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Q9R1N9

- CODA1_MOUSE

UniProt

Q9R1N9 - CODA1_MOUSE

Protein

Collagen alpha-1(XIII) chain

Gene

Col13a1

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 1 (01 May 2000)
      Previous versions | rss
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    Functioni

    Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching morphogenesis of lung. Binds heparin.By similarity3 Publications

    GO - Molecular functioni

    1. heparin binding Source: UniProtKB-KW

    GO - Biological processi

    1. cell differentiation Source: UniProtKB-KW
    2. cell-matrix adhesion Source: UniProtKB
    3. endochondral ossification Source: UniProtKB
    4. morphogenesis of a branching structure Source: UniProtKB
    5. single organismal cell-cell adhesion Source: UniProtKB

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Cell adhesion, Differentiation, Osteogenesis

    Keywords - Ligandi

    Heparin-binding

    Enzyme and pathway databases

    ReactomeiREACT_198984. Collagen biosynthesis and modifying enzymes.
    REACT_199055. Collagen degradation.
    REACT_216309. Integrin cell surface interactions.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Collagen alpha-1(XIII) chain
    Gene namesi
    Name:Col13a1Imported
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 10

    Organism-specific databases

    MGIiMGI:1277201. Col13a1.

    Subcellular locationi

    Cell membrane 1 Publication; Single-pass type II membrane protein 1 Publication

    GO - Cellular componenti

    1. cell-cell junction Source: MGI
    2. collagen trimer Source: UniProtKB-KW
    3. integral component of membrane Source: UniProtKB-KW
    4. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 751751Collagen alpha-1(XIII) chainPRO_0000284680Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi451 – 4511N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    PRIDEiQ9R1N9.

    PTM databases

    PhosphoSiteiQ9R1N9.

    Expressioni

    Developmental stagei

    Expression levels remain fairly constant during early fetal development. This is followed by a marked increase of expression levels during the final stages of organogenesis, with initiation of the rapid fetal growth phase before birth. At mid-gestation, strongly expressed in the central and peripheral nervous systems. Also strongly expressed in developing heart, with localization to cell-cell contacts and accentuated in intercalated disks perinatally. During late fetal development, expressed in many tissues including cartilage, bone, skeletal muscle, lung, intestine and skin. Not detected in endothelia of most blood vessels or the endocardium of the heart.1 Publication

    Gene expression databases

    ArrayExpressiQ9R1N9.
    BgeeiQ9R1N9.
    CleanExiMM_COL13A1.
    GenevestigatoriQ9R1N9.

    Interactioni

    Subunit structurei

    Homotrimer; disulfide-linked. Nucleation of the type XIII collagen triple helix is likely to occur at the N-terminal region with triple helix formation proceeding from the N- to the C-terminus. Interacts with FN1, perlecan/HSPG2 and NID2 By similarity.By similarity

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000090141.

    Structurei

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 4040CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini60 – 751692ExtracellularSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei41 – 5919Helical; Signal-anchor for type II membrane proteinSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni1 – 119119Nonhelical region 1 (NC1)Sequence AnalysisAdd
    BLAST
    Regioni120 – 223104Triple-helical region 1 (COL1)Sequence AnalysisAdd
    BLAST
    Regioni224 – 27350Nonhelical region 2 (NC2)Sequence AnalysisAdd
    BLAST
    Regioni274 – 445172Triple-helical region 2 (COL2)Sequence AnalysisAdd
    BLAST
    Regioni446 – 46722Nonhelical region 3 (NC3)Sequence AnalysisAdd
    BLAST
    Regioni468 – 733266Triple-helical region 3 (COL3)Sequence AnalysisAdd
    BLAST
    Regioni734 – 75118Nonhelical region 4 (NC4)Sequence AnalysisAdd
    BLAST

    Keywords - Domaini

    Collagen, Signal-anchor, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG254293.
    GeneTreeiENSGT00750000117303.
    HOGENOMiHOG000085653.
    HOVERGENiHBG004933.
    InParanoidiQ9R1N9.
    KOiK16617.
    OMAiERQMETA.
    PhylomeDBiQ9R1N9.
    TreeFamiTF338175.

    Family and domain databases

    InterProiIPR008160. Collagen.
    [Graphical view]
    PfamiPF01391. Collagen. 7 hits.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Note: Additional isoforms may exist.Curated

    Isoform 11 Publication (identifier: Q9R1N9-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MVAERTRKAA ASGSRGPGEL GAPGPGTVAL AEQCARLPSP GCCGLLALAL    50
    CSLALSLLAH FRTAELQARV LRLEAERGEQ QMEKAILGRV NQLLDEKWKF 100
    YSRRRREAPK MSPGCNCPPG PPGPTGRPGL PGDKGAIGMP GRVGIKGQPG 150
    EKGAPGDAGM SIVGPRGPPG QPGTRGFPGF PGPIGLDGRP GHPGPKGEMG 200
    LVGPRGQPGP QGQKGEKGQC GEYPHREYPG GMLAALRSNP IMSLKLLPLL 250
    NSVRLAPPPV IKRRTFQGEQ SQTGIQGPPG PPGPPGPSGP LGHPGLPGPI 300
    GPPGLPGPPG PKGDPGIQGY HGRKGERGMP GMPGKHGAKG VPGIAVAGMK 350
    GEPGTPGTKG EKGAAGSPGL LGQKGEKGDA GNAIGGGRGE PGPPGLPGPP 400
    GPKGEAGVDG QAGPPGQQGD KGQPGAAGEQ GPSGPKGAKG EPGKGEMVDY 450
    NGSINEALQE IRTLALMGPP GLPGQTGPPG PPGTPGQRGE IGLPGPPGHD 500
    GDKGPRGKPG DMGPAGPQGP PGKDGPPGMK GEVGPPGSPG EKGETGQAGP 550
    QGLDGPTGEK GEPGDEGRPG ATGLPGPIGL PGFTGEKGEA GEKGDPGAEV 600
    PGPPGPEGPP GPPGLQGFPG PKGEAGLEGS KGEKGSQGEK GDRGPLGLPG 650
    ASGLDGRPGP PGTPGPIGVP GPAGPKGERG SKGDPGMTGP TGAAGLPGLH 700
    GPPGDKGNRG ERGKKGSRGP KGDKGDQGAP GLDAPCPLGE DGLPVQGCWN 750
    K 751
    Length:751
    Mass (Da):73,172
    Last modified:May 1, 2000 - v1
    Checksum:iFBE2443E1CBF51AD
    GO
    Isoform 21 Publication (identifier: Q9R1N9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         651-662: Missing.

    Show »
    Length:739
    Mass (Da):72,110
    Checksum:iF13951061381F017
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei651 – 66212Missing in isoform 2. 1 PublicationVSP_052388Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U30292 mRNA. Translation: AAC24314.1.
    AF063693
    , AF063666, AF063667, AF063668, AF063669, AF063670, AF063671, AF063672, AF063673, AF063674, AF063675, AF063676, AF063677, AF063678, AF063679, AF063680, AF063681, AF063682, AF063683, AF063684, AF063685, AF063686, AF063687, AF063688, AF063689, AF063690, AF063691, AF063692 Genomic DNA. Translation: AAD50327.1.
    CCDSiCCDS35918.1. [Q9R1N9-2]
    RefSeqiNP_031757.1. NM_007731.2. [Q9R1N9-2]
    UniGeneiMm.300931.

    Genome annotation databases

    EnsembliENSMUST00000105454; ENSMUSP00000101094; ENSMUSG00000058806. [Q9R1N9-2]
    GeneIDi12817.
    KEGGimmu:12817.
    UCSCiuc007fgn.1. mouse. [Q9R1N9-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U30292 mRNA. Translation: AAC24314.1 .
    AF063693
    , AF063666 , AF063667 , AF063668 , AF063669 , AF063670 , AF063671 , AF063672 , AF063673 , AF063674 , AF063675 , AF063676 , AF063677 , AF063678 , AF063679 , AF063680 , AF063681 , AF063682 , AF063683 , AF063684 , AF063685 , AF063686 , AF063687 , AF063688 , AF063689 , AF063690 , AF063691 , AF063692 Genomic DNA. Translation: AAD50327.1 .
    CCDSi CCDS35918.1. [Q9R1N9-2 ]
    RefSeqi NP_031757.1. NM_007731.2. [Q9R1N9-2 ]
    UniGenei Mm.300931.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000090141.

    PTM databases

    PhosphoSitei Q9R1N9.

    Proteomic databases

    PRIDEi Q9R1N9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000105454 ; ENSMUSP00000101094 ; ENSMUSG00000058806 . [Q9R1N9-2 ]
    GeneIDi 12817.
    KEGGi mmu:12817.
    UCSCi uc007fgn.1. mouse. [Q9R1N9-2 ]

    Organism-specific databases

    CTDi 1305.
    MGIi MGI:1277201. Col13a1.

    Phylogenomic databases

    eggNOGi NOG254293.
    GeneTreei ENSGT00750000117303.
    HOGENOMi HOG000085653.
    HOVERGENi HBG004933.
    InParanoidi Q9R1N9.
    KOi K16617.
    OMAi ERQMETA.
    PhylomeDBi Q9R1N9.
    TreeFami TF338175.

    Enzyme and pathway databases

    Reactomei REACT_198984. Collagen biosynthesis and modifying enzymes.
    REACT_199055. Collagen degradation.
    REACT_216309. Integrin cell surface interactions.

    Miscellaneous databases

    NextBioi 282282.
    PROi Q9R1N9.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9R1N9.
    Bgeei Q9R1N9.
    CleanExi MM_COL13A1.
    Genevestigatori Q9R1N9.

    Family and domain databases

    InterProi IPR008160. Collagen.
    [Graphical view ]
    Pfami PF01391. Collagen. 7 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Type XIII collagen is identified as a plasma membrane protein."
      Hagg P., Rehn M., Huhtala P., Vaisanen T., Tamminen M., Pihlajaniemi T.
      J. Biol. Chem. 273:15590-15597(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), SUBCELLULAR LOCATION.
      Tissue: Intestine.
    2. "Complete exon-intron organization and chromosomal location of the gene for mouse type XIII collagen (col13a1) and comparison with its human homologue."
      Kvist A.-P., Latvanlehto A., Sund M., Horelli-Kuitunen N., Rehn M., Palotie A., Beier D., Pihlajaniemi T.
      Matrix Biol. 18:261-274(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING (ISOFORM 1).
    3. "Lack of cytosolic and transmembrane domains of type XIII collagen results in progressive myopathy."
      Kvist A.-P., Latvanlehto A., Sund M., Eklund L., Vaisanen T., Hagg P., Sormunen R., Komulainen J., Fassler R., Pihlajaniemi T.
      Am. J. Pathol. 159:1581-1592(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TRANSGENIC MICE.
    4. "Abnormal adherence junctions in the heart and reduced angiogenesis in transgenic mice overexpressing mutant type XIII collagen."
      Sund M., Ylonen R., Tuomisto A., Sormunen R., Tahkola J., Kvist A.-P., Kontusaari S., Autio-Harmainen H., Pihlajaniemi T.
      EMBO J. 20:5153-5164(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TRANSGENIC MICE.
    5. "Distinct expression of type XIII collagen in neuronal structures and other tissues during mouse development."
      Sund M., Vaisanen T., Kaukinen S., Ilves M., Tu H., Autio-Harmainen H., Rauvala H., Pihlajaniemi T.
      Matrix Biol. 20:215-231(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: DEVELOPMENTAL STAGE.
    6. "Type XIII collagen strongly affects bone formation in transgenic mice."
      Ylonen R., Kyronlahti T., Sund M., Ilves M., Lehenkari P., Tuukkanen J., Pihlajaniemi T.
      J. Bone Miner. Res. 20:1381-1393(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiCODA1_MOUSE
    AccessioniPrimary (citable) accession number: Q9R1N9
    Secondary accession number(s): O70575
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 17, 2007
    Last sequence update: May 1, 2000
    Last modified: October 1, 2014
    This is version 90 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Transgenic mice overexpressing COL13A1 with a 90 amino acid in-frame deletion of the COL2 sequence show embryonic lethality due either to a lack of placental formation or to cardiovascular defects in offspring from heterozygous mating. In contrast, transgenic mice expressing an N-terminally altered COL13A1 lacking both cytosolic and transmembrane domains while retaining the collagenous ectodomain are viable and fertile, but display progressive muscular myopathy.2 Publications

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

    External Data

    Dasty 3