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

Gene ID: 23127, updated on 12-Oct-2019

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
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
Expression
Biased expression in brain (RPKM 11.8), adrenal (RPKM 2.5) and 7 other tissues See more
Orthologs

Genomic context

See COLGALT2 in Genome Data Viewer
Location:
1q25.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (183929662..184037728, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183898988..184006904, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene apolipoprotein B mRNA editing enzyme catalytic polypeptide like 4 Neighboring gene ral guanine nucleotide dissociation stimulator like 1 Neighboring gene T-box transcription factor T pseudogene Neighboring gene NFE2L2 motif-containing MPRA enhancer 281 Neighboring gene Sharpr-MPRA regulatory region 13835 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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ37771, FLJ37873, KIAA0584

Gene Ontology Provided by GOA

Function Evidence Code Pubs
procollagen galactosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
procollagen galactosyltransferase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
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)

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
    UniProtKB/Swiss-Prot
    Q8IYK4
    UniProtKB/TrEMBL
    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/Swiss-Prot
    Q8IYK4
    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
    Q8IYK4
    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: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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