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Aliases for COL25A1 Gene

Aliases for COL25A1 Gene

  • Collagen Type XXV Alpha 1 2 3
  • Collagen, Type XXV, Alpha 1 2 3 5
  • Alzheimer Disease Amyloid-Associated Protein 3 4
  • CLAC-P 3 4
  • AMY 3 4
  • Collagen-Like Alzheimer Amyloid Plaque Component 3
  • Collagenous Alzheimer Amyloid Plaque Component 3
  • CFEOM5 3
  • CLACP 3
  • CLAC 3

External Ids for COL25A1 Gene

Previous GeneCards Identifiers for COL25A1 Gene

  • GC04M110125
  • GC04M110203
  • GC04M110193
  • GC04M110092
  • GC04M109954
  • GC04M109731
  • GC04M105467

Summaries for COL25A1 Gene

Entrez Gene Summary for COL25A1 Gene

  • This gene encodes a brain-specific membrane associated collagen. A product of proteolytic processing of the encoded protein, CLAC (collagenous Alzheimer amyloid plaque component), binds to amyloid beta-peptides found in Alzheimer amyloid plaques but CLAC inhibits rather than facilitates amyloid fibril elongation (PMID: 16300410). A study of over-expression of this collagen in mice, however, found changes in pathology and behavior suggesting that the encoded protein may promote amyloid plaque formation (PMID: 19548013). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

GeneCards Summary for COL25A1 Gene

COL25A1 (Collagen Type XXV Alpha 1) is a Protein Coding gene. Diseases associated with COL25A1 include fibrosis of extraocular muscles, congenital, 5 and congenital fibrosis of the extraocular muscles. Among its related pathways are Degradation of the extracellular matrix and ERK Signaling. GO annotations related to this gene include heparin binding and beta-amyloid binding. An important paralog of this gene is COL21A1.

UniProtKB/Swiss-Prot for COL25A1 Gene

  • Inhibits fibrillization of beta amyloid peptide during the elongation phase. Has also been shown to assemble amyloid fibrils into protease-resistant aggregates. Binds heparin.

Gene Wiki entry for COL25A1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for COL25A1 Gene

Genomics for COL25A1 Gene

Regulatory Elements for COL25A1 Gene

Promoters for COL25A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around COL25A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for COL25A1 Gene

Chromosome:
4
Start:
108,808,725 bp from pter
End:
109,302,752 bp from pter
Size:
494,028 bases
Orientation:
Minus strand

Genomic View for COL25A1 Gene

Genes around COL25A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
COL25A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for COL25A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for COL25A1 Gene

Proteins for COL25A1 Gene

  • Protein details for COL25A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BXS0-COPA1_HUMAN
    Recommended name:
    Collagen alpha-1(XXV) chain
    Protein Accession:
    Q9BXS0
    Secondary Accessions:
    • A8MPZ6
    • Q9BXR9

    Protein attributes for COL25A1 Gene

    Size:
    654 amino acids
    Molecular mass:
    64771 Da
    Quaternary structure:
    • Forms homodimers and homotrimers. Binds to the fibrillized forms of beta amyloid peptide 40 (beta-APP40) and beta amyloid peptide 42 (beta-APP42). Found associated with beta-APP42 more frequently than with beta-APP40.

    Alternative splice isoforms for COL25A1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for COL25A1 Gene

Proteomics data for COL25A1 Gene at MOPED

Post-translational modifications for COL25A1 Gene

  • Glycosylated.
  • Hydroxylated on 11% of proline residues and 49% of lysine residues.
  • Undergoes proteolytic cleavage by furin protease to yield the soluble collagen-like Alzheimer amyloid plaque component.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for COL25A1 (Collagen XXV alpha 1)

No data available for DME Specific Peptides for COL25A1 Gene

Domains & Families for COL25A1 Gene

Gene Families for COL25A1 Gene

Protein Domains for COL25A1 Gene

Suggested Antigen Peptide Sequences for COL25A1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BXS0

UniProtKB/Swiss-Prot:

COPA1_HUMAN :
  • Contains 7 collagen-like domains.
Domain:
  • Contains 7 collagen-like domains.
genes like me logo Genes that share domains with COL25A1: view

Function for COL25A1 Gene

Molecular function for COL25A1 Gene

UniProtKB/Swiss-Prot Function:
Inhibits fibrillization of beta amyloid peptide during the elongation phase. Has also been shown to assemble amyloid fibrils into protease-resistant aggregates. Binds heparin.
genes like me logo Genes that share phenotypes with COL25A1: view

Human Phenotype Ontology for COL25A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for COL25A1 Gene

Localization for COL25A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for COL25A1 Gene

Membrane; Single-pass type II membrane protein. Note=After proteolytic cleavage, CLAC is secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for COL25A1 Gene COMPARTMENTS Subcellular localization image for COL25A1 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
plasma membrane 5
cytosol 3
mitochondrion 2
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005886 plasma membrane TAS --
GO:0016021 integral component of membrane IEA,NAS 11927537
genes like me logo Genes that share ontologies with COL25A1: view

Pathways & Interactions for COL25A1 Gene

genes like me logo Genes that share pathways with COL25A1: view

Gene Ontology (GO) - Biological Process for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0022617 extracellular matrix disassembly TAS --
genes like me logo Genes that share ontologies with COL25A1: view

No data available for SIGNOR curated interactions for COL25A1 Gene

Drugs & Compounds for COL25A1 Gene

No Compound Related Data Available

Transcripts for COL25A1 Gene

Unigene Clusters for COL25A1 Gene

Collagen, type XXV, alpha 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for COL25A1 Gene

No ASD Table

Relevant External Links for COL25A1 Gene

GeneLoc Exon Structure for
COL25A1
ECgene alternative splicing isoforms for
COL25A1

Expression for COL25A1 Gene

mRNA expression in normal human tissues for COL25A1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for COL25A1 Gene

This gene is overexpressed in Testis (x11.2), Adipose - Subcutaneous (x4.5), and Adipose - Visceral (Omentum) (x4.4).

Protein differential expression in normal tissues from HIPED for COL25A1 Gene

This gene is overexpressed in Plasma (45.9) and Platelet (23.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for COL25A1 Gene



SOURCE GeneReport for Unigene cluster for COL25A1 Gene Hs.658842

mRNA Expression by UniProt/SwissProt for COL25A1 Gene

Q9BXS0-COPA1_HUMAN
Tissue specificity: Expressed predominantly in brain. Deposited preferentially in primitive or neuritic amyloid plaques which are typical of Alzheimer disease.
genes like me logo Genes that share expression patterns with COL25A1: view

Protein tissue co-expression partners for COL25A1 Gene

Primer Products

In Situ Assay Products

Orthologs for COL25A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for COL25A1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia COL25A1 35
  • 92.2 (n)
  • 94.8 (a)
COL25A1 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia COL25A1 35
  • 92.66 (n)
  • 94.04 (a)
COL25A1 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col25a1 35
  • 89.19 (n)
  • 92.51 (a)
Col25a1 16
Col25a1 36
  • 91 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia COL25A1 35
  • 99.39 (n)
  • 99.08 (a)
COL25A1 36
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia COL25A1 36
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia COL25A1 36
  • 92 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL25A1 35
  • 79.61 (n)
  • 85.1 (a)
COL25A1 36
  • 83 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia COL25A1 36
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col25a1.2 35
  • 75.75 (n)
  • 80.4 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC101882764 35
  • 68.37 (n)
  • 70.13 (a)
COL25A1 36
  • 75 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea col-135 36
  • 33 (a)
OneToMany
Species with no ortholog for COL25A1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 COL25A1 Gene

ENSEMBL:
Gene Tree for COL25A1 (if available)
TreeFam:
Gene Tree for COL25A1 (if available)

Paralogs for COL25A1 Gene

(4) SIMAP similar genes for COL25A1 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with COL25A1: view

Variants for COL25A1 Gene

Sequence variations from dbSNP and Humsavar for COL25A1 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
VAR_073325 Fibrosis of extraocular muscles, congenital, 5 (CFEOM5)
rs763917 -- 109,158,980(-) ATAAA(A/G)TACAA intron-variant
rs917021 -- 109,279,347(-) ctggc(A/G)tgagt intron-variant
rs917022 -- 109,279,188(-) TGTGA(A/C)CCAGT intron-variant
rs921565 -- 108,866,292(+) GGCTC(A/G)GGTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for COL25A1 Gene

Variant ID Type Subtype PubMed ID
nsv879715 CNV Gain 21882294
nsv830034 CNV Loss 17160897
esv2657117 CNV Deletion 23128226
nsv830035 CNV Gain 17160897
nsv519227 CNV Loss 19592680
nsv461613 CNV Gain 19166990
esv7089 CNV Gain 19470904
esv259675 OTHER Complex 20981092
esv8308 CNV Gain 19470904
esv7132 CNV Gain 19470904
nsv293715 CNV Insertion 16902084
esv5466 CNV Gain 19470904
esv26012 CNV Loss 19812545
esv2664386 CNV Deletion 23128226
esv2728123 CNV Deletion 23290073
esv2436931 CNV Insertion 19546169
esv268533 CNV Insertion 20981092
esv273723 CNV Insertion 20981092
esv275332 CNV Loss 21479260
esv269886 CNV Insertion 20981092
esv2728124 CNV Deletion 23290073
esv2728125 CNV Deletion 23290073
nsv461614 CNV Loss 19166990
nsv4459 CNV Insertion 18451855
nsv515893 CNV Loss 19592680

Variation tolerance for COL25A1 Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.60; 45.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for COL25A1 Gene

HapMap Linkage Disequilibrium report
COL25A1
Human Gene Mutation Database (HGMD)
COL25A1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for COL25A1 Gene

Disorders for COL25A1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for COL25A1 Gene - From: OMIM, ClinVar, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
fibrosis of extraocular muscles, congenital, 5
  • cfeom5
congenital fibrosis of the extraocular muscles
  • tukel syndrome
antisocial personality disorder
  • asocial personality
ptosis, congenital
  • congenital ptosis
alzheimer disease
  • alzheimer disease, late-onset
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

COPA1_HUMAN
  • Fibrosis of extraocular muscles, congenital, 5 (CFEOM5) [MIM:616219]: An ocular motility disorder characterized by congenital dysinnervation of various cranial nerves to ocular muscles. Clinical features are ophthalmoplegia, anchoring of the eyes in downward gaze, ptosis, and backward tilt of the head. {ECO:0000269 PubMed:25500261}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for COL25A1

Genetic Association Database (GAD)
COL25A1
Human Genome Epidemiology (HuGE) Navigator
COL25A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
COL25A1
genes like me logo Genes that share disorders with COL25A1: view

No data available for Genatlas for COL25A1 Gene

Publications for COL25A1 Gene

  1. CLAC: a novel Alzheimer amyloid plaque component derived from a transmembrane precursor, CLAC-P/collagen type XXV. (PMID: 11927537) Hashimoto T. … Iwatsubo T. (EMBO J. 2002) 2 3 4 23 67
  2. Genetic association to the amyloid plaque associated protein gene COL25A1 in Alzheimer's disease. (PMID: 18501477) Forsell C. … Graff C. (Neurobiol. Aging 2010) 3 23
  3. Molecular identification of AMY, an Alzheimer disease amyloid- associated protein. (PMID: 14656069) Soederberg L. … Naeslund J. (J. Neuropathol. Exp. Neurol. 2003) 3 23
  4. Recessive mutations in COL25A1 are a cause of congenital cranial dysinnervation disorder. (PMID: 25500261) Shinwari J.M. … Al Tassan N. (Am. J. Hum. Genet. 2015) 3
  5. Genome-wide association studies and heritability estimates of body mass index related phenotypes in Bangladeshi adults. (PMID: 25133637) Scannell Bryan M. … Ahsan H. (PLoS ONE 2014) 3

Products for COL25A1 Gene

Sources for COL25A1 Gene

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