Format

Send to:

Choose Destination

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

Gene ID: 12822, updated on 23-Jun-2021

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
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
endo
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:
44
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (76888013..77002391, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (77052178..77166530, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (76514924..76629275, 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 spermidine synthase pseudogene 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)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
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
 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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_001109991.1NP_001103461.1  collagen alpha-1(XVIII) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_001103461.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC159334, BC064817, CF171159
    Consensus CDS
    CCDS48604.1
    UniProtKB/Swiss-Prot
    P39061
    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_009929.3NP_034059.2  collagen alpha-1(XVIII) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_034059.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, compared to variant 1. These variations cause translation initiation from a start codon in a different exon and result in a shorter protein (isoform 2) with a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    BC064817, CF171159, U11636
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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..77002391 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036155572.1XP_036011465.1  collagen alpha-1(XVIII) chain isoform X4

    Conserved Domains (3) summary
    smart00210
    Location:33221
    TSPN; Thrombospondin N-terminal -like domains
    pfam01391
    Location:613669
    Collagen; Collagen triple helix repeat (20 copies)
    pfam06482
    Location:10031308
    Endostatin; Collagenase NC10 and Endostatin
  2. XM_006513174.4XP_006513237.1  collagen alpha-1(XVIII) chain isoform X2

    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
  3. XM_006513173.5XP_006513236.1  collagen alpha-1(XVIII) chain isoform X1

    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
  4. XM_006513176.4XP_006513239.1  collagen alpha-1(XVIII) chain isoform X6

    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
  5. XM_011243346.4XP_011241648.1  collagen alpha-1(XVIII) chain isoform X3

    Conserved Domains (4) summary
    pfam01391
    Location:778837
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:201389
    TSPN; Thrombospondin N-terminal -like domains
    pfam06482
    Location:11721474
    Endostatin; Collagenase NC10 and Endostatin
    cl02447
    Location:93197
    CRD_FZ; CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain
  6. 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)
Support Center