Human Gene COLGALT1 (uc002nhc.1)
  Description: Homo sapiens collagen beta(1-O)galactosyltransferase 1 (COLGALT1), mRNA.
RefSeq Summary (NM_024656): The protein encoded by this gene is one of two enzymes that transfers galactose moieties to hydroxylysine residues of collagen and mannose binding lectin. This gene is constitutively expressed and encodes a soluble protein that localizes to the endoplasmic reticulum. [provided by RefSeq, Dec 2015]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Transcript (Including UTRs)
   Position: hg19 chr19:17,666,511-17,693,965 Size: 27,455 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr19:17,666,523-17,692,253 Size: 25,731 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:17,666,511-17,693,965)mRNA (may differ from genome)Protein (622 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GT251_HUMAN
DESCRIPTION: RecName: Full=Procollagen galactosyltransferase 1; EC=2.4.1.50; AltName: Full=Glycosyltransferase 25 family member 1; AltName: Full=Hydroxylysine galactosyltransferase 1; Flags: Precursor;
FUNCTION: Has a beta-galactosyltransferase activity; transfers beta-galactose to hydroxylysine residues of collagen.
CATALYTIC ACTIVITY: UDP-alpha-D-galactose + 5-hydroxy-L-lysine- [procollagen] = UDP + 5-(D-galactosyloxy)-L-lysine-[procollagen].
BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=18.7 uM for UDP-galactose;
SUBCELLULAR LOCATION: Endoplasmic reticulum lumen. Note=Colocalized with PLOD3 and mannose binding lectin.
TISSUE SPECIFICITY: Ubiquitous with higher levels in placenta, heart, lung and spleen.
PTM: N-glycosylated.
SIMILARITY: Belongs to the glycosyltransferase 25 family.
CAUTION: Has no glucosyltransferase activity.

-  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

+  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: 63.27 RPKM in Spleen
Total median expression: 1181.03 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -660.831712-0.386 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
IPR002654 - Glyco_trans_25

Pfam Domains:
PF01755 - Glycosyltransferase family 25 (LPS biosynthesis protein)
PF13704 - Glycosyl transferase family 2

SCOP Domains:
53448 - Nucleotide-diphospho-sugar transferases

ModBase Predicted Comparative 3D Structure on Q8NBJ5
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0050211 procollagen galactosyltransferase activity

Biological Process:
GO:1904028 positive regulation of collagen fibril organization

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK074941 - Homo sapiens cDNA FLJ90460 fis, clone NT2RP3001858.
BC108308 - Homo sapiens glycosyltransferase 25 domain containing 1, mRNA (cDNA clone MGC:117270 IMAGE:5138787), complete cds.
AK075541 - Homo sapiens cDNA PSEC0241 fis, clone NT2RP3000234, moderately similar to Homo sapiens cerebral cell adhesion molecule mRNA.
BC071684 - Homo sapiens glycosyltransferase 25 domain containing 1, mRNA (cDNA clone IMAGE:4471843), partial cds.
BC081531 - Homo sapiens cDNA clone IMAGE:4453735.
AK225397 - Homo sapiens mRNA for glycosyltransferase 25 domain containing 1 variant, clone: HRC05659.
AK025982 - Homo sapiens cDNA: FLJ22329 fis, clone HRC05659.
BC020492 - Homo sapiens glycosyltransferase 25 domain containing 1, mRNA (cDNA clone IMAGE:3896681), complete cds.
AK057140 - Homo sapiens cDNA FLJ32578 fis, clone SPLEN2000258, highly similar to Homo sapiens glycosyltransferase 25 domain containing 1 (GLT25D1), mRNA.
JD334969 - Sequence 315993 from Patent EP1572962.
JD241118 - Sequence 222142 from Patent EP1572962.
JD532848 - Sequence 513872 from Patent EP1572962.
JD189135 - Sequence 170159 from Patent EP1572962.
JD410661 - Sequence 391685 from Patent EP1572962.
JD067372 - Sequence 48396 from Patent EP1572962.
JD048692 - Sequence 29716 from Patent EP1572962.
AL831905 - Homo sapiens mRNA; cDNA DKFZp547G169 (from clone DKFZp547G169).
JD145321 - Sequence 126345 from Patent EP1572962.
JD043948 - Sequence 24972 from Patent EP1572962.
JD495531 - Sequence 476555 from Patent EP1572962.
JD265023 - Sequence 246047 from Patent EP1572962.
JD173584 - Sequence 154608 from Patent EP1572962.
JD057757 - Sequence 38781 from Patent EP1572962.
JD407671 - Sequence 388695 from Patent EP1572962.
JD213357 - Sequence 194381 from Patent EP1572962.
JD367665 - Sequence 348689 from Patent EP1572962.
JD110940 - Sequence 91964 from Patent EP1572962.
JD115666 - Sequence 96690 from Patent EP1572962.
JD365296 - Sequence 346320 from Patent EP1572962.
JD120531 - Sequence 101555 from Patent EP1572962.
JD379618 - Sequence 360642 from Patent EP1572962.
JD094091 - Sequence 75115 from Patent EP1572962.
JD311667 - Sequence 292691 from Patent EP1572962.
JD081491 - Sequence 62515 from Patent EP1572962.
JD270422 - Sequence 251446 from Patent EP1572962.
JD357476 - Sequence 338500 from Patent EP1572962.
JD269228 - Sequence 250252 from Patent EP1572962.
JD448405 - Sequence 429429 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00310 - Lysine degradation

Reactome (by CSHL, EBI, and GO)

Protein Q8NBJ5 (Reactome details) participates in the following event(s):

R-HSA-8948228 COLGALT1,COLGALT2 bind Lysyl hydroxylated collagen propeptides
R-HSA-1981120 Galactosylation of collagen propeptide hydroxylysines by procollagen galactosyltransferases 1, 2.
R-HSA-1650814 Collagen biosynthesis and modifying enzymes
R-HSA-1474290 Collagen formation
R-HSA-1474244 Extracellular matrix organization

-  Other Names for This Gene
  Alternate Gene Symbols: GLT25D1, GT251_HUMAN, NM_024656, NP_078932, PSEC0241, Q8NBJ5, Q8NC64
UCSC ID: uc002nhc.1
RefSeq Accession: NM_024656
Protein: Q8NBJ5 (aka GT251_HUMAN)
CCDS: CCDS12363.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_024656.2
exon count: 12CDS single in 3' UTR: no RNA size: 3593
ORF size: 1869CDS single in intron: no Alignment % ID: 99.83
txCdsPredict score: 3348.00frame 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.