Aliases for COLGALT2 Gene

Aliases for COLGALT2 Gene

  • Collagen Beta(1-O)Galactosyltransferase 2 2 3 4 5
  • Glycosyltransferase 25 Domain Containing 2 2 3
  • Glycosyltransferase 25 Family Member 2 3 4
  • Hydroxylysine Galactosyltransferase 2 3 4
  • Procollagen Galactosyltransferase 2 3 4
  • ColGalT 2 3 4
  • KIAA0584 2 4
  • C1orf17 3 4
  • GLT25D2 3 4
  • Chromosome 1 Open Reading Frame 17 2
  • Procollagen Galactosyltransferase 2
  • EC 2.4.1.50 4
  • COLGALT2 5

External Ids for COLGALT2 Gene

Previous HGNC Symbols for COLGALT2 Gene

  • C1orf17
  • GLT25D2

Summaries for COLGALT2 Gene

GeneCards Summary for COLGALT2 Gene

COLGALT2 (Collagen Beta(1-O)Galactosyltransferase 2) is a Protein Coding gene. Diseases associated with COLGALT2 include Porencephaly. Among its related pathways are Degradation of the extracellular matrix and Collagen chain trimerization. Gene Ontology (GO) annotations related to this gene include procollagen galactosyltransferase activity. An important paralog of this gene is COLGALT1.

UniProtKB/Swiss-Prot Summary for COLGALT2 Gene

  • Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of collagen.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for COLGALT2 Gene

Genomics for COLGALT2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for COLGALT2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J184036 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 268.6 +0.8 795 2.7 NCOR1 MYC ZNF600 IKZF1 ZNF580 ZNF592 ZNF223 ZIC2 ZBTB10 NONO COLGALT2 SMG7 TSEN15 RGL1 piR-45035-015 APOBEC4
GH01J184050 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 250.4 -14.3 -14292 3.2 BCLAF1 SP1 ZNF207 MYC ZNF600 SIX5 JUND ZNF592 POLR2A CEBPA TSEN15 COLGALT2 LAMC1-AS1 ENSG00000271387 SMG7 LAMC2 RNF2 HSALNG0008991 C1orf21
GH01J183967 Enhancer 0.9 FANTOM5 Ensembl ENCODE dbSUPER 46.8 +69.6 69559 1.3 ATF4 ATF3 ATF7 COLGALT2 APOBEC4 HSALNG0008989 RF00017-364 HSALNG0008988
GH01J184001 Enhancer 1.1 Ensembl ENCODE dbSUPER 19.2 +35.1 35128 1.6 JUND HOMEZ MAFF SMAD4 SAP130 ETV4 ZNF316 TEAD3 FOSL2 NFE2 COLGALT2 piR-45035-015 APOBEC4
GH01J183911 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 16.1 +126.2 126161 1 BCLAF1 SP1 ZNF207 BCL11A TARDBP TRIM22 IRF4 EBF1 CBFB SMARCA5 COLGALT2 NCF2 APOBEC4 ARPC5 lnc-COLGALT2-1 lnc-APOBEC4-5 RGL1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around COLGALT2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for COLGALT2

Genomic Locations for COLGALT2 Gene

Latest Assembly
chr1:183,929,662-184,037,729
(GRCh38/hg38)
Size:
108,068 bases
Orientation:
Minus strand

Previous Assembly
chr1:183,898,796-184,006,862
(GRCh37/hg19 by Entrez Gene)
Size:
108,067 bases
Orientation:
Minus strand

chr1:183,898,796-184,006,863
(GRCh37/hg19 by Ensembl)
Size:
108,068 bases
Orientation:
Minus strand

Genomic View for COLGALT2 Gene

Genes around COLGALT2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COLGALT2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COLGALT2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COLGALT2 Gene

Proteins for COLGALT2 Gene

  • Protein details for COLGALT2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IYK4-GT252_HUMAN
    Recommended name:
    Procollagen galactosyltransferase 2
    Protein Accession:
    Q8IYK4
    Secondary Accessions:
    • O60327
    • Q9BZR0

    Protein attributes for COLGALT2 Gene

    Size:
    626 amino acids
    Molecular mass:
    72924 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA25510.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for COLGALT2 Gene

Post-translational modifications for COLGALT2 Gene

  • Glycosylation at Asn97, Asn185, Asn382, and Asn580
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • GT252_HUMAN (1632)

Other Protein References for COLGALT2 Gene

No data available for DME Specific Peptides for COLGALT2 Gene

Domains & Families for COLGALT2 Gene

Gene Families for COLGALT2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for COLGALT2 Gene

Suggested Antigen Peptide Sequences for COLGALT2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ37873 fis, clone BRSSN2018447, highly similar to Homo sapiens glycosyltransferase 25 domain containing 2 (GLT25D2), mRNA (B3KT92_HUMAN)
  • Hydroxylysine galactosyltransferase 2 (GT252_HUMAN)
  • GLT25D2 protein (Q8WUS1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IYK4

UniProtKB/Swiss-Prot:

GT252_HUMAN :
  • Belongs to the glycosyltransferase 25 family.
Family:
  • Belongs to the glycosyltransferase 25 family.
genes like me logo Genes that share domains with COLGALT2: view

Function for COLGALT2 Gene

Molecular function for COLGALT2 Gene

UniProtKB/Swiss-Prot Function:
Beta-galactosyltransferase that transfers beta-galactose to hydroxylysine residues of collagen.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(5R)-5-hydroxy-L-lysyl-[procollagen] + UDP-alpha-D-galactose = (5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysyl-[procollagen] + H(+) + UDP; Xref=Rhea:RHEA:12637, Rhea:RHEA-COMP:12752, Rhea:RHEA-COMP:12753, ChEBI:CHEBI:15378, ChEBI:CHEBI:58223, ChEBI:CHEBI:66914, ChEBI:CHEBI:133442, ChEBI:CHEBI:133443; EC=2.4.1.50; Evidence={ECO:0000269|PubMed:19075007};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=33.5 uM for UDP-galactose {ECO:0000269|PubMed:19075007};

Enzyme Numbers (IUBMB) for COLGALT2 Gene

Phenotypes From GWAS Catalog for COLGALT2 Gene

Gene Ontology (GO) - Molecular Function for COLGALT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0016740 transferase activity IEA --
GO:0016757 transferase activity, transferring glycosyl groups IEA --
GO:0050211 procollagen galactosyltransferase activity IBA,TAS --
genes like me logo Genes that share ontologies with COLGALT2: view
genes like me logo Genes that share phenotypes with COLGALT2: view

miRNA for COLGALT2 Gene

miRTarBase miRNAs that target COLGALT2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COLGALT2

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for COLGALT2 Gene

Localization for COLGALT2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COLGALT2 Gene

Endoplasmic reticulum lumen.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for COLGALT2 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 2
nucleus 2
plasma membrane 1
extracellular 1
cytoskeleton 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for COLGALT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with COLGALT2: view

Pathways & Interactions for COLGALT2 Gene

genes like me logo Genes that share pathways with COLGALT2: view

Pathways by source for COLGALT2 Gene

SIGNOR curated interactions for COLGALT2 Gene

Activates:

Gene Ontology (GO) - Biological Process for COLGALT2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0018215 protein phosphopantetheinylation IEA --
genes like me logo Genes that share ontologies with COLGALT2: view

Drugs & Compounds for COLGALT2 Gene

(2) Drugs for COLGALT2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Uridine 5'-diphosphate Experimental Pharma 0
Uridine diphosphategalactose Experimental Pharma 0
genes like me logo Genes that share compounds with COLGALT2: view

Transcripts for COLGALT2 Gene

mRNA/cDNA for COLGALT2 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for COLGALT2

Alternative Splicing Database (ASD) splice patterns (SP) for COLGALT2 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ·
SP1: - - - - - - - - -
SP2: - - - - - - -
SP3: -
SP4: - - -
SP5: - - -
SP6: -
SP7:
SP8: - -
SP9:

ExUns: 16c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for COLGALT2 Gene

GeneLoc Exon Structure for
COLGALT2

Expression for COLGALT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for COLGALT2 Gene

mRNA differential expression in normal tissues according to GTEx for COLGALT2 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x5.5).

Protein differential expression in normal tissues from HIPED for COLGALT2 Gene

This gene is overexpressed in Fetal heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for COLGALT2 Gene



Protein tissue co-expression partners for COLGALT2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for COLGALT2

SOURCE GeneReport for Unigene cluster for COLGALT2 Gene:

Hs.387995

mRNA Expression by UniProt/SwissProt for COLGALT2 Gene:

Q8IYK4-GT252_HUMAN
Tissue specificity: Expressed in brain and skeletal muscle.

Evidence on tissue expression from TISSUES for COLGALT2 Gene

  • Nervous system(4.9)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with COLGALT2: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for COLGALT2 Gene

Orthologs for COLGALT2 Gene

This gene was present in the common ancestor of animals.

Orthologs for COLGALT2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia GLT25D2 29 30
  • 99.73 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia COLGALT2 30
  • 92 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia GLT25D2 29 30
  • 91.8 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Colgalt2 29 16 30
  • 88.87 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia COLGALT2 29 30
  • 87.7 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Colgalt2 29
  • 87.03 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia COLGALT2 30
  • 87 (a)
OneToOne
Chicken
(Gallus gallus)
Aves COLGALT2 30
  • 79 (a)
OneToOne
GLT25D2 29
  • 78.44 (n)
Lizard
(Anolis carolinensis)
Reptilia COLGALT2 30
  • 83 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia colgalt2 29
  • 72.17 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12299 29
Zebrafish
(Danio rerio)
Actinopterygii colgalt2 29 30
  • 65.41 (n)
OneToMany
COLGALT2 (2 of 2) 30
  • 58 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta CG31915 30
  • 41 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea D2045.9 30
  • 34 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 49 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.13713 29
Species where no ortholog for COLGALT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for COLGALT2 Gene

ENSEMBL:
Gene Tree for COLGALT2 (if available)
TreeFam:
Gene Tree for COLGALT2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for COLGALT2: view image
Alliance of Genome Resources:
Additional Orthologs for COLGALT2

Paralogs for COLGALT2 Gene

Paralogs for COLGALT2 Gene

(5) SIMAP similar genes for COLGALT2 Gene using alignment to 4 proteins:

  • GT252_HUMAN
  • F5H3T5_HUMAN
  • Q5SXQ3_HUMAN
  • Q5SXQ5_HUMAN
genes like me logo Genes that share paralogs with COLGALT2: view

Variants for COLGALT2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for COLGALT2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
VAR_036978 A breast cancer sample p.Val475Ile

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for COLGALT2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for COLGALT2 Gene

Variant ID Type Subtype PubMed ID
esv2010262 CNV deletion 18987734
esv24684 CNV loss 19812545
esv3588119 CNV loss 21293372
esv3588120 CNV gain 21293372
nsv525878 CNV gain 19592680
nsv526480 CNV loss 19592680
nsv832026 CNV gain+loss 17160897

Variation tolerance for COLGALT2 Gene

Residual Variation Intolerance Score: 72.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.68; 57.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for COLGALT2 Gene

Human Gene Mutation Database (HGMD)
COLGALT2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COLGALT2
Leiden Open Variation Database (LOVD)
COLGALT2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COLGALT2 Gene

Disorders for COLGALT2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for COLGALT2 Gene - From: COP

Disorder Aliases PubMed IDs
porencephaly
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for COLGALT2

genes like me logo Genes that share disorders with COLGALT2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for COLGALT2 Gene

Publications for COLGALT2 Gene

  1. Core glycosylation of collagen is initiated by two beta(1-O)galactosyltransferases. (PMID: 19075007) Schegg B … Hennet T (Molecular and cellular biology 2009) 2 3 4
  2. Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. (PMID: 11318611) Sood R … Carpten JD (Genomics 2001) 3 4
  3. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. Endogenous Cell Type-Specific Disrupted in Schizophrenia 1 Interactomes Reveal Protein Networks Associated With Neurodevelopmental Disorders. (PMID: 29961565) Wilkinson B … Coba MP (Biological psychiatry 2019) 3

Products for COLGALT2 Gene

Sources for COLGALT2 Gene