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Entry version 139 (02 Dec 2020)
Sequence version 2 (06 Dec 2005)
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Protein

Collagen alpha-1(II) chain

Gene

Col2a1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Type II collagen is specific for cartilaginous tissues. It is essential for the normal embryonic development of the skeleton, for linear growth and for the ability of cartilage to resist compressive forces.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi1233CalciumBy similarity1
Metal bindingi1235CalciumBy similarity1
Metal bindingi1236Calcium; via carbonyl oxygenBy similarity1
Metal bindingi1238Calcium; via carbonyl oxygenBy similarity1
Metal bindingi1241CalciumBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

LigandCalcium, Metal-binding

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-RNO-1442490, Collagen degradation
R-RNO-1474244, Extracellular matrix organization
R-RNO-1650814, Collagen biosynthesis and modifying enzymes
R-RNO-186797, Signaling by PDGF
R-RNO-198933, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-RNO-2022090, Assembly of collagen fibrils and other multimeric structures
R-RNO-216083, Integrin cell surface interactions
R-RNO-3000171, Non-integrin membrane-ECM interactions
R-RNO-3000178, ECM proteoglycans
R-RNO-419037, NCAM1 interactions
R-RNO-8874081, MET activates PTK2 signaling
R-RNO-8948216, Collagen chain trimerization

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Collagen alpha-1(II) chainBy similarity
Alternative name(s):
Alpha-1 type II collagenBy similarity
Cleaved into the following 2 chains:
Collagen alpha-1(II) chainBy similarity
ChondrocalcinBy similarity
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Col2a1Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Unplaced

Organism-specific databases

Rat genome database

More...
RGDi
2375, Col2a1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Extracellular matrix, Secreted

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 25Sequence analysisAdd BLAST25
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section describes a propeptide, which is a part of a protein that is cleaved during maturation or activation. Once cleaved, a propeptide generally has no independent biological function.<p><a href='/help/propep' target='_top'>More...</a></p>PropeptideiPRO_000000573526 – 113N-terminal propeptideBy similarityAdd BLAST88
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_0000005736114 – 1173Collagen alpha-1(II) chainAdd BLAST1060
ChainiPRO_00000434071174 – 1419ChondrocalcinBy similarityAdd BLAST246

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei1225-hydroxylysineBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section specifies the position and type of each covalently attached glycan group (mono-, di-, or polysaccharide).<p><a href='/help/carbohyd' target='_top'>More...</a></p>Glycosylationi122O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei2195-hydroxylysineBy similarity1
Glycosylationi219O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei2315-hydroxylysineBy similarity1
Glycosylationi231O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei2405-hydroxylysineBy similarity1
Glycosylationi240O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei3065-hydroxylysineBy similarity1
Glycosylationi306O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei5405-hydroxylysineBy similarity1
Glycosylationi540O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei5525-hydroxylysineBy similarity1
Glycosylationi552O-linked (Gal...) hydroxylysineBy similarity1
Modified residuei5914-hydroxyproline1 Publication1
Modified residuei6004-hydroxyproline1 Publication1
Modified residuei6023-hydroxyproline; partial1 Publication1
Modified residuei6034-hydroxyproline1 Publication1
Modified residuei6064-hydroxyproline1 Publication1
Modified residuei8393-hydroxyproline; partial1 Publication1
Modified residuei8404-hydroxyproline1 Publication1
Modified residuei8464-hydroxyproline1 Publication1
Modified residuei8524-hydroxyproline1 Publication1
Modified residuei10763-hydroxyproline; partial1 Publication1
Modified residuei11134-hydroxyproline1 Publication1
Modified residuei11183-hydroxyproline1 Publication1
Modified residuei11194-hydroxyproline1 Publication1
Modified residuei11333-hydroxyproline; partial1 Publication1
Modified residuei11344-hydroxyproline1 Publication1
Modified residuei11374-hydroxyproline1 Publication1
Modified residuei11393-hydroxyproline; partial1 Publication1
Modified residuei11404-hydroxyproline1 Publication1
Modified residuei11434-hydroxyproline1 Publication1
Modified residuei11453-hydroxyproline; partial1 Publication1
Modified residuei11464-hydroxyproline1 Publication1
<p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi1215 ↔ 1247PROSITE-ProRule annotation
Disulfide bondi1221Interchain (with C-1238)PROSITE-ProRule annotation
Disulfide bondi1238Interchain (with C-1221)PROSITE-ProRule annotation
Disulfide bondi1255 ↔ 1417PROSITE-ProRule annotation
Glycosylationi1320N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi1325 ↔ 1370PROSITE-ProRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Contains mostly 4-hydroxyproline. Prolines at the third position of the tripeptide repeating unit (G-X-P) are 4-hydroxylated in some or all of the chains.1 Publication
Contains 3-hydroxyproline at a few sites. This modification occurs on the first proline residue in the sequence motif Gly-Pro-Hyp, where Hyp is 4-hydroxyproline.1 Publication
Lysine residues at the third position of the tripeptide repeating unit (G-X-Y) are 5-hydroxylated in some or all of the chains.Curated
O-glycosylated on hydroxylated lysine residues. The O-linked glycan consists of a Glc-Gal disaccharide.Curated

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei113 – 114Cleavage; by procollagen N-endopeptidaseBy similarity2
Sitei1173 – 1174Cleavage; by procollagen C-endopeptidaseBy similarity2

Keywords - PTMi

Disulfide bond, Glycoprotein, Hydroxylation

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P05539

PRoteomics IDEntifications database

More...
PRIDEi
P05539

PTM databases

GlyGen: Computational and Informatics Resources for Glycoscience

More...
GlyGeni
P05539, 8 sites

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified 'at protein level'.<br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed in chondrocytes.1 Publication

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotrimers of alpha 1(II) chains.

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
247447, 1 interactor

Protein interaction database and analysis system

More...
IntActi
P05539, 1 interactor

STRING: functional protein association networks

More...
STRINGi
10116.ENSRNOP00000016044

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P05539

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini1185 – 1419Fibrillar collagen NC1PROSITE-ProRule annotationAdd BLAST235

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni133 – 1146Triple-helical regionAdd BLAST1014
Regioni1147 – 1173Nonhelical region (C-terminal)Add BLAST27

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function (By similarity).By similarity

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the fibrillar collagen family.PROSITE-ProRule annotation

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3544, Eukaryota

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P05539

Database of Orthologous Groups

More...
OrthoDBi
337699at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P05539

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR008160, Collagen
IPR000885, Fib_collagen_C

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01410, COLFI, 1 hit
PF01391, Collagen, 3 hits

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00038, COLFI, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51461, NC1_FIB, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequence (1+)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

P05539-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIRLGAPQSL VLLTLLIATV LQCQGQDARK LGPKGQKGEP GDIKDIIGPK
60 70 80 90 100
GPPGPQGPAG EQGPRGDRGD KGERGAPGPR GRDGEPGTPG NPGPPGPPGP
110 120 130 140 150
PGPPGLGGGN FAAQMAGGFD EKAGGAQMGV MQGPMGPMGP RGPPGPAGAP
160 170 180 190 200
GPQGFQGNPG EPGEPGVSGP IGPRGPPGPA GKPGDDGEAG KPGKAGERGL
210 220 230 240 250
PGPQGARGFP GTPGLPGVKG HRGYPGLDGA KGEAGAPGVK GESGSPGENG
260 270 280 290 300
SPGPMGPRGL PGERGRTGPA GAAGARGNDG QPGPAGPPGP VGPAGGPGFL
310 320 330 340 350
GAPGAKGEAG PTGARGPEGA QGSRGEPGNP GSPGPAGASG NPGTDGIPGA
360 370 380 390 400
KGSAGAPGIA GAPGFPGPRG PPGPQGATGP LGPKGQTGEP GIAGFKGEQG
410 420 430 440 450
PKGETGPAGP QGAPGPAGEE GKRGARGEPG GAGPIGPPGE RGAPGNRGFP
460 470 480 490 500
GQDGLAGPKG APGERGPSGL AGPKGANGDP GRPGEPGLPG ARGLTGRPGD
510 520 530 540 550
AGPQGKVGPS GAPGEDGRPG PPGPQGARGQ PGVMGFPGPK GANGEPGKAG
560 570 580 590 600
EKGLAGAPGL RGLPGKDGET GAAGPPGPSG PAGERGEQGA PGPSGFQGLP
610 620 630 640 650
GPPGPPGEGG KQGDQGIPGE AGAPGLVGPR GERGFPGERG SPGAQGLQGP
660 670 680 690 700
RGLPGTPGTD GPKGAAGPDG PPGAQGPPGL QGMPGERGAA GIAGPKGDRG
710 720 730 740 750
DVGEKGPEGA PGKDGGRGLT GPIGPPGPAG ANGEKGEVGP PGPSGSTGAR
760 770 780 790 800
GAPGERGETG PPGPAGFAGP PGADGQPGAK GDQGEAGQKG DAGAPGPQGP
810 820 830 840 850
SGAPGPQGPT GVTGPKGARG AQGPPGATGF PGAAGRVGPP GSNGNPGPAG
860 870 880 890 900
PPGPAGKDGP KGARGDTGAP GRAGDPGLQG PAGAPGEKGE PGDDGPSGSD
910 920 930 940 950
GPPGPQGLAG QRGIVGLPGQ RGERGFPGLP GPSGEPGKQG APGASGDRGP
960 970 980 990 1000
PGPVGPPGLT GPAGEPGREG SPGADGPPGR DGAAGVKGDR GETGALGAPG
1010 1020 1030 1040 1050
APGPPGSPGP AGPTGKQGDR GEAGAQGPMG PSGPAGARGI AGPQGPRGDK
1060 1070 1080 1090 1100
GEAGEPGERG LKGHRGFTGL QGLPGPPGPS GDQGTSGPAG PSGPRGPPGP
1110 1120 1130 1140 1150
VGPSGKDGSN GIPGPIGPPG PRGRSGETGP AGPPGNPGPP GPPGPPGPGI
1160 1170 1180 1190 1200
DMSAFAGLGQ REKGPDPLQY MRADEADSTL RQHDVEVDAT LKSLNNQIES
1210 1220 1230 1240 1250
IRSPDGSRKN PARTCQDLKL CHPEWKSGDY WIDPNQGCTL DAMKVFCNME
1260 1270 1280 1290 1300
TGESCVYPNP ATVPRKNWWS SKSKEKKHIW FGETMNGGFH FSYGDGNLAP
1310 1320 1330 1340 1350
NTANVQMTFL RLLSTEGSQN ITYHCKNSIA YLDEAAGNLK KALLIQGSND
1360 1370 1380 1390 1400
VEMRAEGNSR FTYTALKDGC TKHTGKWGKT IIEYRSQKTS RLPIVDIAPM
1410
DIGGPDQEFG VDIGPVCFL
Length:1,419
Mass (Da):134,570
Last modified:December 6, 2005 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iB7C63B77819CE50B
GO

<p>In eukaryotic reference proteomes, unreviewed entries that are likely to belong to the same gene are computationally mapped, based on gene identifiers from Ensembl, EnsemblGenomes and model organism databases.<p><a href='/help/gene_centric_isoform_mapping' target='_top'>More...</a></p>Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F1LRM7F1LRM7_RAT
Collagen alpha-1(II) chain
Col2a1
1,419Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti121E → Q in AAA40919 (PubMed:6094525).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
L48440 mRNA Translation: AAA79780.1
K02804 mRNA Translation: AAA40919.1
M10613 Genomic DNA Translation: AAA40920.1
X79816 mRNA Translation: CAA56213.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A05152
I60384

NCBI Reference Sequences

More...
RefSeqi
NP_037061.1, NM_012929.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
25412

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:25412

UCSC genome browser

More...
UCSCi
RGD:2375, rat

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L48440 mRNA Translation: AAA79780.1
K02804 mRNA Translation: AAA40919.1
M10613 Genomic DNA Translation: AAA40920.1
X79816 mRNA Translation: CAA56213.1
PIRiA05152
I60384
RefSeqiNP_037061.1, NM_012929.1

3D structure databases

SMRiP05539
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi247447, 1 interactor
IntActiP05539, 1 interactor
STRINGi10116.ENSRNOP00000016044

PTM databases

GlyGeniP05539, 8 sites

Proteomic databases

PaxDbiP05539
PRIDEiP05539

Protocols and materials databases

ABCD curated depository of sequenced antibodies

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ABCDi
P05539, 18 sequenced antibodies

Genome annotation databases

GeneIDi25412
KEGGirno:25412
UCSCiRGD:2375, rat

Organism-specific databases

Comparative Toxicogenomics Database

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CTDi
1280
RGDi2375, Col2a1

Phylogenomic databases

eggNOGiKOG3544, Eukaryota
InParanoidiP05539
OrthoDBi337699at2759
PhylomeDBiP05539

Enzyme and pathway databases

ReactomeiR-RNO-1442490, Collagen degradation
R-RNO-1474244, Extracellular matrix organization
R-RNO-1650814, Collagen biosynthesis and modifying enzymes
R-RNO-186797, Signaling by PDGF
R-RNO-198933, Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
R-RNO-2022090, Assembly of collagen fibrils and other multimeric structures
R-RNO-216083, Integrin cell surface interactions
R-RNO-3000171, Non-integrin membrane-ECM interactions
R-RNO-3000178, ECM proteoglycans
R-RNO-419037, NCAM1 interactions
R-RNO-8874081, MET activates PTK2 signaling
R-RNO-8948216, Collagen chain trimerization

Miscellaneous databases

Protein Ontology

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PROi
PR:P05539

Family and domain databases

InterProiView protein in InterPro
IPR008160, Collagen
IPR000885, Fib_collagen_C
PfamiView protein in Pfam
PF01410, COLFI, 1 hit
PF01391, Collagen, 3 hits
SMARTiView protein in SMART
SM00038, COLFI, 1 hit
PROSITEiView protein in PROSITE
PS51461, NC1_FIB, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiCO2A1_RAT
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P05539
Secondary accession number(s): Q63123, Q63565, Q78DY3
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: December 6, 2005
Last modified: December 2, 2020
This is version 139 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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