD364743 - Sequence 345767 from Patent EP1572962.
AK127448 - Homo sapiens cDNA FLJ45540 fis, clone BRTHA2033155.
JD218483 - Sequence 199507 from Patent EP1572962.
JD543618 - Sequence 524642 from Patent EP1572962.
JD188539 - Sequence 169563 from Patent EP1572962.
AK293432 - Homo sapiens cDNA FLJ55323 complete cds, highly similar to Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92).
JD269322 - Sequence 250346 from Patent EP1572962.
JD385539 - Sequence 366563 from Patent EP1572962.
JD566596 - Sequence 547620 from Patent EP1572962.
JD390655 - Sequence 371679 from Patent EP1572962.
JD227285 - Sequence 208309 from Patent EP1572962.
JD500386 - Sequence 481410 from Patent EP1572962.
JD417948 - Sequence 398972 from Patent EP1572962.
JD443653 - Sequence 424677 from Patent EP1572962.
JD519615 - Sequence 500639 from Patent EP1572962.
JD417825 - Sequence 398849 from Patent EP1572962.
JD531966 - Sequence 512990 from Patent EP1572962.
JD260233 - Sequence 241257 from Patent EP1572962.
LC273521 - Homo sapiens B4GALNT1 mRNA for beta-1,4-N-acetyl-galactosaminyl transferase 1, complete cds.
AK299845 - Homo sapiens cDNA FLJ60142 complete cds, highly similar to Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92).
LF324138 - JP 2014500723-A/131641: Polycomb-Associated Non-Coding RNAs.
MA559715 - JP 2018138019-A/131641: Polycomb-Associated Non-Coding RNAs.
HQ860788 - Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1 isoform c (B4GALNT1) mRNA, partial cds, alternatively spliced.
HQ860786 - Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1 isoform a (B4GALNT1) mRNA, partial cds, alternatively spliced.
HQ860787 - Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1 isoform b (B4GALNT1) mRNA, partial cds, alternatively spliced.
BC029828 - Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1, mRNA (cDNA clone MGC:34476 IMAGE:5176204), complete cds.
AK289690 - Homo sapiens cDNA FLJ75209 complete cds, highly similar to Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1, mRNA.
JF432494 - Synthetic construct Homo sapiens clone IMAGE:100073715 beta-1,4-N-acetyl-galactosaminyl transferase 1 (B4GALNT1) gene, encodes complete protein.
KJ904466 - Synthetic construct Homo sapiens clone ccsbBroadEn_13860 B4GALNT1 gene, encodes complete protein.
HQ860789 - Homo sapiens beta-1,4-N-acetyl-galactosaminyl transferase 1 isoform d (B4GALNT1) mRNA, partial cds, alternatively spliced.
LF212362 - JP 2014500723-A/19865: Polycomb-Associated Non-Coding RNAs.
MA447939 - JP 2018138019-A/19865: Polycomb-Associated Non-Coding RNAs.
AK302503 - Homo sapiens cDNA FLJ55781 complete cds, highly similar to Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92).
LF213198 - JP 2014500723-A/20701: Polycomb-Associated Non-Coding RNAs.
MA448775 - JP 2018138019-A/20701: Polycomb-Associated Non-Coding RNAs.
KY966277 - Homo sapiens cell line 93T449 B4GALNT1/SLC28A3 isoform1 fusion mRNA, partial sequence.
JD383465 - Sequence 364489 from Patent EP1572962.
JD387428 - Sequence 368452 from Patent EP1572962.
JD386133 - Sequence 367157 from Patent EP1572962.
JD114775 - Sequence 95799 from Patent EP1572962.
JD473089 - Sequence 454113 from Patent EP1572962.
JD179137 - Sequence 160161 from Patent EP1572962.
JD307527 - Sequence 288551 from Patent EP1572962.
JD124672 - Sequence 105696 from Patent EP1572962.
JD191335 - Sequence 172359 from Patent EP1572962.
JD108520 - Sequence 89544 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00604 - Glycosphingolipid biosynthesis - ganglio series
hsa01100 - Metabolic pathways

BioCyc Knowledge Library
PWY-7835 - superpathway of glycosphingolipids biosynthesis
PWY-7836 - ganglio-series glycosphingolipids biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein Q00973 (Reactome details) participates in the following event(s):

R-HSA-8856223 B4GALNT1 dimer transfers GalNAc from UDP-GalNAc to GM3 and GD3 gangliosides
R-HSA-1660662 Glycosphingolipid metabolism
R-HSA-428157 Sphingolipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B4GN1_HUMAN, ENST00000341156.1, ENST00000341156.2, ENST00000341156.3, ENST00000341156.4, ENST00000341156.5, ENST00000341156.6, ENST00000341156.7, ENST00000341156.8, GALGT, NM_001478, Q00973, SIAT2, uc001spg.1, uc001spg.2, uc001spg.3, uc001spg.4
UCSC ID: ENST00000341156.9
RefSeq Accession: NM_001478
Protein: Q00973 (aka B4GN1_HUMAN)
CCDS: CCDS8950.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene B4GALNT1:
hsp (Hereditary Spastic Paraplegia Overview)

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