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    Col18a1 collagen, type XVIII, alpha 1 [ Mus musculus (house mouse) ]

    Gene ID: 12822, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col18a1provided by MGI
    Official Full Name
    collagen, type XVIII, alpha 1provided by MGI
    Primary source
    MGI:MGI:88451
    See related
    Ensembl:ENSMUSG00000001435 AllianceGenome:MGI:88451
    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
    Summary
    Predicted to enable identical protein binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Acts upstream of or within several processes, including endothelial cell morphogenesis; positive regulation of endothelial cell apoptotic process; and positive regulation of vascular endothelial cell proliferation. Located in basement membrane. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Used to study pigment dispersion syndrome. Human ortholog(s) of this gene implicated in primary angle-closure glaucoma. Orthologous to human COL18A1 (collagen type XVIII alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in liver adult (RPKM 128.4), liver E18 (RPKM 40.0) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Col18a1 in Genome Data Viewer
    Location:
    10 C1; 10 39.72 cM
    Exon count:
    48
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (76888013..77002351, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (77052178..77166530, complement)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene predicted gene 10787 Neighboring gene predicted gene, 3137 Neighboring gene solute carrier family 19 (folate transporter), member 1 Neighboring gene STARR-seq mESC enhancer starr_27190 Neighboring gene spermidine synthase pseudogene Neighboring gene STARR-seq mESC enhancer starr_27194 Neighboring gene STARR-seq mESC enhancer starr_27197 Neighboring gene STARR-seq mESC enhancer starr_27199 Neighboring gene predicted gene, 35837 Neighboring gene predicted gene, 40704 Neighboring gene predicted gene, 40703

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (5)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within angiogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of blood vessel endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of endothelial cell apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in endothelial cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within endothelial cell morphogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within extracellular matrix organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of blood vessel endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of endothelial cell apoptotic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within positive regulation of vascular endothelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of vascular endothelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basement membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    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 space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XVIII) chain
    Names
    alpha-1(XVIII) collagen
    endostatin
    procollagen, type XVIII, alpha 1

    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.

    mRNA and Protein(s)

    1. NM_001109991.2NP_001103461.1  collagen alpha-1(XVIII) chain isoform 1 precursor

      See identical proteins and their annotated locations for NP_001103461.1

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
      Consensus CDS
      CCDS48604.1
      UniProtKB/Swiss-Prot
      P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63
      Related
      ENSMUSP00000101049.2, ENSMUST00000105409.8
      Conserved Domains (4) summary
      pfam01391
      Location:822881
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:245433
      TSPN; Thrombospondin N-terminal -like domains
      cd00247
      Location:13501520
      Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...
      pfam06121
      Location:22218
      DUF959; Domain of Unknown Function (DUF959)
    2. NM_001406250.1NP_001393179.1  collagen alpha-1(XVIII) chain isoform 3 precursor

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    3. NM_001406251.1NP_001393180.1  collagen alpha-1(XVIII) chain isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    4. NM_001406252.1NP_001393181.1  collagen alpha-1(XVIII) chain isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    5. NM_001406253.1NP_001393182.1  collagen alpha-1(XVIII) chain isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    6. NM_001406254.1NP_001393183.1  collagen alpha-1(XVIII) chain isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    7. NM_001406255.1NP_001393184.1  collagen alpha-1(XVIII) chain isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
    8. NM_009929.4NP_034059.2  collagen alpha-1(XVIII) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_034059.2

      Status: VALIDATED

      Source sequence(s)
      AC055777, AC159334
      Consensus CDS
      CCDS23953.1
      UniProtKB/Swiss-Prot
      P39061
      Related
      ENSMUSP00000080358.7, ENSMUST00000081654.13
      Conserved Domains (3) summary
      pfam01391
      Location:610669
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:33221
      TSPN; Thrombospondin N-terminal -like domains
      cd00247
      Location:11381308
      Endostatin-like; Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; ...

    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_000076.7 Reference GRCm39 C57BL/6J

      Range
      76888013..77002351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006513174.4XP_006513237.1  collagen alpha-1(XVIII) chain isoform X2

      UniProtKB/Swiss-Prot
      P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63
      Conserved Domains (5) summary
      cd07455
      Location:366488
      CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )
      pfam01391
      Location:10691128
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:492680
      TSPN; Thrombospondin N-terminal -like domains
      pfam06121
      Location:37218
      DUF959; Domain of Unknown Function (DUF959)
      pfam06482
      Location:14621764
      Endostatin; Collagenase NC10 and Endostatin
    2. XM_006513173.5XP_006513236.1  collagen alpha-1(XVIII) chain isoform X1

      UniProtKB/Swiss-Prot
      P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63
      UniProtKB/TrEMBL
      E9QPX1
      Related
      ENSMUSP00000072538.5, ENSMUST00000072755.12
      Conserved Domains (5) summary
      cd07455
      Location:366488
      CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )
      pfam01391
      Location:10691128
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:492680
      TSPN; Thrombospondin N-terminal -like domains
      pfam06121
      Location:37218
      DUF959; Domain of Unknown Function (DUF959)
      pfam06482
      Location:14631765
      Endostatin; Collagenase NC10 and Endostatin
    3. XM_006513176.4XP_006513239.1  collagen alpha-1(XVIII) chain isoform X6

      UniProtKB/Swiss-Prot
      P39061, Q60672, Q61434, Q61437, Q62001, Q62002, Q6NZK9, Q6P1Y4, Q8CCZ8, Q9CRT2, Q9JK63
      Conserved Domains (4) summary
      pfam01391
      Location:822881
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:245433
      TSPN; Thrombospondin N-terminal -like domains
      pfam06121
      Location:37218
      DUF959; Domain of Unknown Function (DUF959)
      pfam06482
      Location:12151517
      Endostatin; Collagenase NC10 and Endostatin
    4. XM_011243347.4XP_011241649.1  collagen alpha-1(XVIII) chain isoform X5

      Conserved Domains (4) summary
      cd07455
      Location:366488
      CRD_Collagen_XVIII; Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 )
      pfam01391
      Location:840875
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:492680
      TSPN; Thrombospondin N-terminal -like domains
      pfam06121
      Location:37218
      DUF959; Domain of Unknown Function (DUF959)