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Col13a1 collagen, type XIII, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12817, updated on 23-May-2018
Official Symbol
Col13a1provided by MGI
Official Full Name
collagen, type XIII, alpha 1provided by MGI
Primary source
MGI:MGI:1277201
See related
Ensembl:ENSMUSG00000058806 Vega:OTTMUSG00000021424
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
Expression
Broad expression in lung adult (RPKM 5.8), limb E14.5 (RPKM 1.5) and 15 other tissues See more
Orthologs
See Col13a1 in Genome Data Viewer
Location:
10 32.29 cM; 10 B4
Exon count:
45
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 10 NC_000076.6 (61838234..61979210, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (61301246..61441856, complement)

Chromosome 10 - NC_000076.6Genomic Context describing neighboring genes Neighboring gene H2A histone family, member Y2 Neighboring gene microRNA 5108 Neighboring gene predicted gene 2137 Neighboring gene predicted gene, 40674 Neighboring gene predicted gene, 30121 Neighboring gene ribosomal protein L7A pseudogene Neighboring gene argininosuccinate synthase pseudogene Neighboring gene family with sequence similarity 241, member B

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

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

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
heparin binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-matrix adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-matrix adhesion ISO
Inferred from Sequence Orthology
more info
 
endochondral ossification IEP
Inferred from Expression Pattern
more info
PubMed 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
morphogenesis of a branching structure IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
morphogenesis of a branching structure IEP
Inferred from Expression Pattern
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
ossification IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell-cell junction IDA
Inferred from Direct Assay
more info
PubMed 
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-1(XIII) chain
Names
procollagen, type XIII, alpha 1
type XIII collagen

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_001304757.1NP_001291686.1  collagen alpha-1(XIII) chain isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks three alternate in-frame exons in the coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AC122315, AC164702
    Consensus CDS
    CCDS78821.1
    UniProtKB/TrEMBL
    D3Z7B8
    Related
    ENSMUSP00000101093.1, OTTMUSP00000023799, ENSMUST00000105453.7, OTTMUST00000050791
    Conserved Domains (1) summary
    pfam01391
    Location:571628
    Collagen; Collagen triple helix repeat (20 copies)
  2. NM_007731.3NP_031757.1  collagen alpha-1(XIII) chain isoform 1

    See identical proteins and their annotated locations for NP_031757.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC122315, AC164702
    Consensus CDS
    CCDS35918.1
    UniProtKB/Swiss-Prot
    Q9R1N9
    Related
    ENSMUSP00000101094.2, OTTMUSP00000023796, ENSMUST00000105454.2, OTTMUST00000050788
    Conserved Domains (1) summary
    pfam01391
    Location:534592
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000076.6 Reference GRCm38.p4 C57BL/6J

    Range
    61838234..61979210 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011243333.1XP_011241635.1  collagen alpha-1(XIII) chain isoform X12

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
  2. XM_011243332.2XP_011241634.1  collagen alpha-1(XIII) chain isoform X11

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
  3. XM_006513171.3XP_006513234.1  collagen alpha-1(XIII) chain isoform X20

    Conserved Domains (1) summary
    pfam01391
    Location:574631
    Collagen; Collagen triple helix repeat (20 copies)
  4. XM_006513170.2XP_006513233.1  collagen alpha-1(XIII) chain isoform X19

    Related
    ENSMUSP00000101092.2, OTTMUSP00000023800, ENSMUST00000105452.8, OTTMUST00000050792
    Conserved Domains (1) summary
    pfam01391
    Location:613672
    Collagen; Collagen triple helix repeat (20 copies)
  5. XM_011243342.1XP_011241644.1  collagen alpha-1(XIII) chain isoform X18

    Conserved Domains (1) summary
    pfam01391
    Location:625684
    Collagen; Collagen triple helix repeat (20 copies)
  6. XM_011243339.1XP_011241641.1  collagen alpha-1(XIII) chain isoform X16

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
  7. XM_011243325.2XP_011241627.1  collagen alpha-1(XIII) chain isoform X4

    Conserved Domains (1) summary
    pfam01391
    Location:506564
    Collagen; Collagen triple helix repeat (20 copies)
  8. XM_011243341.1XP_011241643.1  collagen alpha-1(XIII) chain isoform X17

    Conserved Domains (1) summary
    pfam01391
    Location:468526
    Collagen; Collagen triple helix repeat (20 copies)
  9. XM_011243337.1XP_011241639.1  collagen alpha-1(XIII) chain isoform X15

    Conserved Domains (1) summary
    pfam01391
    Location:477535
    Collagen; Collagen triple helix repeat (20 copies)
  10. XM_011243328.1XP_011241630.1  collagen alpha-1(XIII) chain isoform X7

    Conserved Domains (1) summary
    pfam01391
    Location:494552
    Collagen; Collagen triple helix repeat (20 copies)
  11. XM_011243336.1XP_011241638.1  collagen alpha-1(XIII) chain isoform X14

    Conserved Domains (1) summary
    pfam01391
    Location:480538
    Collagen; Collagen triple helix repeat (20 copies)
  12. XM_011243331.1XP_011241633.1  collagen alpha-1(XIII) chain isoform X10

    Conserved Domains (1) summary
    pfam01391
    Location:489547
    Collagen; Collagen triple helix repeat (20 copies)
  13. XM_011243324.1XP_011241626.1  collagen alpha-1(XIII) chain isoform X3

    Conserved Domains (1) summary
    pfam01391
    Location:506564
    Collagen; Collagen triple helix repeat (20 copies)
  14. XM_011243326.2XP_011241628.1  collagen alpha-1(XIII) chain isoform X5

    Conserved Domains (1) summary
    pfam01391
    Location:503561
    Collagen; Collagen triple helix repeat (20 copies)
  15. XM_011243329.1XP_011241631.1  collagen alpha-1(XIII) chain isoform X8

    Conserved Domains (1) summary
    pfam01391
    Location:493551
    Collagen; Collagen triple helix repeat (20 copies)
  16. XM_011243335.1XP_011241637.1  collagen alpha-1(XIII) chain isoform X13

    Conserved Domains (1) summary
    pfam01391
    Location:625676
    Collagen; Collagen triple helix repeat (20 copies)
  17. XM_011243327.1XP_011241629.1  collagen alpha-1(XIII) chain isoform X6

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
  18. XM_011243322.1XP_011241624.1  collagen alpha-1(XIII) chain isoform X1

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
  19. XM_011243323.1XP_011241625.1  collagen alpha-1(XIII) chain isoform X2

    Conserved Domains (1) summary
    pfam01391
    Location:512570
    Collagen; Collagen triple helix repeat (20 copies)
  20. XM_011243343.1XP_011241645.1  collagen alpha-1(XIII) chain isoform X21

    Conserved Domains (1) summary
    pfam01391
    Location:403461
    Collagen; Collagen triple helix repeat (20 copies)
  21. XM_011243344.1XP_011241646.1  collagen alpha-1(XIII) chain isoform X22

    Conserved Domains (1) summary
    pfam01391
    Location:394452
    Collagen; Collagen triple helix repeat (20 copies)
  22. XM_011243330.1XP_011241632.1  collagen alpha-1(XIII) chain isoform X9

    Conserved Domains (1) summary
    pfam01391
    Location:515573
    Collagen; Collagen triple helix repeat (20 copies)
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