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

Summary

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. Acts upstream of or within axonogenesis involved in innervation. Located in collagen-containing extracellular matrix. Is expressed in retina layer; skeletal muscle; telencephalon; 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, Nov 2024]
Expression: Biased expression in bladder adult (RPKM 7.3), limb E14.5 (RPKM 4.6) and 10 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (1) 1 citation

General gene information

Go to the top of the page Help

Markers

D3Mit357 (e-PCR), detects polymorphism
- UniSTS:129798

15.MHAa56f3.seq (e-PCR)
- UniSTS:123241

21.MMHAP7FLG3.seq (e-PCR)
- UniSTS:123539

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 amyloid-beta binding	ISS Inferred from Sequence or Structural Similarity 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 heparin binding	ISS Inferred from Sequence or Structural Similarity 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 more info	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 extracellular space	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(XXV) chain

Names: collagen-like Alzheimer amyloid plaque component; procollagen, type XXV, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

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)
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)
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

NC_000069.7 Reference GRCm39 C57BL/6J

Range

129973992..130393533

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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)
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)
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
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)
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
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
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)
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)
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)
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
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
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)
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)
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)
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)