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

    Gene ID: 84570, updated on 5-Mar-2024

    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; AllianceGenome:HGNC:18603
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See COL25A1 in Genome Data Viewer
    Location:
    4q25
    Exon count:
    49
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (108808725..109302658, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (112110611..112604870, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (109729881..110223814, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:109708719-109709219 Neighboring gene ethanolamine-phosphate phospho-lyase Neighboring gene regulator of chromosome condensation 2 pseudogene 8 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:109852739-109853343 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71593 Neighboring gene uncharacterized LOC124900756 Neighboring gene Sharpr-MPRA regulatory region 6815 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71618 Neighboring gene Sharpr-MPRA regulatory region 12117 Neighboring gene uncharacterized LOC124900754 Neighboring gene NANOG hESC enhancer GRCh37_chr4:110107576-110108103 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71641 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71659 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71681 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15620 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:110223886-110224668 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
    Fibrosis of extraocular muscles, congenital, 5
    MedGen: C4015552 OMIM: 616219 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    Genome-wide association analysis of age at onset in schizophrenia in a European-American sample
    EBI GWAS Catalog
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

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

    NEW Try the new Transcript table

    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
      A8MPZ6, Q9BXR9, 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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      108808725..109302658 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      See identical proteins and their annotated locations for XP_011530637.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Conserved Domains (1) summary
      pfam01391
      Location:592646
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_011532334.3XP_011530636.1  collagen alpha-1(XXV) chain isoform X1

      See identical proteins and their annotated locations for XP_011530636.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Conserved Domains (1) summary
      pfam01391
      Location:592646
      Collagen; Collagen triple helix repeat (20 copies)
    3. XM_011532333.3XP_011530635.1  collagen alpha-1(XXV) chain isoform X1

      See identical proteins and their annotated locations for XP_011530635.1

      UniProtKB/TrEMBL
      A0A2R8Y760
      Related
      ENSP00000495847.1, ENST00000642955.1
      Conserved Domains (1) summary
      pfam01391
      Location:592646
      Collagen; Collagen triple helix repeat (20 copies)
    4. XM_017008737.2XP_016864226.1  collagen alpha-1(XXV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:479533
      Collagen; Collagen triple helix repeat (20 copies)
    5. XM_011532356.3XP_011530658.1  collagen alpha-1(XXV) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:473527
      Collagen; Collagen triple helix repeat (20 copies)
    6. XM_011532355.3XP_011530657.1  collagen alpha-1(XXV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:479533
      Collagen; Collagen triple helix repeat (20 copies)
    7. XM_011532358.2XP_011530660.1  collagen alpha-1(XXV) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:431485
      Collagen; Collagen triple helix repeat (20 copies)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      112110611..112604870 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351103.1XP_054207078.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760
    2. XM_054351101.1XP_054207076.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760
    3. XM_054351102.1XP_054207077.1  collagen alpha-1(XXV) chain isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y760
    4. XM_054351105.1XP_054207080.1  collagen alpha-1(XXV) chain isoform X2

    5. XM_054351106.1XP_054207081.1  collagen alpha-1(XXV) chain isoform X3

    6. XM_054351104.1XP_054207079.1  collagen alpha-1(XXV) chain isoform X2

    7. XM_054351107.1XP_054207082.1  collagen alpha-1(XXV) chain isoform X4