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

Gene ID: 77018, updated on 21-Apr-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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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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