U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from OMIM

    • Showing Current items.

    COLGALT2 collagen beta(1-O)galactosyltransferase 2 [ Homo sapiens (human) ]

    Gene ID: 23127, updated on 27-Nov-2024

    Summary

    Official Symbol
    COLGALT2provided by HGNC
    Official Full Name
    collagen beta(1-O)galactosyltransferase 2provided by HGNC
    Primary source
    HGNC:HGNC:16790
    See related
    Ensembl:ENSG00000198756 MIM:617533; AllianceGenome:HGNC:16790
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C1orf17; GLT25D2; ColGalT 2
    Summary
    Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 11.8), adrenal (RPKM 2.5) and 7 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See COLGALT2 in Genome Data Viewer
    Location:
    1q25.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (183929662..184037728, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (183289012..183400897, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183898796..184006862, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183653331-183653832 Neighboring gene ral guanine nucleotide dissociation stimulator like 1 Neighboring gene T-box transcription factor T pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183692952-183693452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2228 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183887920-183888109 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:183913934-183914776 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:183914777-183915619 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183924966-183925130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2229 Neighboring gene NFE2L2 motif-containing MPRA enhancer 281 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:183993995-183994734 Neighboring gene Sharpr-MPRA regulatory region 12313 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1636 Neighboring gene Sharpr-MPRA regulatory region 13835 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:184037463-184038001 Neighboring gene tRNA splicing endonuclease subunit 15 Neighboring gene uncharacterized LOC102724830

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Addition of peripheral sugar residues such as galactose, N-acetylglucosamine, and sialic acid to HIV-1 gp120 is processed by specific glycosyltransferase PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ37771, FLJ37873, KIAA0584

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables procollagen galactosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables procollagen galactosyltransferase activity TAS
    Traceable Author Statement
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in collagen fibril organization TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    procollagen galactosyltransferase 2
    Names
    glycosyltransferase 25 domain containing 2
    glycosyltransferase 25 family member 2
    hydroxylysine galactosyltransferase 2
    NP_001290349.1
    NP_001290350.1
    NP_055916.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001303420.2NP_001290349.1  procollagen galactosyltransferase 2 isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 3' terminal exon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK293973, BC035672
      Consensus CDS
      CCDS91126.1
      UniProtKB/TrEMBL
      A0A3B3IT37, B4DF84
      Related
      ENSP00000497601.1, ENST00000649786.1
      Conserved Domains (2) summary
      cl01298
      Location:341526
      Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...
      cl11394
      Location:62175
      Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold
    2. NM_001303421.2NP_001290350.1  procollagen galactosyltransferase 2 isoform 3

      See identical proteins and their annotated locations for NP_001290350.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal exon, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      AB011156, AK095192, BQ477485
      UniProtKB/TrEMBL
      B3KT92
      Conserved Domains (1) summary
      cl01298
      Location:221406
      Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...
    3. NM_015101.4NP_055916.1  procollagen galactosyltransferase 2 isoform 1precursor

      See identical proteins and their annotated locations for NP_055916.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB011156, BC035672, BQ477485
      Consensus CDS
      CCDS1360.1
      UniProtKB/Swiss-Prot
      O60327, Q8IYK4, Q9BZR0
      UniProtKB/TrEMBL
      B4DF84
      Related
      ENSP00000354960.4, ENST00000361927.9
      Conserved Domains (2) summary
      pfam13704
      Location:62175
      Glyco_tranf_2_4; Glycosyl transferase family 2
      cl01298
      Location:341526
      Glyco_transf_25; Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      183929662..184037728 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      183289012..183400897 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)