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

Gene ID: 1305, updated on 22-Nov-2014
Official Symbol
COL13A1provided by HGNC
Official Full Name
collagen, type XIII, alpha 1provided by HGNC
Primary source
HGNC:HGNC:2190
See related
Ensembl:ENSG00000197467; HPRD:00383; 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
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]
See COL13A1 in Epigenomics, MapViewer
Location:
10q22
Exon count:
41
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 10 NC_000010.11 (69801883..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 chromosome 10 open reading frame 35 Neighboring gene ribosomal protein L5 pseudogene 26 Neighboring gene uncharacterized LOC102723350 Neighboring gene H2A histone family, member Y2 Neighboring gene apoptosis-inducing factor, mitochondrion-associated, 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
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 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 disassembly TAS
Traceable Author Statement
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
 
single organismal cell-cell adhesion IEP
Inferred from Expression Pattern
more info
PubMed 
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
 
Preferred Names
collagen alpha-1(XIII) chain
Names
collagen alpha-1(XIII) chain
COL13A1

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_001130103.1NP_001123575.1  collagen alpha-1(XIII) chain isoform 1

    See proteins identical to 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, OTTHUMP00000019731, ENST00000398978, OTTHUMT00000048468
    Conserved Domains (1) summary
    pfam01391
    Location:643702
    Collagen; Collagen triple helix repeat (20 copies)
  2. NM_080798.3NP_542988.3  collagen alpha-1(XIII) chain isoform 21

    See proteins identical to 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
    Conserved Domains (1) summary
    pfam01391
    Location:571630
    Collagen; Collagen triple helix repeat (20 copies)
  3. 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
    Conserved Domains (1) summary
    pfam01391
    Location:594651
    Collagen; Collagen triple helix repeat (20 copies)
  4. 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, OTTHUMP00000019732, ENST00000354547, OTTHUMT00000048469
    Conserved Domains (1) summary
    pfam01391
    Location:621680
    Collagen; Collagen triple helix repeat (20 copies)
  5. 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
    Conserved Domains (1) summary
    pfam01391
    Location:576633
    Collagen; Collagen triple helix repeat (20 copies)
  6. 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
    Conserved Domains (1) summary
    pfam01391
    Location:547603
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Alternate HuRef

Genomic

  1. AC_000142.1 

    Range
    65553122..65710673
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000010.11 

    Range
    69801883..69959148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006717632.1XP_006717695.1  

    Conserved Domains (1) summary
    pfam01391
    Location:585642
    Collagen; Collagen triple helix repeat (20 copies)

Alternate CHM1_1.1

Genomic

  1. NC_018921.2 

    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.