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Protein

Collagen alpha-1(IX) chain

Gene

COL9A1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Structural component of hyaline cartilage and vitreous of the eye.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi213Zinc1
Metal bindingi215Zinc1
Metal bindingi253Zinc1

GO - Molecular functioni

  • extracellular matrix structural constituent conferring tensile strength Source: BHF-UCL
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • animal organ morphogenesis Source: ProtInc
  • extracellular matrix organization Source: Reactome
Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112280-MONOMER.
ReactomeiR-HSA-1442490. Collagen degradation.
R-HSA-1650814. Collagen biosynthesis and modifying enzymes.
R-HSA-186797. Signaling by PDGF.
R-HSA-216083. Integrin cell surface interactions.
R-HSA-3000178. ECM proteoglycans.
R-HSA-419037. NCAM1 interactions.

Names & Taxonomyi

Protein namesi
Recommended name:
Collagen alpha-1(IX) chain
Gene namesi
Name:COL9A1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:2217. COL9A1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Involvement in diseasei

Multiple epiphyseal dysplasia 6 (EDM6)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal.
See also OMIM:614135
Stickler syndrome 4 (STL4)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn autosomal recessive form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Pierre Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable.
See also OMIM:614134

Keywords - Diseasei

Deafness, Stickler syndrome

Organism-specific databases

DisGeNETi1297.
MalaCardsiCOL9A1.
MIMi614134. phenotype.
614135. phenotype.
OpenTargetsiENSG00000112280.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26733.

Polymorphism and mutation databases

BioMutaiCOL9A1.
DMDMi296439373.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Add BLAST23
ChainiPRO_000000576524 – 921Collagen alpha-1(IX) chainAdd BLAST898

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi44 ↔ 2421 Publication
Glycosylationi171N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi198 ↔ 2521 Publication
Disulfide bondi411Interchain1 Publication
Disulfide bondi415Interchain1 Publication

Post-translational modificationi

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.

Keywords - PTMi

Disulfide bond, Glycoprotein, Hydroxylation

Proteomic databases

PaxDbiP20849.
PeptideAtlasiP20849.
PRIDEiP20849.

PTM databases

iPTMnetiP20849.
PhosphoSitePlusiP20849.

Expressioni

Gene expression databases

BgeeiENSG00000112280.
GenevisibleiP20849. HS.

Interactioni

Subunit structurei

Heterotrimer of an alpha 1(IX), an alpha 2(IX) and an alpha 3(IX) chain.

Protein-protein interaction databases

BioGridi107694. 8 interactors.
STRINGi9606.ENSP00000349790.

Structurei

Secondary structure

1921
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi56 – 58Combined sources3
Helixi59 – 62Combined sources4
Helixi65 – 69Combined sources5
Turni70 – 72Combined sources3
Beta strandi76 – 78Combined sources3
Beta strandi85 – 89Combined sources5
Beta strandi96 – 98Combined sources3
Helixi99 – 102Combined sources4
Beta strandi109 – 118Combined sources10
Helixi121 – 125Combined sources5
Beta strandi127 – 134Combined sources8
Beta strandi140 – 147Combined sources8
Helixi148 – 150Combined sources3
Beta strandi152 – 159Combined sources8
Beta strandi164 – 169Combined sources6
Helixi173 – 175Combined sources3
Beta strandi177 – 179Combined sources3
Beta strandi181 – 188Combined sources8
Beta strandi191 – 196Combined sources6
Beta strandi199 – 205Combined sources7
Beta strandi215 – 225Combined sources11
Beta strandi233 – 242Combined sources10
Helixi246 – 249Combined sources4
Helixi759 – 771Combined sources13
Helixi774 – 781Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2UURX-ray1.80A24-268[»]
5CTDX-ray1.60A754-789[»]
5CTIX-ray1.90A754-789[»]
5CVAX-ray2.10A/D754-789[»]
5CVBX-ray2.25A/D754-789[»]
ProteinModelPortaliP20849.
SMRiP20849.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20849.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini50 – 244Laminin G-likeAdd BLAST195
Domaini269 – 324Collagen-like 1Add BLAST56
Domaini325 – 356Collagen-like 2Add BLAST32
Domaini358 – 403Collagen-like 3Add BLAST46
Domaini416 – 472Collagen-like 4Add BLAST57
Domaini473 – 516Collagen-like 5Add BLAST44
Domaini587 – 643Collagen-like 6Add BLAST57
Domaini655 – 712Collagen-like 7Add BLAST58
Domaini713 – 755Collagen-like 8Add BLAST43
Domaini790 – 847Collagen-like 9Add BLAST58
Domaini848 – 899Collagen-like 10Add BLAST52

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni24 – 268Nonhelical region (NC4)Add BLAST245
Regioni269 – 405Triple-helical region (COL3)Add BLAST137
Regioni406 – 417Nonhelical region (NC3)Add BLAST12
Regioni418 – 756Triple-helical region (COL2)Add BLAST339
Regioni757 – 786Nonhelical region (NC2)Add BLAST30
Regioni787 – 901Triple-helical region (COL1)Add BLAST115
Regioni902 – 921Nonhelical region (NC1)Add BLAST20

Domaini

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.

Sequence similaritiesi

Contains 10 collagen-like domains.Curated
Contains 1 laminin G-like domain.Curated

Keywords - Domaini

Collagen, Repeat, Signal

Phylogenomic databases

eggNOGiKOG3544. Eukaryota.
ENOG410Y4B3. LUCA.
GeneTreeiENSGT00840000129701.
HOVERGENiHBG004933.
InParanoidiP20849.
KOiK08131.
OMAiIKPRGQI.
OrthoDBiEOG091G0ESN.
PhylomeDBiP20849.
TreeFamiTF332900.

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR008160. Collagen.
IPR013320. ConA-like_dom.
IPR001791. Laminin_G.
[Graphical view]
PfamiPF01391. Collagen. 8 hits.
[Graphical view]
SMARTiSM00210. TSPN. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P20849-1) [UniParc]FASTAAdd to basket
Also known as: Long

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

        10         20         30         40         50
MKTCWKIPVF FFVCSFLEPW ASAAVKRRPR FPVNSNSNGG NELCPKIRIG
60 70 80 90 100
QDDLPGFDLI SQFQVDKAAS RRAIQRVVGS ATLQVAYKLG NNVDFRIPTR
110 120 130 140 150
NLYPSGLPEE YSFLTTFRMT GSTLKKNWNI WQIQDSSGKE QVGIKINGQT
160 170 180 190 200
QSVVFSYKGL DGSLQTAAFS NLSSLFDSQW HKIMIGVERS SATLFVDCNR
210 220 230 240 250
IESLPIKPRG PIDIDGFAVL GKLADNPQVS VPFELQWMLI HCDPLRPRRE
260 270 280 290 300
TCHELPARIT PSQTTDERGP PGEQGPPGPP GPPGVPGIDG IDGDRGPKGP
310 320 330 340 350
PGPPGPAGEP GKPGAPGKPG TPGADGLTGP DGSPGSIGSK GQKGEPGVPG
360 370 380 390 400
SRGFPGRGIP GPPGPPGTAG LPGELGRVGP VGDPGRRGPP GPPGPPGPRG
410 420 430 440 450
TIGFHDGDPL CPNACPPGRS GYPGLPGMRG HKGAKGEIGE PGRQGHKGEE
460 470 480 490 500
GDQGELGEVG AQGPPGAQGL RGITGIVGDK GEKGARGLDG EPGPQGLPGA
510 520 530 540 550
PGDQGQRGPP GEAGPKGDRG AEGARGIPGL PGPKGDTGLP GVDGRDGIPG
560 570 580 590 600
MPGTKGEPGK PGPPGDAGLQ GLPGVPGIPG AKGVAGEKGS TGAPGKPGQM
610 620 630 640 650
GNSGKPGQQG PPGEVGPRGP QGLPGSRGEL GPVGSPGLPG KLGSLGSPGL
660 670 680 690 700
PGLPGPPGLP GMKGDRGVVG EPGPKGEQGA SGEEGEAGER GELGDIGLPG
710 720 730 740 750
PKGSAGNPGE PGLRGPEGSR GLPGVEGPRG PPGPRGVQGE QGATGLPGVQ
760 770 780 790 800
GPPGRAPTDQ HIKQVCMRVI QEHFAEMAAS LKRPDSGATG LPGRPGPPGP
810 820 830 840 850
PGPPGENGFP GQMGIRGLPG IKGPPGALGL RGPKGDLGEK GERGPPGRGP
860 870 880 890 900
NGLPGAIGLP GDPGPASYGR NGRDGERGPP GVAGIPGVPG PPGPPGLPGF
910 920
CEPASCTMQA GQRAFNKGPD P
Length:921
Mass (Da):91,869
Last modified:May 18, 2010 - v3
Checksum:iA69BF076127283D0
GO
Isoform 2 (identifier: P20849-2) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     1-243: Missing.
     244-267: PLRPRRETCHELPARITPSQTTDE → MAWTARDRGALGLLLLGLCLCAAQ

Show »
Length:678
Mass (Da):64,372
Checksum:iAD0E99997DF2896E
GO
Isoform 3 (identifier: P20849-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     326-328: GLT → TSP
     329-921: Missing.

Note: No experimental confirmation available.
Show »
Length:328
Mass (Da):35,509
Checksum:iBDD662939FECAD21
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti279 – 280PP → AS in CAA38276 (PubMed:2209617).Curated2
Sequence conflicti279 – 280PP → AS in CAA38277 (PubMed:2209617).Curated2
Sequence conflicti476I → L in CAA38276 (PubMed:2209617).Curated1
Sequence conflicti570Q → H in AAC33527 (PubMed:9707347).Curated1
Sequence conflicti570Q → H in AAC33528 (PubMed:9707347).Curated1
Sequence conflicti910 – 921AGQRA…KGPDP → LVSEHLTKGLTLERLTAAWL SA in AAA53475 (PubMed:2209617).CuratedAdd BLAST12

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026463339S → P.1 PublicationCorresponds to variant rs592121dbSNPEnsembl.1
Natural variantiVAR_026464621Q → R.2 PublicationsCorresponds to variant rs1135056dbSNPEnsembl.1
Natural variantiVAR_055668684E → K.Corresponds to variant rs35470562dbSNPEnsembl.1
Natural variantiVAR_055669767M → V.Corresponds to variant rs6910140dbSNPEnsembl.1
Natural variantiVAR_023326870R → K.3 PublicationsCorresponds to variant rs1056921dbSNPEnsembl.1
Natural variantiVAR_023327882V → L.3 PublicationsCorresponds to variant rs1056923dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0011411 – 243Missing in isoform 2. 2 PublicationsAdd BLAST243
Alternative sequenceiVSP_001142244 – 267PLRPR…QTTDE → MAWTARDRGALGLLLLGLCL CAAQ in isoform 2. 2 PublicationsAdd BLAST24
Alternative sequenceiVSP_015250326 – 328GLT → TSP in isoform 3. 1 Publication3
Alternative sequenceiVSP_015251329 – 921Missing in isoform 3. 1 PublicationAdd BLAST593

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54412 mRNA. Translation: CAA38276.1.
X54413 mRNA. Translation: CAA38277.1.
AF036130
, AF036110, AF036111, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA. Translation: AAC33527.1.
AF036130
, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA. Translation: AAC33528.1.
AL080275, AL160262 Genomic DNA. Translation: CAI19590.1.
AL080275 Genomic DNA. Translation: CAI19591.1.
AL160262, AL080275 Genomic DNA. Translation: CAI42321.1.
BC015409 mRNA. Translation: AAH15409.1.
BC063646 mRNA. Translation: AAH63646.1.
M32137, M32133 Genomic DNA. Translation: AAA53474.1.
M32137, M32135 Genomic DNA. Translation: AAA53475.1.
CCDSiCCDS47447.1. [P20849-2]
CCDS4971.1. [P20849-1]
PIRiS13580.
S13581.
RefSeqiNP_001842.3. NM_001851.4. [P20849-1]
NP_511040.2. NM_078485.3. [P20849-2]
UniGeneiHs.590892.

Genome annotation databases

EnsembliENST00000320755; ENSP00000315252; ENSG00000112280. [P20849-2]
ENST00000357250; ENSP00000349790; ENSG00000112280. [P20849-1]
ENST00000370496; ENSP00000359527; ENSG00000112280. [P20849-3]
GeneIDi1297.
KEGGihsa:1297.
UCSCiuc003pff.5. human. [P20849-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X54412 mRNA. Translation: CAA38276.1.
X54413 mRNA. Translation: CAA38277.1.
AF036130
, AF036110, AF036111, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA. Translation: AAC33527.1.
AF036130
, AF036112, AF036113, AF036114, AF036115, AF036116, AF036117, AF036118, AF036119, AF036120, AF036121, AF036122, AF036123, AF036124, AF036125, AF036126, AF036127, AF036128, AF036129 Genomic DNA. Translation: AAC33528.1.
AL080275, AL160262 Genomic DNA. Translation: CAI19590.1.
AL080275 Genomic DNA. Translation: CAI19591.1.
AL160262, AL080275 Genomic DNA. Translation: CAI42321.1.
BC015409 mRNA. Translation: AAH15409.1.
BC063646 mRNA. Translation: AAH63646.1.
M32137, M32133 Genomic DNA. Translation: AAA53474.1.
M32137, M32135 Genomic DNA. Translation: AAA53475.1.
CCDSiCCDS47447.1. [P20849-2]
CCDS4971.1. [P20849-1]
PIRiS13580.
S13581.
RefSeqiNP_001842.3. NM_001851.4. [P20849-1]
NP_511040.2. NM_078485.3. [P20849-2]
UniGeneiHs.590892.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2UURX-ray1.80A24-268[»]
5CTDX-ray1.60A754-789[»]
5CTIX-ray1.90A754-789[»]
5CVAX-ray2.10A/D754-789[»]
5CVBX-ray2.25A/D754-789[»]
ProteinModelPortaliP20849.
SMRiP20849.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi107694. 8 interactors.
STRINGi9606.ENSP00000349790.

PTM databases

iPTMnetiP20849.
PhosphoSitePlusiP20849.

Polymorphism and mutation databases

BioMutaiCOL9A1.
DMDMi296439373.

Proteomic databases

PaxDbiP20849.
PeptideAtlasiP20849.
PRIDEiP20849.

Protocols and materials databases

DNASUi1297.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000320755; ENSP00000315252; ENSG00000112280. [P20849-2]
ENST00000357250; ENSP00000349790; ENSG00000112280. [P20849-1]
ENST00000370496; ENSP00000359527; ENSG00000112280. [P20849-3]
GeneIDi1297.
KEGGihsa:1297.
UCSCiuc003pff.5. human. [P20849-1]

Organism-specific databases

CTDi1297.
DisGeNETi1297.
GeneCardsiCOL9A1.
GeneReviewsiCOL9A1.
HGNCiHGNC:2217. COL9A1.
MalaCardsiCOL9A1.
MIMi120210. gene.
614134. phenotype.
614135. phenotype.
neXtProtiNX_P20849.
OpenTargetsiENSG00000112280.
Orphaneti250984. Autosomal recessive Stickler syndrome.
166002. Multiple epiphyseal dysplasia due to collagen 9 anomaly.
PharmGKBiPA26733.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3544. Eukaryota.
ENOG410Y4B3. LUCA.
GeneTreeiENSGT00840000129701.
HOVERGENiHBG004933.
InParanoidiP20849.
KOiK08131.
OMAiIKPRGQI.
OrthoDBiEOG091G0ESN.
PhylomeDBiP20849.
TreeFamiTF332900.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112280-MONOMER.
ReactomeiR-HSA-1442490. Collagen degradation.
R-HSA-1650814. Collagen biosynthesis and modifying enzymes.
R-HSA-186797. Signaling by PDGF.
R-HSA-216083. Integrin cell surface interactions.
R-HSA-3000178. ECM proteoglycans.
R-HSA-419037. NCAM1 interactions.

Miscellaneous databases

ChiTaRSiCOL9A1. human.
EvolutionaryTraceiP20849.
GeneWikiiCollagen,_type_IX,_alpha_1.
GenomeRNAii1297.
PROiP20849.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000112280.
GenevisibleiP20849. HS.

Family and domain databases

Gene3Di2.60.120.200. 1 hit.
InterProiIPR008160. Collagen.
IPR013320. ConA-like_dom.
IPR001791. Laminin_G.
[Graphical view]
PfamiPF01391. Collagen. 8 hits.
[Graphical view]
SMARTiSM00210. TSPN. 1 hit.
[Graphical view]
SUPFAMiSSF49899. SSF49899. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCO9A1_HUMAN
AccessioniPrimary (citable) accession number: P20849
Secondary accession number(s): Q13699
, Q13700, Q5TF52, Q6P467, Q96BM8, Q99225, Q9H151, Q9H152, Q9Y6P2, Q9Y6P3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: May 18, 2010
Last modified: November 30, 2016
This is version 190 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.