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Col28a1 collagen, type XXVIII, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 213945, updated on 11-Apr-2024

Summary

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Official Symbol
Col28a1provided by MGI
Official Full Name
collagen, type XXVIII, alpha 1provided by MGI
Primary source
MGI:MGI:2685312
See related
Ensembl:ENSMUSG00000068794 AllianceGenome:MGI:2685312
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Col28; Gm466
Summary
Predicted to be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell adhesion and negative regulation of peptidase activity. Located in basement membrane. Is expressed in several structures, including main olfactory bulb; metapodial pad; peripheral nervous system; skeletal muscle; and skin. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in bladder adult (RPKM 1.7), mammary gland adult (RPKM 0.6) and 14 other tissues See more
Orthologs
human all
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Genomic context

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Location:
6 A1; 6 3.44 cM
Exon count:
39
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (7997100..8193709, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (7997100..8193709, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 35246 Neighboring gene STARR-seq mESC enhancer starr_15106 Neighboring gene RNA binding protein with serine rich domain 1, pseudogene Neighboring gene predicted gene, 35446 Neighboring gene predicted gene, 35384 Neighboring gene STARR-seq mESC enhancer starr_15110 Neighboring gene STARR-seq mESC enhancer starr_15111 Neighboring gene STARR-seq mESC enhancer starr_15112 Neighboring gene meiosis regulator for oocyte development Neighboring gene STARR-positive B cell enhancer ABC_E1064 Neighboring gene replication protein A3

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. Type XXVIII Collagen Regulates Renal Interstitial Fibrosis and Epithelial-Mesenchymal Transition by SREBP1-Mediated HKDC1 Expression. Li L, et al. J Renin Angiotensin Aldosterone Syst, 2022. PMID 36518326, Free PMC Article
  2. COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells. Li L, et al. Ren Fail, 2023 Dec. PMID 36883360, Free PMC Article
  3. Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain. Veit G, et al. J Biol Chem, 2006 Feb 10. PMID 16330543
  4. Collagen XXVIII is a distinctive component of the peripheral nervous system nodes of ranvier and surrounds nonmyelinating glial cells. Grimal S, et al. Glia, 2010 Dec. PMID 20830809
  5. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Naba A, et al. Mol Cell Proteomics, 2012 Apr. PMID 22159717, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
    Title: COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
  2. Type XXVIII Collagen Regulates Renal Interstitial Fibrosis and Epithelial-Mesenchymal Transition by SREBP1-Mediated HKDC1 Expression.
    Title: Type XXVIII Collagen Regulates Renal Interstitial Fibrosis and Epithelial-Mesenchymal Transition by SREBP1-Mediated HKDC1 Expression.
  3. The correlation between the absence of myelin and the presence of collagen XXVIII is confirmed in a mouse model of Charcot-Marie-Tooth characterized by dysmyelinated nerve fibers, in which enhancement of collagen XXVIII labeling is observed
    Title: Collagen XXVIII is a distinctive component of the peripheral nervous system nodes of ranvier and surrounds nonmyelinating glial cells.
  4. Collagen XXVIII is a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain
    Title: Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain.
Submit: New GeneRIF Correction

Variation

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Alleles

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

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
enables serine-type endopeptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of peptidase activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in basement membrane IDA
Inferred from Direct Assay
more info
 PubMed 
part_of collagen trimer IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
collagen alpha-1(XXVIII) chain
Names
collagen 28

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_001037865.1 → NP_001032954.1  collagen alpha-1(XXVIII) chain precursor

    See identical proteins and their annotated locations for NP_001032954.1

    Status: PROVISIONAL

    Source sequence(s)
    AJ890449
    Consensus CDS
    CCDS39424.1
    UniProtKB/Swiss-Prot
    Q2UY10, Q2UY11
    Related
    ENSMUSP00000111199.2, ENSMUST00000115537.2
    Conserved Domains (5) summary
    pfam01391
    Location:575 → 636
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:1086 → 1139
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47 → 212
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799 → 974
    VWA; von Willebrand factor type A domain
    pfam03157
    Location:361 → 763
    Glutenin_hmw; High molecular weight glutenin subunit

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_000072.7 Reference GRCm39 C57BL/6J

    Range
    7997100..8193709 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017321502.1 → XP_017176991.1  collagen alpha-1(XXVIII) chain isoform X1

    UniProtKB/Swiss-Prot
    Q2UY10, Q2UY11
    Conserved Domains (5) summary
    pfam01391
    Location:575 → 636
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:1086 → 1139
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47 → 212
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799 → 974
    VWA; von Willebrand factor type A domain
    pfam03157
    Location:361 → 763
    Glutenin_hmw; High molecular weight glutenin subunit

  2. XM_036166011.1 → XP_036021904.1  collagen alpha-1(XXVIII) chain isoform X2

    Conserved Domains (4) summary
    cd00109
    Location:1017 → 1070
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47 → 212
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:730 → 905
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:500 → 567
    Collagen; Collagen triple helix repeat (20 copies)

  3. XM_006505031.2 → XP_006505094.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_006505094.1

    UniProtKB/Swiss-Prot
    Q2UY10, Q2UY11
    Conserved Domains (5) summary
    pfam01391
    Location:575 → 636
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:1086 → 1139
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47 → 212
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799 → 974
    VWA; von Willebrand factor type A domain
    pfam03157
    Location:361 → 763
    Glutenin_hmw; High molecular weight glutenin subunit

  4. XM_006505033.4 → XP_006505096.1  collagen alpha-1(XXVIII) chain isoform X3

    Conserved Domains (4) summary
    pfam01391
    Location:32 → 96
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:861 → 914
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    pfam09606
    Location:162 → 411
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00092
    Location:574 → 749
    VWA; von Willebrand factor type A domain

  5. XM_017321503.3 → XP_017176992.1  collagen alpha-1(XXVIII) chain isoform X3

    Conserved Domains (4) summary
    pfam01391
    Location:32 → 96
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:861 → 914
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    pfam09606
    Location:162 → 411
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam00092
    Location:574 → 749
    VWA; von Willebrand factor type A domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q2UY11.1 GenPept UniProtKB/Swiss-Prot:Q2UY11

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