Q9R1N9 (CODA1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Collagen alpha-1(XIII) chain

Gene names

Name:

Col13a1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	751 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	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. Ref.3 Ref.4 Ref.6 UniProtKB Q5TAT6
Subunit structure	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. UniProtKB Q5TAT6
Subcellular location	Cell membrane; Single-pass type II membrane protein Ref.1.
Developmental stage	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. Ref.5
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. Ref.3 Ref.4

Ontologies

Keywords
Biological process	Cell adhesion Differentiation Osteogenesis
Cellular component	Cell membrane Membrane
Coding sequence diversity	Alternative splicing
Domain	Collagen Signal-anchor Transmembrane Transmembrane helix
Ligand	Heparin-binding
Molecular function	Developmental protein
PTM	Disulfide bond Glycoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW cell-cell adhesion Inferred from sequence or structural similarity. Source: UniProtKB cell-matrix adhesion Inferred from sequence or structural similarity. Source: UniProtKB endochondral ossification Inferred from expression pattern Ref.5. Source: UniProtKB morphogenesis of a branching structure Inferred from expression pattern Ref.5. Source: UniProtKB
Cellular_component	cell-cell junction Inferred from direct assay Ref.5. Source: MGI collagen Inferred from electronic annotation. Source: UniProtKB-KW integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	heparin binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms may exist.

Isoform 1 Ref.2 (identifier: Q9R1N9-1)

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.

Isoform 2 Ref.1 (identifier: Q9R1N9-2)

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

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 751	751	Collagen alpha-1(XIII) chain		PRO_0000284680
Regions
	Topological domain	1 – 40	40	Cytoplasmic Potential
	Transmembrane	41 – 59	19	Helical; Signal-anchor for type II membrane protein; Potential
	Topological domain	60 – 751	692	Extracellular Potential
	Region	1 – 119	119	Nonhelical region 1 (NC1)
	Region	120 – 223	104	Triple-helical region 1 (COL1)
	Region	224 – 273	50	Nonhelical region 2 (NC2)
	Region	274 – 445	172	Triple-helical region 2 (COL2)
	Region	446 – 467	22	Nonhelical region 3 (NC3)
	Region	468 – 733	266	Triple-helical region 3 (COL3)
	Region	734 – 751	18	Nonhelical region 4 (NC4)
Amino acid modifications
	Glycosylation	451	1	N-linked (GlcNAc...) Potential
Natural variations
	Alternative sequence	651 – 662	12	Missing in isoform 2. Ref.1		VSP_052388

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: FBE2443E1CBF51AD	FASTA	751	73,172
	10 20 30 40 50 60 MVAERTRKAA ASGSRGPGEL GAPGPGTVAL AEQCARLPSP GCCGLLALAL CSLALSLLAH 70 80 90 100 110 120 FRTAELQARV LRLEAERGEQ QMEKAILGRV NQLLDEKWKF YSRRRREAPK MSPGCNCPPG 130 140 150 160 170 180 PPGPTGRPGL PGDKGAIGMP GRVGIKGQPG EKGAPGDAGM SIVGPRGPPG QPGTRGFPGF 190 200 210 220 230 240 PGPIGLDGRP GHPGPKGEMG LVGPRGQPGP QGQKGEKGQC GEYPHREYPG GMLAALRSNP 250 260 270 280 290 300 IMSLKLLPLL NSVRLAPPPV IKRRTFQGEQ SQTGIQGPPG PPGPPGPSGP LGHPGLPGPI 310 320 330 340 350 360 GPPGLPGPPG PKGDPGIQGY HGRKGERGMP GMPGKHGAKG VPGIAVAGMK GEPGTPGTKG 370 380 390 400 410 420 EKGAAGSPGL LGQKGEKGDA GNAIGGGRGE PGPPGLPGPP GPKGEAGVDG QAGPPGQQGD 430 440 450 460 470 480 KGQPGAAGEQ GPSGPKGAKG EPGKGEMVDY NGSINEALQE IRTLALMGPP GLPGQTGPPG 490 500 510 520 530 540 PPGTPGQRGE IGLPGPPGHD GDKGPRGKPG DMGPAGPQGP PGKDGPPGMK GEVGPPGSPG 550 560 570 580 590 600 EKGETGQAGP QGLDGPTGEK GEPGDEGRPG ATGLPGPIGL PGFTGEKGEA GEKGDPGAEV 610 620 630 640 650 660 PGPPGPEGPP GPPGLQGFPG PKGEAGLEGS KGEKGSQGEK GDRGPLGLPG ASGLDGRPGP 670 680 690 700 710 720 PGTPGPIGVP GPAGPKGERG SKGDPGMTGP TGAAGLPGLH GPPGDKGNRG ERGKKGSRGP 730 740 750 KGDKGDQGAP GLDAPCPLGE DGLPVQGCWN K
	Isoform 2 [UniParc]. Checksum: F13951061381F017	FASTA	739	72,110
	10 20 30 40 50 60 MVAERTRKAA ASGSRGPGEL GAPGPGTVAL AEQCARLPSP GCCGLLALAL CSLALSLLAH 70 80 90 100 110 120 FRTAELQARV LRLEAERGEQ QMEKAILGRV NQLLDEKWKF YSRRRREAPK MSPGCNCPPG 130 140 150 160 170 180 PPGPTGRPGL PGDKGAIGMP GRVGIKGQPG EKGAPGDAGM SIVGPRGPPG QPGTRGFPGF 190 200 210 220 230 240 PGPIGLDGRP GHPGPKGEMG LVGPRGQPGP QGQKGEKGQC GEYPHREYPG GMLAALRSNP 250 260 270 280 290 300 IMSLKLLPLL NSVRLAPPPV IKRRTFQGEQ SQTGIQGPPG PPGPPGPSGP LGHPGLPGPI 310 320 330 340 350 360 GPPGLPGPPG PKGDPGIQGY HGRKGERGMP GMPGKHGAKG VPGIAVAGMK GEPGTPGTKG 370 380 390 400 410 420 EKGAAGSPGL LGQKGEKGDA GNAIGGGRGE PGPPGLPGPP GPKGEAGVDG QAGPPGQQGD 430 440 450 460 470 480 KGQPGAAGEQ GPSGPKGAKG EPGKGEMVDY NGSINEALQE IRTLALMGPP GLPGQTGPPG 490 500 510 520 530 540 PPGTPGQRGE IGLPGPPGHD GDKGPRGKPG DMGPAGPQGP PGKDGPPGMK GEVGPPGSPG 550 560 570 580 590 600 EKGETGQAGP QGLDGPTGEK GEPGDEGRPG ATGLPGPIGL PGFTGEKGEA GEKGDPGAEV 610 620 630 640 650 660 PGPPGPEGPP GPPGLQGFPG PKGEAGLEGS KGEKGSQGEK GDRGPLGLPG TPGPIGVPGP 670 680 690 700 710 720 AGPKGERGSK GDPGMTGPTG AAGLPGLHGP PGDKGNRGER GKKGSRGPKG DKGDQGAPGL 730 DAPCPLGEDG LPVQGCWNK

References

[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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00620475. IPI00844674.
RefSeq	NP_031757.1. NM_007731.2.
UniGene	Mm.300931.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	10090.ENSMUSP00000090141.
PTM databases
PhosphoSite	Q9R1N9.
Proteomic databases
PRIDE	Q9R1N9.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000105454; ENSMUSP00000101094; ENSMUSG00000058806.
GeneID	12817.
KEGG	mmu:12817.
UCSC	uc007fgn.1. mouse.
Organism-specific databases
CTD	1305.
MGI	MGI:1277201. Col13a1.
Phylogenomic databases
eggNOG	NOG254293.
GeneTree	ENSGT00530000063274.
HOGENOM	HOG000085653.
HOVERGEN	HBG004933.
InParanoid	Q9R1N9.
KO	K16617.
OMA	YPHREYP.
OrthoDB	EOG4894NC.
Gene expression databases
ArrayExpress	Q9R1N9.
Bgee	Q9R1N9.
CleanEx	MM_COL13A1.
Genevestigator	Q9R1N9.
Family and domain databases
InterPro	IPR008160. Collagen. [Graphical view]
Pfam	PF01391. Collagen. 7 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	282282.
SOURCE	Search...

Entry information

Entry name

CODA1_MOUSE

Accession

Primary (citable) accession number: Q9R1N9
Secondary accession number(s): O70575

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 17, 2007
Last sequence update:	May 1, 2000
Last modified:	April 3, 2013
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program