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    Col25a1 collagen, type XXV, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 77018, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Col25a1provided by MGI
    Official Full Name
    collagen, type XXV, alpha 1provided by MGI
    Primary source
    MGI:MGI:1924268
    See related
    Ensembl:ENSMUSG00000058897 AllianceGenome:MGI:1924268
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CLAC-P; 2700062B08Rik
    Summary
    Predicted to enable amyloid-beta binding activity; heparin binding activity; and identical protein binding activity. Predicted to be an extracellular matrix structural constituent. Acts upstream of or within axonogenesis involved in innervation. Located in collagen-containing extracellular matrix. Is expressed in retina layer and ureter. Human ortholog(s) of this gene implicated in congenital fibrosis of the extraocular muscles 5. Orthologous to human COL25A1 (collagen type XXV alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in bladder adult (RPKM 7.3), limb E14.5 (RPKM 4.6) and 10 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Col25a1 in Genome Data Viewer
    Location:
    3 G3; 3 59.99 cM
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (129973992..130393533)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (130180358..130599884)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene 9396 Neighboring gene makorin, ring finger protein, 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_08983 Neighboring gene predicted gene, 22682 Neighboring gene STARR-seq mESC enhancer starr_08984 Neighboring gene STARR-seq mESC enhancer starr_08985 Neighboring gene ethanolamine phosphate phospholyase Neighboring gene predicted gene, 36322 Neighboring gene STARR-positive B cell enhancer ABC_E4590 Neighboring gene predicted gene, 36373

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. COL25A1 triggers and promotes Alzheimer's disease-like pathology in vivo. Tong Y, et al. Neurogenetics, 2010 Feb. PMID 19548013, Free PMC Article
    2. Three-dimensional mapping reveals heterochronic development of the neuromuscular system in postnatal mouse skeletal muscles. Xu J, et al. Commun Biol, 2022 Nov 8. PMID 36347940, Free PMC Article
    3. CLAC: a novel Alzheimer amyloid plaque component derived from a transmembrane precursor, CLAC-P/collagen type XXV. Hashimoto T, et al. EMBO J, 2002 Apr 2. PMID 11927537, Free PMC Article
    4. CLAC-P/collagen type XXV is required for the intramuscular innervation of motoneurons during neuromuscular development. Tanaka T, et al. J Neurosci, 2014 Jan 22. PMID 24453327, Free PMC Article
    5. Roles of Collagen XXV and Its Putative Receptors PTPσ/δ in Intramuscular Motor Innervation and Congenital Cranial Dysinnervation Disorder. Munezane H, et al. Cell Rep, 2019 Dec 24. PMID 31875546

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Roles of Collagen XXV and Its Putative Receptors PTPsigma/delta in Intramuscular Motor Innervation and Congenital Cranial Dysinnervation Disorder.
      Title: Roles of Collagen XXV and Its Putative Receptors PTPσ/δ in Intramuscular Motor Innervation and Congenital Cranial Dysinnervation Disorder.
    2. CLAC-P/collagen XXV is a novel essential factor that regulates the initial phase of intramuscular motor innervation, which is required for subsequent target-dependent motoneuron survival and neuromuscular junction formation during development.
      Title: CLAC-P/collagen type XXV is required for the intramuscular innervation of motoneurons during neuromuscular development.
    3. COL25A1 leads to Alzheimer's disease-like pathology in vivo
      Title: COL25A1 triggers and promotes Alzheimer's disease-like pathology in vivo.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1)  1 citation
    • Endonuclease-mediated (2) 

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables amyloid-beta binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables amyloid-beta binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables extracellular matrix structural constituent conferring tensile strength RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    enables heparin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within axonogenesis involved in innervation IMP
    Inferred from Mutant Phenotype
    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 extracellular region ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    collagen alpha-1(XXV) chain
    Names
    collagen-like Alzheimer amyloid plaque component
    procollagen, type XXV, alpha 1

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001244952.1 → NP_001231881.1  collagen alpha-1(XXV) chain isoform 3

      See identical proteins and their annotated locations for NP_001231881.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two in-frame exons in the coding region, compared to variant 1. The resulting isoform (3) lacks two internal segments, compared to isoform 1.
      Source sequence(s)
      AC110540, AK035562, BC138051, CJ117861
      UniProtKB/TrEMBL
      B2RQR7
      Conserved Domains (1) summary
      pfam01391
      Location:553 → 610
      Collagen; Collagen triple helix repeat (20 copies)

    2. NM_029838.4 → NP_084114.2  collagen alpha-1(XXV) chain isoform 1

      See identical proteins and their annotated locations for NP_084114.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC110540, AK035562, BC138051, CJ117861
      Consensus CDS
      CCDS38637.1
      UniProtKB/Swiss-Prot
      G3X9H6, Q99MQ5
      Related
      ENSMUSP00000079210.5, ENSMUST00000080335.11
      Conserved Domains (1) summary
      pfam01391
      Location:565 → 623
      Collagen; Collagen triple helix repeat (20 copies)

    3. NM_198711.3 → NP_942004.1  collagen alpha-1(XXV) chain isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, and has a shorter 3' UTR, compared to variant 1. The resulting isoform (2) is shorter than the full-length of isoform 1, but has a longer C-terminus than that of isoform 1.
      Source sequence(s)
      AC110540, AK012466, AK035562, CJ117861
      Consensus CDS
      CCDS38636.1
      UniProtKB/TrEMBL
      E9Q5L6
      Related
      ENSMUSP00000101960.2, ENSMUST00000106353.2
      Conserved Domains (1) summary
      pfam01391
      Location:528 → 586
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      129973992..130393533
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006502266.5 → XP_006502329.1  collagen alpha-1(XXV) chain isoform X3

      Conserved Domains (2) summary
      pfam01391
      Location:579 → 638
      Collagen; Collagen triple helix repeat (20 copies)
      PHA03169
      Location:209 → 396
      PHA03169; hypothetical protein; Provisional

    2. XM_006502276.5 → XP_006502339.1  collagen alpha-1(XXV) chain isoform X14

      Conserved Domains (1) summary
      pfam01391
      Location:564 → 623
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_006502286.5 → XP_006502349.1  collagen alpha-1(XXV) chain isoform X29

      Conserved Domains (1) summary
      pfam01391
      Location:555 → 614
      Collagen; Collagen triple helix repeat (20 copies)

    4. XM_006502269.5 → XP_006502332.1  collagen alpha-1(XXV) chain isoform X6

      Conserved Domains (2) summary
      pfam01391
      Location:574 → 633
      Collagen; Collagen triple helix repeat (20 copies)
      PHA03169
      Location:252 → 400
      PHA03169; hypothetical protein; Provisional

    5. XM_017319804.3 → XP_017175293.1  collagen alpha-1(XXV) chain isoform X7

      Conserved Domains (1) summary
      pfam01391
      Location:573 → 632
      Collagen; Collagen triple helix repeat (20 copies)

    6. XM_006502280.5 → XP_006502343.1  collagen alpha-1(XXV) chain isoform X19

      Conserved Domains (2) summary
      pfam01391
      Location:553 → 612
      Collagen; Collagen triple helix repeat (20 copies)
      pfam09606
      Location:152 → 390
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    7. XM_006502281.5 → XP_006502344.1  collagen alpha-1(XXV) chain isoform X20

      Conserved Domains (2) summary
      pfam01391
      Location:552 → 611
      Collagen; Collagen triple helix repeat (20 copies)
      PHA03169
      Location:209 → 396
      PHA03169; hypothetical protein; Provisional

    8. XM_006502268.5 → XP_006502331.1  collagen alpha-1(XXV) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:574 → 633
      Collagen; Collagen triple helix repeat (20 copies)

    9. XM_006502272.5 → XP_006502335.1  collagen alpha-1(XXV) chain isoform X10

      Conserved Domains (1) summary
      pfam01391
      Location:577 → 634
      Collagen; Collagen triple helix repeat (20 copies)

    10. XM_006502274.5 → XP_006502337.1  collagen alpha-1(XXV) chain isoform X12

      Conserved Domains (1) summary
      pfam01391
      Location:568 → 627
      Collagen; Collagen triple helix repeat (20 copies)

    11. XM_006502275.5 → XP_006502338.1  collagen alpha-1(XXV) chain isoform X13

      Conserved Domains (2) summary
      pfam01391
      Location:568 → 627
      Collagen; Collagen triple helix repeat (20 copies)
      PHA03169
      Location:252 → 394
      PHA03169; hypothetical protein; Provisional

    12. XM_006502277.5 → XP_006502340.1  collagen alpha-1(XXV) chain isoform X16

      Conserved Domains (2) summary
      pfam01391
      Location:559 → 618
      Collagen; Collagen triple helix repeat (20 copies)
      pfam09606
      Location:158 → 396
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    13. XM_006502267.5 → XP_006502330.1  collagen alpha-1(XXV) chain isoform X4

      Conserved Domains (1) summary
      pfam01391
      Location:577 → 636
      Collagen; Collagen triple helix repeat (20 copies)

    14. XM_006502264.5 → XP_006502327.1  collagen alpha-1(XXV) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:583 → 642
      Collagen; Collagen triple helix repeat (20 copies)

    15. XM_006502265.5 → XP_006502328.1  collagen alpha-1(XXV) chain isoform X2

      Conserved Domains (1) summary
      pfam01391
      Location:592 → 650
      Collagen; Collagen triple helix repeat (20 copies)

    16. XM_006502271.5 → XP_006502334.1  collagen alpha-1(XXV) chain isoform X9

      Conserved Domains (1) summary
      pfam01391
      Location:574 → 633
      Collagen; Collagen triple helix repeat (20 copies)

    17. XM_006502282.5 → XP_006502345.1  collagen alpha-1(XXV) chain isoform X22

      Conserved Domains (1) summary
      pfam01391
      Location:592 → 651
      Collagen; Collagen triple helix repeat (20 copies)

    18. XM_030252886.2 → XP_030108746.1  collagen alpha-1(XXV) chain isoform X21

      Conserved Domains (2) summary
      pfam01391
      Location:556 → 610
      Collagen; Collagen triple helix repeat (20 copies)
      PHA03169
      Location:211 → 395
      PHA03169; hypothetical protein; Provisional

    19. XM_006502283.5 → XP_006502346.1  collagen alpha-1(XXV) chain isoform X23

      Conserved Domains (1) summary
      pfam01391
      Location:553 → 607
      Collagen; Collagen triple helix repeat (20 copies)

    20. XM_006502270.5 → XP_006502333.1  collagen alpha-1(XXV) chain isoform X8

      Related
      ENSMUSP00000158974.2, ENSMUST00000238846.2
      Conserved Domains (1) summary
      pfam01391
      Location:583 → 642
      Collagen; Collagen triple helix repeat (20 copies)

    21. XM_006502284.5 → XP_006502347.1  collagen alpha-1(XXV) chain isoform X24

      Conserved Domains (1) summary
      pfam01391
      Location:592 → 650
      Collagen; Collagen triple helix repeat (20 copies)

    22. XM_006502279.5 → XP_006502342.1  collagen alpha-1(XXV) chain isoform X18

      Conserved Domains (1) summary
      pfam01391
      Location:592 → 650
      Collagen; Collagen triple helix repeat (20 copies)

    23. XM_006502278.5 → XP_006502341.1  collagen alpha-1(XXV) chain isoform X17

      Conserved Domains (1) summary
      pfam01391
      Location:556 → 615
      Collagen; Collagen triple helix repeat (20 copies)

    24. XM_006502285.5 → XP_006502348.1  collagen alpha-1(XXV) chain isoform X25

      Conserved Domains (1) summary
      pfam01391
      Location:553 → 611
      Collagen; Collagen triple helix repeat (20 copies)

    25. XM_006502273.5 → XP_006502336.1  collagen alpha-1(XXV) chain isoform X11

      Conserved Domains (1) summary
      pfam01391
      Location:592 → 650
      Collagen; Collagen triple helix repeat (20 copies)

    26. XM_030252884.2 → XP_030108744.1  collagen alpha-1(XXV) chain isoform X15

      Conserved Domains (1) summary
      pfam01391
      Location:574 → 633
      Collagen; Collagen triple helix repeat (20 copies)

    27. XM_030252888.2 → XP_030108748.1  collagen alpha-1(XXV) chain isoform X27

      Conserved Domains (1) summary
      pfam01391
      Location:553 → 607
      Collagen; Collagen triple helix repeat (20 copies)

    28. XM_030252887.2 → XP_030108747.1  collagen alpha-1(XXV) chain isoform X26

      Conserved Domains (1) summary
      pfam01391
      Location:556 → 614
      Collagen; Collagen triple helix repeat (20 copies)

    29. XM_017319806.3 → XP_017175295.1  collagen alpha-1(XXV) chain isoform X28

      Conserved Domains (1) summary
      pfam01391
      Location:553 → 611
      Collagen; Collagen triple helix repeat (20 copies)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99MQ5.2 GenPept UniProtKB/Swiss-Prot:Q99MQ5

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