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COLGALT1 Gene

protein-coding   GIFtS: 44
GCID: GC19P017916

Collagen Beta(1-O)Galactosyltransferase 1

(Previous name: glycosyltransferase 25 domain containing 1)
(Previous symbol: GLT25D1)
  Search for COLGALT1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Collagen Beta(1-O)Galactosyltransferase 11 2 3     Hydroxylysine Galactosyltransferase 12 3
GLT25D11 2 3     Procollagen Galactosyltransferase 12
Glycosyltransferase 25 Domain Containing 11 2     EC 2.4.1.503
Glycosyltransferase 25 Family Member 12 3     

External Ids:    HGNC: 261821   Entrez Gene: 797092   Ensembl: ENSG000001303097   UniProtKB: Q8NBJ53   

Export aliases for COLGALT1 gene to outside databases

Previous GC identifer: GC19P017747


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for COLGALT1 Gene:
COLGALT1 (collagen beta(1-O)galactosyltransferase 1) is a protein-coding gene. GO annotations related to this gene include procollagen galactosyltransferase activity. An important paralog of this gene is COLGALT2.

UniProtKB/Swiss-Prot: GT251_HUMAN, Q8NBJ5
Function: Has a beta-galactosyltransferase activity; transfers beta-galactose to hydroxylysine residues of
collagen




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011295.12  NC_018930.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for COLGALT1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCOLGALT1 promoter sequence
   Search Chromatin IP Primers for COLGALT1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat COLGALT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.11

COLGALT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
COLGALT1 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P017916:  view genomic region     (about GC identifiers)

Start:
17,666,403 bp from pter      End:
17,693,971 bp from pter
Size:
27,569 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: GT251_HUMAN, Q8NBJ5 (See protein sequence)
Recommended Name: Procollagen galactosyltransferase 1 precursor  
Size: 622 amino acids; 71636 Da
Caution: Has no glucosyltransferase activity
Secondary accessions: Q8NC64

Explore the universe of human proteins at neXtProt for COLGALT1: NX_Q8NBJ5

Explore proteomics data for COLGALT1 at MOPED

Post-translational modifications: 

  • N-glycosylated1
  • Glycosylation2 at Asn96, Asn184, Asn381

  • See COLGALT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_078932.2  
    ENSEMBL proteins: 
     ENSP00000252599   ENSP00000469817   ENSP00000468947  
    Reactome Protein details: Q8NBJ5

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR002654 Glyco_trans_25

    Graphical View of Domain Structure for InterPro Entry Q8NBJ5

    ProtoNet protein and cluster: Q8NBJ5

    UniProtKB/Swiss-Prot: GT251_HUMAN, Q8NBJ5
    Similarity: Belongs to the glycosyltransferase 25 family


    Find genes that share domains with COLGALT1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: GT251_HUMAN, Q8NBJ5
    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;

         Enzyme Number (IUBMB): EC 2.4.1.501

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0050211procollagen galactosyltransferase activity IEA--
         
    Find genes that share ontologies with COLGALT1           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for COLGALT1:
     Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for COLGALT1
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for COLGALT1

    miRNA
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    miRTarBase miRNAs that target COLGALT1:
    hsa-mir-124-3p (MIRT022180), hsa-mir-532-3p (MIRT037931), hsa-mir-744-5p (MIRT037553), hsa-mir-155-5p (MIRT020546), hsa-mir-98-5p (MIRT027402)

    Block miRNA regulation of human, mouse, rat COLGALT1 using miScript Target Protectors
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    GT251_HUMAN, Q8NBJ5: Endoplasmic reticulum lumen. Note=Colocalized with PLOD3 and mannose binding lectin

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005788endoplasmic reticulum lumen TAS--

    Find genes that share ontologies with COLGALT1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for COLGALT1 About    
    See pathways by source

    SuperPathContained pathways About
    1Collagen biosynthesis and modifying enzymes
    Collagen biosynthesis and modifying enzymes0.75
    Collagen formation0.75
    2Degradation of the extracellular matrix
    Extracellular matrix organization0.34
    3Other types of O-glycan biosynthesis
    Other types of O-glycan biosynthesis
    4Lysine degradation
    Lysine degradation


    Find genes that share SuperPaths with COLGALT1           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for COLGALT1
        Collagen biosynthesis and modifying enzymes


    2 Kegg Pathways  (Kegg details for COLGALT1):
        Lysine degradation
    Other types of O-glycan biosynthesis

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for COLGALT1
    Interactions:

        Search GeneGlobe Interaction Network for COLGALT1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    Selected Interacting proteins for COLGALT1 (Q8NBJ52, 3 ENSP000002525994) via UniProtKB, MINT, STRING, and/or I2D (see all 74)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PLOD3O605682, ENSP000002231274MINT-8415355 STRING: ENSP00000223127
    ASNA1O436813I2D: score=3 
    CTSDP073393I2D: score=3 
    SGTAO437653I2D: score=3 
    LMNAP025453I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009103lipopolysaccharide biosynthetic process IEA--
    GO:0030198extracellular matrix organization TAS--

    Find genes that share ontologies with COLGALT1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for COLGALT1 (GT251)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for COLGALT1 gene: 
    NM_024656.2  

    Unigene Cluster for COLGALT1:

    Collagen beta(1-O)galactosyltransferase 1
    Hs.418795  [show with all ESTs]
    Unigene Representative Sequence: BC108308
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000252599(uc002nhc.1 uc010eax.1) ENST00000600474 ENST00000601354
    ENST00000597147 ENST00000597075 ENST00000593832
    miRNA
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    Inhib. RNA
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    OriGene qPCR primer pairs and template standards for COLGALT1
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      QuantiTect SYBR Green Assays in human, mouse, rat COLGALT1
      QuantiFast Probe-based Assays in human, mouse, rat COLGALT1

    Additional mRNA sequence: 

    AK025982.1 AK057140.1 AK074941.1 AK075541.1 AK225397.1 AL831905.1 BC020492.1 BC071684.1 
    BC081531.1 BC108308.1 

    12 DOTS entries:

    DT.91767159  DT.100774260  DT.91767156  DT.87016810  DT.121431832  DT.100694801  DT.95270682  DT.100817267 
    DT.65284234  DT.121431963  DT.121431767  DT.121431945 

    Selected AceView cDNA sequences (see all 202):

    BX952345 CB158320 BQ004637 AA742493 BM987375 BG682126 BM787519 CR624961 
    AW957059 AA369058 AI391456 BM701478 BQ008195 BF195356 BG818044 BM725438 
    BP367844 F06304 Z39207 BE896382 CA416134 BM716868 AW089003 BU633637 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for COLGALT1 (see all 6)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d · 13e ^ 14a · 14b
    SP1:                    -                       -     -           -                             -                                       
    SP2:                                                              -                             -                                       
    SP3:                                            -     -     -     -                             -                                       
    SP4:                                                                                            -                                       
    SP5:                                                                                                                                    


    ECgene alternative splicing isoforms for COLGALT1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    COLGALT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    COLGALT1 Expression
    About this image

    COLGALT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    COLGALT1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.418795

    UniProtKB/Swiss-Prot: GT251_HUMAN, Q8NBJ5
    Tissue specificity: Ubiquitous with higher levels in placenta, heart, lung and spleen

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for COLGALT1 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Glt25d11 , 5 glycosyltransferase 25 domain containing 11, 5 86.79(n)1
    93.71(a)1
      8 (34.43 cM)5
    2344071  NM_146211.31  NP_666323.21 
     716110245 
    chicken
    (Gallus gallus)
    Aves --
    Uncharacterized protein
    84(a)
    many ↔ many
    AADN03012068.1(359-1409)
    lizard
    (Anolis carolinensis)
    Reptilia COLGALT16
    collagen beta(1-O)galactosyltransferase 1
    76(a)
    1 ↔ 1
    GL343326.1(545429-590171)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.136132 Xenopus laevis transcribed sequence with weak similarity more 73.89(n)    CA787866.1 
    zebrafish
    (Danio rerio)
    Actinopterygii colgalt11 collagen beta(1-O)galactosyltransferase 1 68.37(n)
    72.74(a)
      565862  XM_689125.2  XP_694217.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG319156
    --
    41(a)
    1 → many
    2L(5528087-5530682)
    worm
    (Caenorhabditis elegans)
    Secernentea D2045.96
    Protein D2045.9 (D2045.9) mRNA, complete cds
    34(a)
    1 → many
    III(10475970-10479753) WBGene00008426


    ENSEMBL Gene Tree for COLGALT1 (if available)
    TreeFam Gene Tree for COLGALT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for COLGALT1 gene
    COLGALT22  PLOD22  PLOD32  CERCAM2  PLOD12  
    5 SIMAP similar genes for COLGALT1 using alignment to 3 protein entries:     GT251_HUMAN (see all proteins):
    GLT25D1    COLGALT2    GLT25D2    CERCAM    PLOD3

    Find genes that share paralogs with COLGALT1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for COLGALT1 (see all 737)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs129822811,2
    C,F--17665245(+) gatcaT/Cgtgat 1 -- us2k17Minor allele frequency- C:0.25NA WA EA 250
    rs104237591,2
    C,H--17665253(+) gatcaC/Tgccac 1 -- us2k19Minor allele frequency- T:0.09NA WA CSA EA 368
    rs1160749081,2
    F--17665294(+) CCTCTC/TTGTGA 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs2017980231,2
    C--17665314(+) AAGCT-/GGCC  
            
    GGGCG
    1 -- us2k10--------
    rs347635731,2
    C--17665549(+) GCGCCA/CCTGTA 1 -- us2k11Minor allele frequency- C:0.00NA 2
    rs667826751,2
    C,F--17665603(+) AAAAA-/A/AA  
            
    GAAAA
    1 -- us2k12NA 4
    rs785481981,2
    F--17665780(+) CAATTT/GGAAAA 1 -- us2k11Minor allele frequency- G:0.33NA 6
    rs1875843231,2
    --17665788(+) AAATGC/GGGCTC 1 -- us2k10--------
    rs104187311,2
    C,A,H--17665867(+) TGTGCC/TCAGAA 1 -- us2k15Minor allele frequency- T:0.06NS EA WA 522
    rs1486831991,2
    --17665920(+) ATAGGA/GTCTCT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for COLGALT1 (17666403 - 17693971 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for COLGALT1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing COLGALT1
    DNA2.0 Custom Variant and Variant Library Synthesis for COLGALT1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for COLGALT1 gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with COLGALT1)
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    1. Core glycosylation of collagen is initiated by two beta(1- O)galactosyltransferases. (PubMed id 19075007)1, 2, 3 Schegg B.... Hennet T. (Mol. Cell. Biol. 2009)
    2. The human collagen beta(1-O)galactosyltransferase, GLT25D1, is a soluble endoplasmic reticulum localized protein. (PubMed id 20470363)1, 2 Liefhebber J.M.... van Leeuwen H.C. (BMC Cell Biol. 2010)
    3. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
    4. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    5. Unassembled CD147 is an endogenous endoplasmic reticulum-associated degradation substrate. (PubMed id 23097496)1 Tyler R.E....Kopito R.R. (Mol. Biol. Cell 2012)
    6. PKCI/ promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. (PubMed id 22304920)1 Lau E....Ronai Z.A. (Cell 2012)
    7. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 JAoger S....Krogan N.J. (Nature 2012)
    8. Proteomic identification of common SCF ubiquitin ligase FBXO6-interacting glycoproteins in three kinds of cells. (PubMed id 22268729)1 Liu B....Wang L.S. (J. Proteome Res. 2012)
    9. Proteomic dissection of the von Hippel-Lindau (VHL) interactome. (PubMed id 21942715)1 Lai Y....Shiio Y. (J. Proteome Res. 2011)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 79709 HGNC: 26182 AceView: GLT25D1 Ensembl:ENSG00000130309 euGenes: HUgn79709
    ECgene: COLGALT1 Kegg: 79709 H-InvDB: COLGALT1

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for COLGALT1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for COLGALT1 gene:
    Search GeneIP for patents involving COLGALT1

    GeneCards and IP:
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