Human Gene C1GALT1 (uc003srb.3) Description and Page Index
  Description: Homo sapiens core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 (C1GALT1), mRNA.
RefSeq Summary (NM_020156): The protein encoded by this gene generates the common core 1 O-glycan structure, Gal-beta-1-3GalNAc-R, by the transfer of Gal from UDP-Gal to GalNAc-alpha-1-R. Core 1 is a precursor for many extended mucin-type O-glycans on cell surface and secreted glycoproteins. Studies in mice suggest that this gene plays a key role in thrombopoiesis and kidney homeostasis.[provided by RefSeq, Sep 2010]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR7346977.2784355.1, SRR7346977.2348202.1 [ECO:0000332] ##Evidence-Data-END## ##RefSeq-Attributes-START## CDS uses downstream in-frame AUG :: upstream AUG and CDS extension is not conserved RefSeq Select criteria :: based on manual assertion, conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr7:7,222,246-7,288,280 Size: 66,035 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr7:7,273,951-7,283,358 Size: 9,408 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:7,222,246-7,288,280)mRNA (may differ from genome)Protein (363 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1; EC=; AltName: Full=B3Gal-T8; AltName: Full=Core 1 O-glycan T-synthase; AltName: Full=Core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase 1; Short=Beta-1,3-galactosyltransferase; AltName: Full=Core 1 beta1,3-galactosyltransferase 1; Short=C1GalT1; Short=Core 1 beta3-Gal-T1;
FUNCTION: Glycosyltransferase that generates the core 1 O-glycan Gal-beta1-3GalNAc-alpha1-Ser/Thr (T antigen), which is a precursor for many extended O-glycans in glycoproteins. Plays a central role in many processes, such as angiogenesis, thrombopoiesis and kidney homeostasis development.
CATALYTIC ACTIVITY: UDP-alpha-D-galactose + glycoprotein N-acetyl- D-galactosamine = UDP + glycoprotein D-galactosyl-(1->3)-N-acetyl- D-galactosamine.
COFACTOR: Magnesium (By similarity).
PATHWAY: Protein modification; protein glycosylation.
SUBUNIT: Homodimer; disulfide-linked (By similarity). Interacts with the C1GALT1C1 chaperone; required for galactosyltransferase activity.
SUBCELLULAR LOCATION: Membrane; Single-pass type II membrane protein (By similarity).
TISSUE SPECIFICITY: Widely expressed. Highly expressed in kidney, heart, placenta and liver.
MISCELLANEOUS: Aberrant O-galactosylation of IgA1 molecules plays a role in the development and progression of IgA nephropathy (IgAN). Genetic interactions of C1GALT1 and ST6GALNAC2 variants influence IgA1 O-glycosylation, disease predisposition, and disease severity, and may contribute to the polygenic nature of IgAN.
SIMILARITY: Belongs to the glycosyltransferase 31 family. Beta3- Gal-T subfamily.
WEB RESOURCE: Name=Functional Glycomics Gateway - GTase; Note=Core1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3- galactosyltransferase; URL="";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): C1GALT1
CDC HuGE Published Literature: C1GALT1
Positive Disease Associations: Behcet Syndrome , Bipolar Disorder , Lipids , Metabolism , Multiple Sclerosis , multiple sclerosis (severity) , nephropathy, IgA
Related Studies:
  1. Behcet Syndrome
    Elaine F Remmers et al. Nature genetics 2010, , Nature genetics. [PubMed 20622878]
  2. Bipolar Disorder
    , , . [PubMed 0]
  3. Bipolar Disorder
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: C1GALT1
Diseases sorted by gene-association score: iga glomerulonephritis (9), hypersensitivity vasculitis (5)

-  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: 7.53 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 174.64 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 -114.50223-0.513 Picture PostScript Text
3' UTR -1252.894922-0.255 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
IPR026842 - C1GALT1
IPR003378 - Fringe-like

Pfam Domains:
PF01762 - Galactosyltransferase
PF02434 - Fringe-like

ModBase Predicted Comparative 3D Structure on Q9NS00
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    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0016263 glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0046872 metal ion binding

Biological Process:
GO:0001525 angiogenesis
GO:0001822 kidney development
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0007275 multicellular organism development
GO:0016266 O-glycan processing
GO:0016267 O-glycan processing, core 1
GO:0030154 cell differentiation
GO:0060576 intestinal epithelial cell development

Cellular Component:
GO:0000139 Golgi membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  GQ891407 - Homo sapiens clone HEL-S-125 epididymis secretory sperm binding protein mRNA, complete cds.
LF384080 - JP 2014500723-A/191583: Polycomb-Associated Non-Coding RNAs.
AK309328 - Homo sapiens cDNA, FLJ99369.
AF155582 - Homo sapiens core1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase (C1GALT1) mRNA, complete cds.
AJ132443 - Homo sapiens mRNA for beta-1,3-galactosyltransferase b3Gal-T8.
AJ243256 - Homo sapiens mRNA for beta-1,3-Galactosyltransferase.
AJ278960 - Homo sapiens mRNA for beta 1,3-galactosyltransferase (core-1-beta 1, 3-galactosyltransferase gene).
BC003174 - Homo sapiens core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1, mRNA (cDNA clone IMAGE:2957836), partial cds.
LF360407 - JP 2014500723-A/167910: Polycomb-Associated Non-Coding RNAs.
LF360408 - JP 2014500723-A/167911: Polycomb-Associated Non-Coding RNAs.
LF360409 - JP 2014500723-A/167912: Polycomb-Associated Non-Coding RNAs.
LF360410 - JP 2014500723-A/167913: Polycomb-Associated Non-Coding RNAs.
LF360412 - JP 2014500723-A/167915: Polycomb-Associated Non-Coding RNAs.
LF360413 - JP 2014500723-A/167916: Polycomb-Associated Non-Coding RNAs.
JD311413 - Sequence 292437 from Patent EP1572962.
JD204253 - Sequence 185277 from Patent EP1572962.
JD316287 - Sequence 297311 from Patent EP1572962.
JD146609 - Sequence 127633 from Patent EP1572962.
JD534484 - Sequence 515508 from Patent EP1572962.
AK023557 - Homo sapiens cDNA FLJ13495 fis, clone PLACE1004425.
LF360414 - JP 2014500723-A/167917: Polycomb-Associated Non-Coding RNAs.
JD362984 - Sequence 344008 from Patent EP1572962.
JD413664 - Sequence 394688 from Patent EP1572962.
JD367256 - Sequence 348280 from Patent EP1572962.
JD325964 - Sequence 306988 from Patent EP1572962.
JD153376 - Sequence 134400 from Patent EP1572962.
JD161829 - Sequence 142853 from Patent EP1572962.
JD161830 - Sequence 142854 from Patent EP1572962.
JD547958 - Sequence 528982 from Patent EP1572962.
JD228420 - Sequence 209444 from Patent EP1572962.
JD525363 - Sequence 506387 from Patent EP1572962.
JD388805 - Sequence 369829 from Patent EP1572962.
JD388807 - Sequence 369831 from Patent EP1572962.
JD457396 - Sequence 438420 from Patent EP1572962.
JD522992 - Sequence 504016 from Patent EP1572962.
JD388809 - Sequence 369833 from Patent EP1572962.
JD514090 - Sequence 495114 from Patent EP1572962.
JD514089 - Sequence 495113 from Patent EP1572962.
JD070123 - Sequence 51147 from Patent EP1572962.
JD070122 - Sequence 51146 from Patent EP1572962.
JD397747 - Sequence 378771 from Patent EP1572962.
JD416237 - Sequence 397261 from Patent EP1572962.
JD128140 - Sequence 109164 from Patent EP1572962.
JD336862 - Sequence 317886 from Patent EP1572962.
JD505175 - Sequence 486199 from Patent EP1572962.
JD552349 - Sequence 533373 from Patent EP1572962.
JD294867 - Sequence 275891 from Patent EP1572962.
JD560471 - Sequence 541495 from Patent EP1572962.
JD475583 - Sequence 456607 from Patent EP1572962.
JD085765 - Sequence 66789 from Patent EP1572962.
JD312187 - Sequence 293211 from Patent EP1572962.
JD346668 - Sequence 327692 from Patent EP1572962.
JD301706 - Sequence 282730 from Patent EP1572962.
JD534480 - Sequence 515504 from Patent EP1572962.
JD510250 - Sequence 491274 from Patent EP1572962.
JD557935 - Sequence 538959 from Patent EP1572962.
JD491431 - Sequence 472455 from Patent EP1572962.
JD308562 - Sequence 289586 from Patent EP1572962.
JD113865 - Sequence 94889 from Patent EP1572962.
JD431603 - Sequence 412627 from Patent EP1572962.
JD270477 - Sequence 251501 from Patent EP1572962.
JD353770 - Sequence 334794 from Patent EP1572962.
JD260066 - Sequence 241090 from Patent EP1572962.
JD054288 - Sequence 35312 from Patent EP1572962.
JD123128 - Sequence 104152 from Patent EP1572962.
JD237027 - Sequence 218051 from Patent EP1572962.
JD120901 - Sequence 101925 from Patent EP1572962.
JD099883 - Sequence 80907 from Patent EP1572962.
JD305285 - Sequence 286309 from Patent EP1572962.
JD331555 - Sequence 312579 from Patent EP1572962.
JD325543 - Sequence 306567 from Patent EP1572962.
JD184769 - Sequence 165793 from Patent EP1572962.
JD333971 - Sequence 314995 from Patent EP1572962.
JD299578 - Sequence 280602 from Patent EP1572962.
LF360415 - JP 2014500723-A/167918: Polycomb-Associated Non-Coding RNAs.
LF360416 - JP 2014500723-A/167919: Polycomb-Associated Non-Coding RNAs.
MA619657 - JP 2018138019-A/191583: Polycomb-Associated Non-Coding RNAs.
MA595984 - JP 2018138019-A/167910: Polycomb-Associated Non-Coding RNAs.
MA595985 - JP 2018138019-A/167911: Polycomb-Associated Non-Coding RNAs.
MA595986 - JP 2018138019-A/167912: Polycomb-Associated Non-Coding RNAs.
MA595987 - JP 2018138019-A/167913: Polycomb-Associated Non-Coding RNAs.
MA595989 - JP 2018138019-A/167915: Polycomb-Associated Non-Coding RNAs.
MA595990 - JP 2018138019-A/167916: Polycomb-Associated Non-Coding RNAs.
MA595991 - JP 2018138019-A/167917: Polycomb-Associated Non-Coding RNAs.
MA595992 - JP 2018138019-A/167918: Polycomb-Associated Non-Coding RNAs.
MA595993 - JP 2018138019-A/167919: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00512 - O-Glycan biosynthesis
hsa01100 - Metabolic pathways

Reactome (by CSHL, EBI, and GO)

Protein Q9NS00 (Reactome details) participates in the following event(s):

R-HSA-1964505 C1GALT1 transfers Galactose to the Tn antigen forming Core 1 glycoproteins (T antigens)
R-HSA-913709 O-linked glycosylation of mucins
R-HSA-5173105 O-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: C1GLT_HUMAN, NM_020156, NP_064541, Q96QH4, Q9BTU1, Q9NS00, uc003srb.2
UCSC ID: uc003srb.3
RefSeq Accession: NM_020156
Protein: Q9NS00 (aka C1GLT_HUMAN)
CCDS: CCDS5355.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_020156.4
exon count: 4CDS single in 3' UTR: no RNA size: 6244
ORF size: 1092CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2372.00frame shift in genome: no % Coverage: 99.89
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.