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
  • C1orf17 3 4
  • GLT25D2 3 4
  • Chromosome 1 Open Reading Frame 17 2
  • Procollagen Galactosyltransferase 2
  • EC 2.4.1.50 4
  • KIAA0584 4

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 Collagen chain trimerization and Other types of O-glycan biosynthesis. 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.

Additional gene information for COLGALT2 Gene

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 for COLGALT2 Gene

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 768.3 +14.7 14677 2.7 ZBTB6 ZNF701 HLF L3MBTL2 ZNF652 GTF2F1 ZFX ZNF384 MLLT1 ZSCAN21 COLGALT2 RGL1 SMG7 TSEN15 piR-45035-015
GH01J184050 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 750.6 -0.4 -410 3.2 ZNF785 ZNF24 SP1 ZBTB40 SIX5 ZBTB6 SMARCE1 RBPJ POLR2A HDAC2 TSEN15 COLGALT2 ENSG00000271387 SMG7 LAMC1-AS1 RGL1 RNF2 RF00994-071
GH01J183967 Enhancer 0.7 FANTOM5 Ensembl ENCODE dbSUPER 46.8 +83.4 83441 1.3 HSALNG0008988 COLGALT2 APOBEC4 RF00017-420
GH01J184001 Enhancer 1.1 Ensembl ENCODE dbSUPER 19.2 +48.9 48911 1.8 L3MBTL2 ELF3 MAFK CBFA2T2 TFE3 BACH1 SMARCA4 ZNF639 ZNF644 KAT8 COLGALT2 piR-45035-015
GH01J183911 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 16.1 +140.0 140043 1 ZNF24 SP1 ETV6 RELA NKRF MLLT1 ZNF687 CREM ZBED1 IKZF1 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for COLGALT2 Gene

Genomic Locations for COLGALT2 Gene
chr1:183,929,662-184,051,611
(GRCh38/hg38)
Size:
121,950 bases
Orientation:
Minus strand
chr1:183,898,796-184,006,863
(GRCh37/hg19)
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=Translation N-terminally shortened.; 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
  • Predicted secreted 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=. ;.
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

Animal Model Products

CRISPR Products

miRNA for COLGALT2 Gene

miRTarBase miRNAs that target COLGALT2

Inhibitory RNA Products

  • 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
extracellular 0
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (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

Gene Ontology (GO) - Biological Process for COLGALT2 Gene

None

No data available for SIGNOR curated interactions for COLGALT2 Gene

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

CRISPR Products

Inhibitory RNA Products

  • 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
ECgene alternative splicing isoforms for
COLGALT2

Expression for COLGALT2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of COLGALT2 Gene:

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

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 33 32
  • 99.73 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COLGALT2 33
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia GLT25D2 33 32
  • 91.8 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Colgalt2 17 33 32
  • 88.87 (n)
dog
(Canis familiaris)
Mammalia COLGALT2 33 32
  • 87.7 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Colgalt2 32
  • 87.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COLGALT2 33
  • 87 (a)
OneToOne
chicken
(Gallus gallus)
Aves COLGALT2 33
  • 79 (a)
OneToOne
GLT25D2 32
  • 78.44 (n)
lizard
(Anolis carolinensis)
Reptilia COLGALT2 33
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia colgalt2 32
  • 72.17 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.12299 32
zebrafish
(Danio rerio)
Actinopterygii colgalt2 33 32
  • 65.41 (n)
OneToMany
COLGALT2 (2 of 2) 33
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG31915 33
  • 41 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea D2045.9 33
  • 34 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 49 (a)
OneToMany
Cin.13713 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13713 32
Species where no ortholog for COLGALT2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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

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 from dbSNP and Humsavar for COLGALT2 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
VAR_036978 A breast cancer sample p.Val475Ile
rs1000000445 -- 183,946,922(-) T/C intron_variant
rs1000007086 -- 183,989,208(-) A/T intron_variant
rs1000110919 -- 184,016,547(-) G/C intron_variant
rs1000143237 -- 183,947,160(-) A/T intron_variant

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

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: HGMD and DISEASES

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 56
  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 56
  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 56
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 56
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 56

Products for COLGALT2 Gene

Sources for COLGALT2 Gene