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UniProtKB - F1LQ93 (F1LQ93_RAT)

Entry version 69 (02 Dec 2020)
Sequence version 3 (22 Jul 2015)
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Protein
Submitted name:

Collagen alpha-1(IX) chain

Gene

Col9a1

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

Annotation score:1 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>-Protein predictedi <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

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...Reactomei		R-RNO-1650814, Collagen biosynthesis and modifying enzymes
R-RNO-186797, Signaling by PDGF
R-RNO-2022090, Assembly of collagen fibrils and other multimeric structures
R-RNO-216083, Integrin cell surface interactions
R-RNO-3000178, ECM proteoglycans
R-RNO-419037, NCAM1 interactions
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
Submitted name:
Collagen alpha-1(IX) chainImported
<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:Col9a1Imported
<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)Imported
<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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus
<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: Chromosome 9

Organism-specific databases

Rat genome database

More...RGDi		1309425, Col9a1

<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

<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

Proteomic databases

PRoteomics IDEntifications database

More...PRIDEi		F1LQ93

<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

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...Bgeei		ENSRNOG00000012920, Expressed in pancreas and 14 other tissues

<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		F1LQ93

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>Domaini63 – 257LAM_G_DOMAINInterPro annotationAdd BLAST195

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>Regioni266 – 772DisorderedSequence analysisAdd BLAST507
Regioni796 – 934DisorderedSequence analysisAdd BLAST139

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi285 – 299Pro-richSequence analysisAdd BLAST15
Compositional biasi310 – 330Pro-richSequence analysisAdd BLAST21
Compositional biasi398 – 412Pro-richSequence analysisAdd BLAST15
Compositional biasi446 – 467PolyampholyteSequence analysisAdd BLAST22
Compositional biasi804 – 820Pro-richSequence analysisAdd BLAST17
Compositional biasi897 – 914Pro-richSequence analysisAdd BLAST18

Phylogenomic databases

Ensembl GeneTree

More...GeneTreei		ENSGT00940000157935

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_001074_18_1_1

Identification of Orthologs from Complete Genome Data

More...OMAi		QGENGPT

Database of Orthologous Groups

More...OrthoDBi		1295141at2759

TreeFam database of animal gene trees

More...TreeFami		TF332900

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR008160, Collagen
IPR013320, ConA-like_dom_sf
IPR001791, Laminin_G

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01391, Collagen, 10 hits

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00210, TSPN, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF49899, SSF49899, 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.

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

F1LQ93-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVTLINPREP TGKMKNFWKI PLFFFACSFL GPCVSATPKR RARFPANSVS 
        60         70         80         90        100
HGGSELCPKI RIGQDDLPGF DLISQFQIEK AASRRTIQRV VGSTALQVAY 
       110        120        130        140        150
KLGSNVDFRI PTRHLYPSGL PEEYSFLTTF RMTGSTLEKQ WNIWQIQDSS 
       160        170        180        190        200
GREQVGVKIN GQTKSVAFSY KGLDGSLQTA AFLNLQSLFD SRWHKLMIGV 
       210        220        230        240        250
ERTRATLFID CIQIDSLPIK PRAQIDADGF AVLGKLVDNP QVSVPFELQW 
       260        270        280        290        300
MLIHCDPLRP RRETCHELPV RITTSQTTDE RGPPGEQGPP GPPGPPGVPG 
       310        320        330        340        350
IDGIDGDRGP KGPPGPPGPP GDPGKPGAPG KPGTPGADGL TGPDGSPGSV 
       360        370        380        390        400
GPRGQKGEPG VPGSRGFPGR GIPGPPGPPG TTGLPGELGR VGPAGDPGKR 
       410        420        430        440        450
GPPGPPGPPG PSGTIGFHDG DPLCPNSCPP GRSGYPGLPG MRGHKGAKGE 
       460        470        480        490        500
IGEPGRQGHK GEEGDQGELG EVGAQGPPGA QGLRGITGIV GDKGEKGARG 
       510        520        530        540        550
FDGDPGPQGV PGAAGDQGQR GPPGETGPKG DRGIQGSRGI PGSPGPKGDT 
       560        570        580        590        600
GLPGVDGRDG IPGMPGTKGE AGKPGPPGDA GLQGLPGVPG IPGAKGVAGE 
       610        620        630        640        650
KGNTGPPGKP GQLGSSGKPG QQGPPGEVGP RGPRGLPGSR GPVGPEGSPG 
       660        670        680        690        700
IPGKLGPLGS PGLPGLPGPP GLPGMKGDRG VFGEPGPKGE QGASGEEGEA 
       710        720        730        740        750
GVRGDLGDMG QPGPKGSVGN PGEPGLRGPE GIRGLPGVEG PRGPPGPRGV 
       760        770        780        790        800
QGEQGATGLP GIQGPPGRAP TDQHIKQVCM RVVQEHFAEM AASLKRPDTG 
       810        820        830        840        850
ASGLPGRPGP PGPPGPPGEN GFPGQMGIRG LPGIKGPPGA LGLRGPKGDL 
       860        870        880        890        900
GEKGERGPPG RGPKGLPGAI GLPGDPGPAS YGKNGRDGEQ GPPGVAGIPG 
       910        920        930 
VPGPPGPPGP PGFCEPASCT LQAGQRAFSK GPDK
Length:934
Mass (Da):93,466
Last modified:July 22, 2015 - v3
<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:i4D5F0AEA480EE7FD
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
P20850CO9A1_RAT
Collagen alpha-1(IX) chain
Col9a1
325Annotation 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>

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
AABR07067099 Genomic DNA No translation available.
AABR07067100 Genomic DNA No translation available.

NCBI Reference Sequences

More...RefSeqi		NP_001094312.1, NM_001100842.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...Ensembli		ENSRNOT00000018116; ENSRNOP00000018116; ENSRNOG00000012920

Database of genes from NCBI RefSeq genomes

More...GeneIDi		305104

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		rno:305104

<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
AABR07067099 Genomic DNA No translation available.
AABR07067100 Genomic DNA No translation available.
RefSeqiNP_001094312.1, NM_001100842.1

3D structure databases

SMRiF1LQ93
ModBaseiSearch...

Proteomic databases

PRIDEiF1LQ93

Genome annotation databases

EnsembliENSRNOT00000018116; ENSRNOP00000018116; ENSRNOG00000012920
GeneIDi305104
KEGGirno:305104

Organism-specific databases

Comparative Toxicogenomics Database

More...CTDi		1297
RGDi1309425, Col9a1

Phylogenomic databases

GeneTreeiENSGT00940000157935
HOGENOMiCLU_001074_18_1_1
OMAiQGENGPT
OrthoDBi1295141at2759
TreeFamiTF332900

Enzyme and pathway databases

ReactomeiR-RNO-1650814, Collagen biosynthesis and modifying enzymes
R-RNO-186797, Signaling by PDGF
R-RNO-2022090, Assembly of collagen fibrils and other multimeric structures
R-RNO-216083, Integrin cell surface interactions
R-RNO-3000178, ECM proteoglycans
R-RNO-419037, NCAM1 interactions
R-RNO-8948216, Collagen chain trimerization

Gene expression databases

BgeeiENSRNOG00000012920, Expressed in pancreas and 14 other tissues

Family and domain databases

InterProiView protein in InterPro
IPR008160, Collagen
IPR013320, ConA-like_dom_sf
IPR001791, Laminin_G
PfamiView protein in Pfam
PF01391, Collagen, 10 hits
SMARTiView protein in SMART
SM00210, TSPN, 1 hit
SUPFAMiSSF49899, SSF49899, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...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 nameiF1LQ93_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: F1LQ93
<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/TrEMBL: May 3, 2011
Last sequence update: July 22, 2015
Last modified: December 2, 2020
This is version 69 of the entry and version 3 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

<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>Keywords - Technical termi

Reference proteomeImported
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Main funding by: National Institutes of Health

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