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Aliases for COL25A1 Gene

Aliases for COL25A1 Gene

  • Collagen Type XXV Alpha 1 Chain 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
  • Collagen, Type XXV, Alpha 1 2
  • Collagen Alpha-1(XXV) Chain 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 Chain) is a Protein Coding gene. Diseases associated with COL25A1 include Fibrosis Of Extraocular Muscles, Congenital, 5 and Ptosis, Congenital. Among its related pathways are Collagen biosynthesis and modifying enzymes and Phospholipase-C Pathway. GO annotations related to this gene include heparin binding and beta-amyloid binding. An important paralog of this gene is COL13A1.

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

Enhancers for COL25A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04F108830 0.5 ENCODE 11.6 +472.0 471973 0.2 INSM2 FEZF1 ZNF600 ZNF391 GFI1B ZNF501 ZNF843 OSR2 BCL11A ZNF610 COL25A1 ZCCHC23 ETNPPL GC04M108805 GC04M108908
GH04F109367 0.4 ENCODE 10.9 -65.8 -65844 1.2 COL25A1 ZCCHC23 SEC24B GC04P109364 PIR37678
GH04F109365 0.4 ENCODE 10.9 -63.4 -63369 0.8 ZNF792 JUN FOSL1 ZNF316 ZFHX2 CBX5 EED ETV6 ZNF600 NFE2 ZCCHC23 COL25A1 SEC24B-AS1 GC04P109364 PIR37678
GH04F108884 1.4 FANTOM5 ENCODE 5.3 +417.8 417812 1.6 ZNF316 COL25A1 GC04M108908 GC04M108805
GH04F108880 0.9 Ensembl ENCODE 5 +421.3 421308 1.9 FEZF1 RAD21 YY1 RARA FOS CREM MIXL1 NFYC NFIL3 CEBPA COL25A1 GC04M108908 GC04M108805
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around COL25A1 on UCSC Golden Path with GeneCards custom track

Promoters for COL25A1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001247177 -148 1400 TBP ARNT ZNF76 KLF17 FEZF1 ZNF2 GLIS2 ZNF366 SCRT2 SP3

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

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

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.

Gene Ontology (GO) - Molecular Function for COL25A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 beta-amyloid binding IDA 11927537
GO:0008201 heparin binding IEA,IDA 15522881
genes like me logo Genes that share ontologies with COL25A1: view
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 Models for COL25A1 Gene

MGI Knock Outs for COL25A1:

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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:0005576 extracellular region TAS --
GO:0005581 collagen trimer IEA --
GO:0005615 extracellular space IDA 11927537
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005886 plasma membrane TAS --
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:0030574 collagen catabolic process TAS --
GO:0060385 axonogenesis involved in innervation IEA --
genes like me logo Genes that share ontologies with COL25A1: view

No data available for SIGNOR curated interactions for COL25A1 Gene

Transcripts for COL25A1 Gene

Unigene Clusters for COL25A1 Gene

Collagen, type XXV, alpha 1:
Representative Sequences:

Inhibitory RNA Products

Clone 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



Protein tissue co-expression partners for COL25A1 Gene

NURSA nuclear receptor signaling pathways regulating expression of COL25A1 Gene:

COL25A1

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

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia COL25A1 34 35
  • 99.39 (n)
dog
(Canis familiaris)
Mammalia COL25A1 34 35
  • 92.66 (n)
cow
(Bos Taurus)
Mammalia COL25A1 34 35
  • 92.2 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia COL25A1 35
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Col25a1 34 16 35
  • 89.19 (n)
oppossum
(Monodelphis domestica)
Mammalia COL25A1 35
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves COL25A1 34 35
  • 79.61 (n)
lizard
(Anolis carolinensis)
Reptilia COL25A1 35
  • 86 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia col25a1.2 34
  • 75.75 (n)
zebrafish
(Danio rerio)
Actinopterygii COL25A1 35
  • 75 (a)
OneToOne
LOC101882764 34
  • 68.37 (n)
worm
(Caenorhabditis elegans)
Secernentea col-135 35
  • 33 (a)
OneToMany
Species where no ortholog for COL25A1 was found in the sources mined by GeneCards:
  • 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
rs780209390 Fibrosis of extraocular muscles, congenital, 5 (CFEOM5) [MIM:616219], Pathogenic 108,863,327(+) TGGTC(C/T)GGGGG nc-transcript-variant, reference, missense
rs10001049 -- 108,988,646(+) AAAGA(A/G)TTATT intron-variant
rs10001134 -- 108,859,974(+) AAATA(C/T)GATTT intron-variant
rs10001706 -- 108,997,039(+) aaaat(C/T)gacac intron-variant
rs10002294 -- 108,997,694(+) caata(C/T)acctg intron-variant

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

Variant ID Type Subtype PubMed ID
dgv113e19 CNV gain 19470904
dgv2875n106 CNV deletion 24896259
esv2436931 CNV insertion 19546169
esv26012 CNV loss 19812545
esv2657117 CNV deletion 23128226
esv2664386 CNV deletion 23128226
esv2728123 CNV deletion 23290073
esv2728124 CNV deletion 23290073
esv2728125 CNV deletion 23290073
esv275332 CNV loss 21479260
esv3302701 CNV tandem duplication 20981092
esv3304254 CNV mobile element insertion 20981092
esv3305609 CNV mobile element insertion 20981092
esv3309451 CNV mobile element insertion 20981092
esv3329381 CNV insertion 20981092
esv3365857 CNV insertion 20981092
esv3380051 CNV insertion 20981092
esv3564424 CNV deletion 23714750
esv3569650 CNV loss 25503493
esv3569651 CNV loss 25503493
esv3601731 CNV loss 21293372
esv3601732 CNV loss 21293372
esv3601734 OTHER inversion 21293372
esv7089 CNV gain 19470904
esv8308 CNV gain 19470904
nsv1073790 CNV deletion 25765185
nsv1128086 CNV deletion 24896259
nsv1136899 CNV deletion 24896259
nsv1143102 CNV tandem duplication 24896259
nsv1153416 CNV insertion 26484159
nsv293715 CNV insertion 16902084
nsv4459 CNV insertion 18451855
nsv461613 CNV gain 19166990
nsv461614 CNV loss 19166990
nsv476458 CNV novel sequence insertion 20440878
nsv515893 CNV loss 19592680
nsv519227 CNV loss 19592680
nsv595128 CNV loss 21841781
nsv595129 CNV gain 21841781
nsv595130 CNV loss 21841781
nsv595131 CNV loss 21841781
nsv830034 CNV loss 17160897
nsv830035 CNV gain 17160897

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

Human Gene Mutation Database (HGMD)
COL25A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
COL25A1

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

Disorders for COL25A1 Gene

MalaCards: The human disease database

(7) 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
ptosis, congenital
  • congenital ptosis
duane retraction syndrome 1
  • duane retraction syndrome
ptosis
  • blepharoptosis
antisocial personality disorder
  • asocial personality
- 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 22 64
  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 22 46 64
  3. Molecular identification of AMY, an Alzheimer disease amyloid- associated protein. (PMID: 14656069) Soederberg L. … Naeslund J. (J. Neuropathol. Exp. Neurol. 2003) 3 4 22 64
  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 4 64
  5. A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts. (PMID: 20332099) Kalsi G. … Riley B.P. (Hum. Mol. Genet. 2010) 3 46 64

Products for COL25A1 Gene

Sources for COL25A1 Gene

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