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    COL13A1 collagen type XIII alpha 1 chain [ Homo sapiens (human) ]

    Gene ID: 1305, updated on 15-Aug-2017
    Official Symbol
    COL13A1provided by HGNC
    Official Full Name
    collagen type XIII alpha 1 chainprovided by HGNC
    Primary source
    HGNC:HGNC:2190
    See related
    Ensembl:ENSG00000197467 MIM:120350; Vega:OTTHUMG00000018394
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CMS19; COLXIIIA1
    Summary
    This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    10q22.1
    Exon count:
    43
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (69801885..69959148)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (71561644..71718904)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378346 Neighboring gene uncharacterized LOC105378347 Neighboring gene ribosomal protein L5 pseudogene 26 Neighboring gene uncharacterized LOC107984242 Neighboring gene uncharacterized LOC102723350 Neighboring gene H2A histone family member Y2 Neighboring gene apoptosis inducing factor, mitochondria associated 2

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Myasthenic syndrome, congenital, 19
    MedGen: C4225235 OMIM: 616720 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.
    NHGRI GWA Catalog
    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    NHGRI GWA Catalog
    Parkinson disease loci in the mid-western Amish.
    NHGRI GWA Catalog
    • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
      Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
    • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
      Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
    • Collagen degradation, organism-specific biosystem (from REACTOME)
      Collagen degradation, organism-specific biosystemCollagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknow...
    • Collagen formation, organism-specific biosystem (from REACTOME)
      Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
    • Degradation of the extracellular matrix, organism-specific biosystem (from REACTOME)
      Degradation of the extracellular matrix, organism-specific biosystemMatrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the...
    • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
      Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
    • Integrin cell surface interactions, organism-specific biosystem (from REACTOME)
      Integrin cell surface interactions, organism-specific biosystemThe extracellular matrix (ECM) is a network of macro-molecules that underlies all epithelia and endothelia and that surrounds all connective tissue cells. This matrix provides the mechanical strength...
    • Protein digestion and absorption, organism-specific biosystem (from KEGG)
      Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    • Protein digestion and absorption, conserved biosystem (from KEGG)
      Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ42485

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    heparin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    cell-matrix adhesion IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    collagen catabolic process TAS
    Traceable Author Statement
    more info
     
    endochondral ossification ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    extracellular matrix organization TAS
    Traceable Author Statement
    more info
     
    morphogenesis of a branching structure ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cell-cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    collagen type XIII trimer TAS
    Traceable Author Statement
    more info
    PubMed 
    endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    postsynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    collagen alpha-1(XIII) chain
    Names
    collagen, type XIII, alpha 1

    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.

    Genomic

    1. NG_046344.1 RefSeqGene

      Range
      5001..162261
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130103.1NP_001123575.1  collagen alpha-1(XIII) chain isoform 1

      See identical proteins and their annotated locations for NP_001123575.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC025426, AI741175, AJ293624, AL138925, BY796799, CN297094
      Consensus CDS
      CCDS44419.1
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000381949.3, OTTHUMP00000019731, ENST00000398978.7, OTTHUMT00000048468
      Conserved Domains (1) summary
      pfam01391
      Location:643702
      Collagen; Collagen triple helix repeat (20 copies)
    2. NM_001320951.1NP_001307880.1  collagen alpha-1(XIII) chain isoform 22

      Status: REVIEWED

      Source sequence(s)
      AC024601, AC025426, AI741175, AL138925, BY796799, HY104799
      Conserved Domains (1) summary
      pfam01391
      Location:588645
      Collagen; Collagen triple helix repeat (20 copies)
    3. NM_080798.3NP_542988.3  collagen alpha-1(XIII) chain isoform 21

      See identical proteins and their annotated locations for NP_542988.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (21) does not contain exons 3B, 4, 5, 12, and 29, based on the exon numbering used in PMID: 1894651. Isoform 21 lacks three internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44427.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000428057.1, OTTHUMP00000227634, ENST00000520267.5, OTTHUMT00000380458
      Conserved Domains (1) summary
      pfam01391
      Location:571630
      Collagen; Collagen triple helix repeat (20 copies)
    4. NM_080800.3NP_542990.3  collagen alpha-1(XIII) chain isoform 11

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) does not contain exon 12 and 33, based on the exon numbering used in PMID: 1894651. Isoform 11 lacks two internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44425.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000428342.1, OTTHUMP00000227636, ENST00000522165.5, OTTHUMT00000380460
      Conserved Domains (1) summary
      pfam01391
      Location:594651
      Collagen; Collagen triple helix repeat (20 copies)
    5. NM_080801.3NP_542991.3  collagen alpha-1(XIII) chain isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) does not contain exon 13, based on the exon numbering used in PMID: 1894651. Isoform 5 lacks an internal 22 aa compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44424.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000346553.3, OTTHUMP00000019732, ENST00000354547.7, OTTHUMT00000048469
      Conserved Domains (1) summary
      pfam01391
      Location:621680
      Collagen; Collagen triple helix repeat (20 copies)
    6. NM_080802.3NP_542992.3  collagen alpha-1(XIII) chain isoform 15

      Status: REVIEWED

      Description
      Transcript Variant: This variant (15) does not contain exons 13, 29, and 33, based on the exon numbering used in PMID: 1894651. Isoform 15 lacks three internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44423.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000430061.1, OTTHUMP00000227635, ENST00000517713.5, OTTHUMT00000380459
      Conserved Domains (1) summary
      pfam01391
      Location:576633
      Collagen; Collagen triple helix repeat (20 copies)
    7. NM_080805.3NP_542995.3  collagen alpha-1(XIII) chain isoform 19

      Status: REVIEWED

      Description
      Transcript Variant: This variant (19) does not contain exons 4, 5, 13, 29, 33, and 37, based on the exon numbering used in PMID: 1894651. Isoform 19 lacks five internal segments, compared to isoform 1.
      Source sequence(s)
      AC024601, AC025426, AL138925
      Consensus CDS
      CCDS44428.2
      UniProtKB/Swiss-Prot
      Q5TAT6
      Related
      ENSP00000430173.1, OTTHUMP00000227637, ENST00000520133.5, OTTHUMT00000380461
      Conserved Domains (1) summary
      pfam01391
      Location:547603
      Collagen; Collagen triple helix repeat (20 copies)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

      Range
      69801885..69959148
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011539292.2XP_011537594.1  collagen alpha-1(XIII) chain isoform X1

      Conserved Domains (1) summary
      pfam01391
      Location:654713
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_017015676.1XP_016871165.1  collagen alpha-1(XIII) chain isoform X2

    3. XM_017015677.1XP_016871166.1  collagen alpha-1(XIII) chain isoform X4

    4. XM_011539293.2XP_011537595.1  collagen alpha-1(XIII) chain isoform X3

      Conserved Domains (1) summary
      pfam01391
      Location:639698
      Collagen; Collagen triple helix repeat (20 copies)
    5. XM_017015679.1XP_016871168.1  collagen alpha-1(XIII) chain isoform X8

    6. XM_017015687.1XP_016871176.1  collagen alpha-1(XIII) chain isoform X16

    7. XM_017015680.1XP_016871169.1  collagen alpha-1(XIII) chain isoform X9

    8. XM_017015682.1XP_016871171.1  collagen alpha-1(XIII) chain isoform X11

    9. XM_011539294.2XP_011537596.1  collagen alpha-1(XIII) chain isoform X5

      Conserved Domains (1) summary
      pfam01391
      Location:633692
      Collagen; Collagen triple helix repeat (20 copies)
    10. XM_017015681.1XP_016871170.1  collagen alpha-1(XIII) chain isoform X10

    11. XM_017015689.1XP_016871178.1  collagen alpha-1(XIII) chain isoform X18

    12. XM_017015691.1XP_016871180.1  collagen alpha-1(XIII) chain isoform X20

    13. XM_017015685.1XP_016871174.1  collagen alpha-1(XIII) chain isoform X14

    14. XM_017015686.1XP_016871175.1  collagen alpha-1(XIII) chain isoform X15

    15. XM_017015693.1XP_016871182.1  collagen alpha-1(XIII) chain isoform X22

    16. XM_017015688.1XP_016871177.1  collagen alpha-1(XIII) chain isoform X17

    17. XM_017015684.1XP_016871173.1  collagen alpha-1(XIII) chain isoform X13

    18. XM_017015678.1XP_016871167.1  collagen alpha-1(XIII) chain isoform X7

    19. XM_017015683.1XP_016871172.1  collagen alpha-1(XIII) chain isoform X12

    20. XM_017015692.1XP_016871181.1  collagen alpha-1(XIII) chain isoform X21

    21. XM_017015690.1XP_016871179.1  collagen alpha-1(XIII) chain isoform X19

    22. XM_017015694.1XP_016871183.1  collagen alpha-1(XIII) chain isoform X23

    23. XM_017015695.1XP_016871184.1  collagen alpha-1(XIII) chain isoform X24

    24. XM_011539295.2XP_011537597.1  collagen alpha-1(XIII) chain isoform X6

      Conserved Domains (1) summary
      pfam01391
      Location:609666
      Collagen; Collagen triple helix repeat (20 copies)
    25. XM_017015697.1XP_016871186.1  collagen alpha-1(XIII) chain isoform X26

    26. XM_017015696.1XP_016871185.1  collagen alpha-1(XIII) chain isoform X25

      Conserved Domains (1) summary
      pfam01391
      Location:433492
      Collagen; Collagen triple helix repeat (20 copies)

    RNA

    1. XR_001747024.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      71843392..72000665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_005203.3: Suppressed sequence

      Description
      NM_005203.3: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.
    2. NM_080799.2: Suppressed sequence

      Description
      NM_080799.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.
    3. NM_080803.2: Suppressed sequence

      Description
      NM_080803.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.
    4. NM_080804.2: Suppressed sequence

      Description
      NM_080804.2: This RefSeq was permanently suppressed because currently there is not sufficient full-length data to support this transcript.
    5. NM_080806.2: Suppressed sequence

      Description
      NM_080806.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    6. NM_080807.2: Suppressed sequence

      Description
      NM_080807.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    7. NM_080808.2: Suppressed sequence

      Description
      NM_080808.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    8. NM_080809.2: Suppressed sequence

      Description
      NM_080809.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    9. NM_080810.2: Suppressed sequence

      Description
      NM_080810.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    10. NM_080811.2: Suppressed sequence

      Description
      NM_080811.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    11. NM_080812.2: Suppressed sequence

      Description
      NM_080812.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    12. NM_080813.2: Suppressed sequence

      Description
      NM_080813.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    13. NM_080814.2: Suppressed sequence

      Description
      NM_080814.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
    14. NM_080815.2: Suppressed sequence

      Description
      NM_080815.2: This RefSeq was temporarily suppressed because currently there is not sufficient full-length data to support this transcript.
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