Collagen alpha-1(IX) chain precursor

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Sequences

References

Cross-references

Entry information

Relevant documents

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Sequences

References

Cross-references

Entry information

Relevant documents

Molecule processing

Regions

Sites

Amino acid modifications

Natural variations

Experimental info

Preferred order of sections

Molecule processing

Regions

Sites

Amino acid modifications

Natural variations

Experimental info

Sequence databases

3D structure databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

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Q05722 (CO9A1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 117. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Protein names

Recommended name:
Collagen alpha-1(IX) chain

Gene names

Name:

Col9a1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Sequence length	921 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

Function	Structural component of hyaline cartilage and vitreous of the eye.
Subunit structure	Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.
Subcellular location	Secreted › extracellular space › extracellular matrix By similarity.
Domain	Each subunit is composed of three triple-helical domains interspersed with non-collagenous domains. The globular domain at the N-terminus of type IX collagen molecules represents the NC4 domain which may participate in electrostatic interactions with polyanionic glycosaminoglycans in cartilage.
Post-translational modification	Covalently linked to the telopeptides of type II collagen by lysine-derived cross-links. Prolines at the third position of the tripeptide repeating unit (G-X-Y) are hydroxylated in some or all of the chains.
Sequence similarities	Belongs to the fibril-associated collagens with interrupted helices (FACIT) family. Contains 9 collagen-like domains. Contains 1 laminin G-like domain.

Keywords
Cellular component	Extracellular matrix Secreted
Coding sequence diversity	Alternative splicing
Domain	Collagen Repeat Signal
Ligand	Metal-binding Zinc
PTM	Disulfide bond Hydroxylation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	growth plate cartilage development Inferred from mutant phenotype PubMed 18467703. Source: MGI tissue homeostasis Inferred from mutant phenotype PubMed 8197187. Source: MGI
Cellular_component	collagen Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Signal peptide

1 – 23

Potential

Chain

24 – 921

898

Collagen alpha-1(IX) chain

PRO_0000005766

Domain

50 – 244

195

Laminin G-like

Domain

269 – 325

Collagen-like 1

Domain

326 – 356

Collagen-like 2

Domain

358 – 403

Collagen-like 3

Domain

416 – 472

Collagen-like 4

Domain

473 – 512

Collagen-like 5

Domain

604 – 656

Collagen-like 6

Domain

657 – 711

Collagen-like 7

Domain

712 – 755

Collagen-like 8

Domain

790 – 847

Collagen-like 9

Region

24 – 268

245

Nonhelical region (NC4)

Region

269 – 405

137

Triple-helical region (COL3)

Region

406 – 417

Nonhelical region (NC3)

Region

418 – 756

339

Triple-helical region (COL2)

Region

757 – 786

Nonhelical region (NC2)

Region

787 – 901

115

Triple-helical region (COL1)

Region

902 – 921

Nonhelical region (NC1)

Metal binding

213

Zinc By similarity

Metal binding

215

Zinc By similarity

Metal binding

253

Zinc By similarity

Disulfide bond

44 ↔ 242

By similarity

Disulfide bond

198 ↔ 252

By similarity

Disulfide bond

411

Interchain By similarity

Disulfide bond

415

Interchain By similarity

Alternative sequence

1 – 260

260

Missing in isoform Short.

VSP_001143

Alternative sequence

261

T → MAWAAWGRGVLGLSLMLSGL RLCAAQT in isoform Short.

VSP_001144

Sequence conflict

110

E → R in AAA21834. Ref.2

Sequence conflict

238

M → V in AAA21834. Ref.2

Sequence conflict

289

D → G in AAA21834. Ref.2

Sequence conflict

461

A → D in AAA21834. Ref.2

Sequence conflict

516

K → E in AAA21834. Ref.2

Sequence conflict

569 – 570

LQ → IA in AAA21834. Ref.2

Sequence conflict

740

E → D in AAA21834. Ref.2

Sequence conflict

775

V → A in AAA21834. Ref.2

Sequence conflict

775

V → A in CAA41049. Ref.3

Sequence		Length	Mass (Da)
Isoform Long [UniParc]. Last modified July 15, 1999. Version 2. Checksum: BC79177D36DCFFFC Show »	FASTA	921	92,092
10 20 30 40 50 60 MKNFWKISVF FCVCSCLGPW VSATLKRRAR FPANSISNGG SELCPKIRIG QDDLPGFDLI 70 80 90 100 110 120 SQFQIEKAAS RRTIQRVVGS TALQVAYKLG SNVDFRIPTR HLYPSGLPEE YSFLTTFRMT 130 140 150 160 170 180 GSTLEKHWNI WQIQDSAGRE QVGVKINGQT KSVAFSYKGL DGSLQTAAFL NLPSLFDSRW 190 200 210 220 230 240 HKLMIGVERT SATLFIDCIR IESLPIKPRG QIDADGFAVL GKLVDNPQVS VPFELQWMLI 250 260 270 280 290 300 HCDPLRPRRE TCHELPIRIT TSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP 310 320 330 340 350 360 PGPPGPPGDP GKPGAPGKPG TPGADGLTGP DGSPGSVGPR GQKGEPGVPG SRGFPGRGIP 370 380 390 400 410 420 GPPGPPGTTG LPGELGRVGP IGDPGKRGPP GPPGPPGPSG TIGFHDGDPL CPNSCPPGRS 430 440 450 460 470 480 GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE GDQGELGEVG AQGPPGPQGL RGITGIVGDK 490 500 510 520 530 540 GEKGARGFDG EPGPQGIPGA AGDQGQRGPP GETGPKGDRG IQGSRGIPGS PGPKGDTGLP 550 560 570 580 590 600 GVDGRDGIPG MPGTKGEAGK PGPPGDVGLQ GLPGVPGIPG AKGVAGEKGN TGAPGKPGQL 610 620 630 640 650 660 GSSGKPGQQG PPGEVGPRGP RGLPGSRGPV GPEGSPGIPG KLGSVGSPGL PGLPGPPGLP 670 680 690 700 710 720 GMKGDRGVFG EPGPKGEQGA SGEEGEAGAR GDLGDMGQPG PKGSVGNPGE PGLRGPEGIR 730 740 750 760 770 780 GLPGVEGPRG PPGPRGMQGE QGATGLPGIQ GPPGRAPTDQ HIKQVCMRVV QEHFVEMAAS 790 800 810 820 830 840 LKRPDTGASG LPGRPGPPGP PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK 850 860 870 880 890 900 GERGPPGRGP KGLPGAIGLP GDPGPASYGK NGRDGEQGPP GVAGIPGVPG PPGPPGPPGF 910 920 CEPASCTLQS GQRAFSKGPD K « Hide
Isoform Short [UniParc]. Checksum: 9F20E93756155B19 Show »	FASTA	687	65,493
10 20 30 40 50 60 MAWAAWGRGV LGLSLMLSGL RLCAAQTSQT TDERGPPGEQ GPPGPPGPPG VPGIDGIDGD 70 80 90 100 110 120 RGPKGPPGPP GPPGDPGKPG APGKPGTPGA DGLTGPDGSP GSVGPRGQKG EPGVPGSRGF 130 140 150 160 170 180 PGRGIPGPPG PPGTTGLPGE LGRVGPIGDP GKRGPPGPPG PPGPSGTIGF HDGDPLCPNS 190 200 210 220 230 240 CPPGRSGYPG LPGMRGHKGA KGEIGEPGRQ GHKGEEGDQG ELGEVGAQGP PGPQGLRGIT 250 260 270 280 290 300 GIVGDKGEKG ARGFDGEPGP QGIPGAAGDQ GQRGPPGETG PKGDRGIQGS RGIPGSPGPK 310 320 330 340 350 360 GDTGLPGVDG RDGIPGMPGT KGEAGKPGPP GDVGLQGLPG VPGIPGAKGV AGEKGNTGAP 370 380 390 400 410 420 GKPGQLGSSG KPGQQGPPGE VGPRGPRGLP GSRGPVGPEG SPGIPGKLGS VGSPGLPGLP 430 440 450 460 470 480 GPPGLPGMKG DRGVFGEPGP KGEQGASGEE GEAGARGDLG DMGQPGPKGS VGNPGEPGLR 490 500 510 520 530 540 GPEGIRGLPG VEGPRGPPGP RGMQGEQGAT GLPGIQGPPG RAPTDQHIKQ VCMRVVQEHF 550 560 570 580 590 600 VEMAASLKRP DTGASGLPGR PGPPGPPGPP GENGFPGQMG IRGLPGIKGP PGALGLRGPK 610 620 630 640 650 660 GDLGEKGERG PPGRGPKGLP GAIGLPGDPG PASYGKNGRD GEQGPPGVAG IPGVPGPPGP 670 680 PGPPGFCEPA SCTLQSGQRA FSKGPDK « Hide

[1]	"The complete primary structure of the long form of mouse alpha 1(IX) collagen chain and its expression during limb development." Abe N., Yoshioka H., Inoue H., Ninomiya Y. Biochim. Biophys. Acta 1204:61-67(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG).
[2]	"Assembly and sequencing of a cDNA covering the entire mouse alpha 1(IX) collagen chain." Rokos I., Muragaki Y., Warman M., Olsen B.R. Matrix Biol. 14:1-8(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM LONG). Tissue: Embryo.
[3]	"Specific hybridization probes for mouse type I, II, III and IX collagen mRNAs." Metsaeranta M., Toman D., de Crombrugghe B., Vuorio E. Biochim. Biophys. Acta 1089:241-243(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 759-906.
[4]	"The alpha 1 (IX) collagen gene gives rise to two different transcripts in both mouse embryonic and human fetal RNA." Muragaki Y., Nishimura I., Henney A., Ninomiya Y., Olsen B.R. Proc. Natl. Acad. Sci. U.S.A. 87:2400-2404(1990) [PubMed] [Europe PMC] [Abstract] Cited for: ALTERNATIVE SPLICING. Strain: BALB/c. Tissue: Liver and Spleen.
+	Additional computationally mapped references.

Sequence databases
EMBL GenBank DDBJ	D17511 mRNA. Translation: BAA04463.1. L12215 mRNA. Translation: AAA21834.1. X57984 Genomic DNA. Translation: CAA41049.1. M32136, M32132 Genomic DNA. Translation: AAA53523.1. M32136, M32134 Genomic DNA. Translation: AAA53522.1.
IPI	IPI00230262. IPI00758037.
PIR	A35980. S40495. S42617.
RefSeq	NP_031766.3. NM_007740.3.
UniGene	Mm.154662.
3D structure databases
ProteinModelPortal	Q05722.
SMR	Q05722. Positions 42-256.
ModBase	Search...
PTM databases
PhosphoSite	Q05722.
Proteomic databases
PaxDb	Q05722.
PRIDE	Q05722.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	12839.
KEGG	mmu:12839.
Organism-specific databases
CTD	1297.
MGI	MGI:88465. Col9a1.
Phylogenomic databases
eggNOG	NOG12793.
HOGENOM	HOG000085653.
HOVERGEN	HBG004933.
InParanoid	Q05722.
KO	K08131.
OrthoDB	EOG4P2Q36.
Gene expression databases
CleanEx	MM_COL9A1.
Genevestigator	Q05722.
GermOnline	ENSMUSG00000026147. Mus musculus.
Family and domain databases
InterPro	IPR008160. Collagen. IPR008985. ConA-like_lec_gl_sf. IPR001791. Laminin_G. [Graphical view]
Pfam	PF01391. Collagen. 9 hits. [Graphical view]
SMART	SM00210. TSPN. 1 hit. [Graphical view]
SUPFAM	SSF49899. ConA_like_lec_gl. 1 hit.
PROSITE	PS50025. LAM_G_DOMAIN. False negative. [Graphical view]
ProtoNet	Search...
Other
NextBio	282364.
SOURCE	Search...

Entry name

CO9A1_MOUSE

Accession

Primary (citable) accession number: Q05722
Secondary accession number(s): Q61269

Q61940

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	July 15, 1999
Last modified:	April 3, 2013
This is version 117 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

MGD cross-references

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

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

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

Note: Additional isoforms seem to exist.

Isoform Long (identifier: Q05722-1)

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 Short (identifier: Q05722-2)

The sequence of this isoform differs from the canonical sequence as follows:
1-260: Missing.
261-261: T → MAWAAWGRGVLGLSLMLSGLRLCAAQT