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COL25A1 collagen type XXV alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 84570, updated on 22-Aug-2020

Summary

Official Symbol
COL25A1provided by HGNC
Official Full Name
collagen type XXV alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:18603
See related
Ensembl:ENSG00000188517 MIM:610004
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AMY; CLAC; CLACP; CFEOM5; CLAC-P
Summary
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]
Expression
Biased expression in testis (RPKM 1.9), fat (RPKM 1.8) and 13 other tissues See more
Orthologs

Genomic context

See COL25A1 in Genome Data Viewer
Location:
4q25
Exon count:
48
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (108808725..109302737, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (109731877..110223799, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ethanolamine-phosphate phospho-lyase Neighboring gene regulator of chromosome condensation 2 pseudogene 8 Neighboring gene Sharpr-MPRA regulatory region 12117 Neighboring gene COL25A1 divergent transcript Neighboring gene RBMX pseudogene 4

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

Associated conditions

Description Tests
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
GeneReviews: Not available
Fibrosis of extraocular muscles, congenital, 5
MedGen: C4015552 OMIM: 616219 GeneReviews: Not available
Compare labs
Genome-wide association analysis of age at onset in schizophrenia in a European-American sample
GeneReviews: Not available
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
amyloid-beta binding IDA
Inferred from Direct Assay
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
heparin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
axonogenesis involved in innervation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
collagen-containing extracellular matrix HDA PubMed 
collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
collagen alpha-1(XXV) chain
Names
alzheimer disease amyloid-associated protein
collagen-like Alzheimer amyloid plaque component
collagenous Alzheimer amyloid plaque component

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.

Genomic

  1. NG_047204.1 RefSeqGene

    Range
    5095..499028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256074.3NP_001243003.1  collagen alpha-1(XXV) chain isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has multiple differences in the coding region but maintains the reading frame, and also differs in the 5' and 3' UTRs, compared to variant 1. The resulting isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC004051, AC097473, BC030649
    Consensus CDS
    CCDS58922.1
    UniProtKB/TrEMBL
    A8MWQ5
    Related
    ENSP00000382078.1, ENST00000399127.5
    Conserved Domains (1) summary
    pfam01391
    Location:547606
    Collagen; Collagen triple helix repeat (20 copies)
  2. NM_032518.4NP_115907.2  collagen alpha-1(XXV) chain isoform 2

    See identical proteins and their annotated locations for NP_115907.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks three 3' exons but includes an alternate 3' exon, resulting in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC004051, AC097473, AF293341, BC030649
    Consensus CDS
    CCDS43259.1
    UniProtKB/Swiss-Prot
    Q9BXS0
    Related
    ENSP00000382077.1, ENST00000399126.1
    Conserved Domains (1) summary
    pfam01391
    Location:553611
    Collagen; Collagen triple helix repeat (20 copies)
  3. NM_198721.4NP_942014.1  collagen alpha-1(XXV) chain isoform 1

    See identical proteins and their annotated locations for NP_942014.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC004051, AC097473, AF293340, AF293341, BC030649, KF457803
    Consensus CDS
    CCDS43258.1
    UniProtKB/Swiss-Prot
    Q9BXS0
    Related
    ENSP00000382083.1, ENST00000399132.6
    Conserved Domains (1) summary
    pfam01391
    Location:553611
    Collagen; Collagen triple helix repeat (20 copies)

RNA

  1. NR_045756.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' exon, lacks three exons and uses an alternate splice site in the central region, and uses alternate exon structure in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC004051, AC097473, BC036669
    Related
    ENST00000494183.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    108808725..109302737 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008735.1XP_016864224.1  collagen alpha-1(XXV) chain isoform X3

  2. XM_017008736.1XP_016864225.1  collagen alpha-1(XXV) chain isoform X4

  3. XM_011532335.2XP_011530637.1  collagen alpha-1(XXV) chain isoform X1

    See identical proteins and their annotated locations for XP_011530637.1

    Conserved Domains (1) summary
    pfam01391
    Location:592646
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_011532334.2XP_011530636.1  collagen alpha-1(XXV) chain isoform X1

    See identical proteins and their annotated locations for XP_011530636.1

    Conserved Domains (1) summary
    pfam01391
    Location:592646
    Collagen; Collagen triple helix repeat (20 copies)
  5. XM_011532333.2XP_011530635.1  collagen alpha-1(XXV) chain isoform X1

    See identical proteins and their annotated locations for XP_011530635.1

    Related
    ENSP00000495847.1, ENST00000642955.1
    Conserved Domains (1) summary
    pfam01391
    Location:592646
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_011532338.2XP_011530640.1  collagen alpha-1(XXV) chain isoform X2

    Conserved Domains (1) summary
    pfam01391
    Location:586640
    Collagen; Collagen triple helix repeat (20 copies)
  7. XM_017008737.1XP_016864226.1  collagen alpha-1(XXV) chain isoform X5

    Conserved Domains (1) summary
    pfam01391
    Location:479533
    Collagen; Collagen triple helix repeat (20 copies)
  8. XM_011532356.2XP_011530658.1  collagen alpha-1(XXV) chain isoform X6

    Conserved Domains (1) summary
    pfam01391
    Location:473527
    Collagen; Collagen triple helix repeat (20 copies)
  9. XM_011532355.2XP_011530657.1  collagen alpha-1(XXV) chain isoform X5

    Conserved Domains (1) summary
    pfam01391
    Location:479533
    Collagen; Collagen triple helix repeat (20 copies)
  10. XM_011532358.2XP_011530660.1  collagen alpha-1(XXV) chain isoform X7

    Related
    ENSP00000484110.1, ENST00000622134.4
    Conserved Domains (1) summary
    pfam01391
    Location:431485
    Collagen; Collagen triple helix repeat (20 copies)
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