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Protein

Proto-oncogene tyrosine-protein kinase receptor Ret

Gene

Ret

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Receptor tyrosine-protein kinase involved in numerous cellular mechanisms including cell proliferation, neuronal navigation, cell migration, and cell differentiation upon binding with glial cell derived neurotrophic factor family ligands. Phosphorylates PTK2/FAK1. Regulates both cell death/survival balance and positional information. Required for the molecular mechanisms orchestration during intestine organogenesis; involved in the development of enteric nervous system and renal organogenesis during embryonic life, and promotes the formation of Peyer's patch-like structures, a major component of the gut-associated lymphoid tissue. Modulates cell adhesion via its cleavage by caspase in sympathetic neurons and mediates cell migration in an integrin (e.g. ITGB1 and ITGB3)-dependent manner. Involved in the development of the neural crest. Active in the absence of ligand, triggering apoptosis through a mechanism that requires receptor intracellular caspase cleavage. Acts as a dependence receptor; in the presence of the ligand GDNF in somatotrophs (within pituitary), promotes survival and down regulates growth hormone (GH) production, but triggers apoptosis in absence of GDNF. Regulates nociceptor survival and size. Triggers the differentiation of rapidly adapting (RA) mechanoreceptors. Mediator of several diseases such as neuroendocrine cancers; these diseases are characterized by aberrant integrins-regulated cell migration.2 Publications

Catalytic activityi

ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate.PROSITE-ProRule annotation

Enzyme regulationi

Repressed by withaferin A (WA).1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei759ATPPROSITE-ProRule annotation1
Active sitei875Proton acceptorPROSITE-ProRule annotation1
Binding sitei893InhibitorBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi731 – 739ATPPROSITE-ProRule annotation9

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • calcium ion binding Source: MGI
  • transmembrane receptor protein tyrosine kinase activity Source: MGI

GO - Biological processi

  • anatomical structure morphogenesis Source: MGI
  • cellular response to retinoic acid Source: MGI
  • embryonic epithelial tube formation Source: MGI
  • enteric nervous system development Source: MGI
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • innervation Source: Ensembl
  • MAPK cascade Source: MGI
  • membrane protein proteolysis Source: MGI
  • nervous system development Source: MGI
  • neural crest cell migration Source: MGI
  • neuron cell-cell adhesion Source: UniProtKB
  • neuron differentiation Source: MGI
  • neuron maturation Source: MGI
  • Peyer's patch morphogenesis Source: UniProtKB
  • positive regulation of cell adhesion mediated by integrin Source: MGI
  • positive regulation of cell migration Source: MGI
  • positive regulation of cell size Source: MGI
  • positive regulation of gene expression Source: MGI
  • positive regulation of metanephric glomerulus development Source: UniProtKB
  • positive regulation of neuron maturation Source: Ensembl
  • positive regulation of neuron projection development Source: MGI
  • positive regulation of serine phosphorylation of STAT3 protein Source: MGI
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • regulation of axonogenesis Source: MGI
  • regulation of cell adhesion Source: MGI
  • response to drug Source: Ensembl
  • response to pain Source: UniProtKB
  • retina development in camera-type eye Source: Ensembl
  • transmembrane receptor protein tyrosine kinase signaling pathway Source: MGI
  • ureteric bud development Source: MGI
  • ureter maturation Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase, Tyrosine-protein kinase

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.10.1. 3474.
ReactomeiR-MMU-5673001. RAF/MAP kinase cascade.
R-MMU-8853659. RET signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
Proto-oncogene tyrosine-protein kinase receptor Ret (EC:2.7.10.1)
Alternative name(s):
Proto-oncogene c-Ret
Cleaved into the following 2 chains:
Gene namesi
Name:Ret
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:97902. Ret.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini29 – 637ExtracellularSequence analysisAdd BLAST609
Transmembranei638 – 659HelicalSequence analysisAdd BLAST22
Topological domaini660 – 1115CytoplasmicSequence analysisAdd BLAST456

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endosome, Membrane

Pathology & Biotechi

Disruption phenotypei

Exclusive loss in nociceptors results in a reduction in nociceptor number and size with a reduced epidermal innervation, but increased sensitivity to cold and increased formalin-induced pain.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1063Y → F: Abolishes interaction with DOK proteins. 1 Publication1

Keywords - Diseasei

Proto-oncogene

Chemistry databases

ChEMBLiCHEMBL2034799.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 28Sequence analysisAdd BLAST28
ChainiPRO_000002445129 – 1115Proto-oncogene tyrosine-protein kinase receptor RetAdd BLAST1087
ChainiPRO_000041529429 – 708Extracellular cell-membrane anchored RET cadherin 120 kDa fragmentBy similarityAdd BLAST680
ChainiPRO_0000415295709 – 1018Soluble RET kinase fragmentBy similarityAdd BLAST310

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi89N-linked (GlcNAc...)Sequence analysis1
Glycosylationi98N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi137 ↔ 142By similarity
Glycosylationi151N-linked (GlcNAc...)By similarity1
Glycosylationi156N-linked (GlcNAc...)Sequence analysis1
Glycosylationi199N-linked (GlcNAc...)Sequence analysis1
Glycosylationi345N-linked (GlcNAc...)Sequence analysis1
Glycosylationi360N-linked (GlcNAc...)Sequence analysis1
Glycosylationi378N-linked (GlcNAc...)Sequence analysis1
Glycosylationi396N-linked (GlcNAc...)Sequence analysis1
Glycosylationi450N-linked (GlcNAc...)Sequence analysis1
Glycosylationi470N-linked (GlcNAc...)Sequence analysis1
Glycosylationi556N-linked (GlcNAc...)Sequence analysis1
Modified residuei697PhosphoserineBy similarity1
Modified residuei807Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei810Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei901Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei906Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei982Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei1016Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei1063Phosphotyrosine; by autocatalysis1 Publication1
Modified residuei1091Phosphotyrosine; by autocatalysisBy similarity1
Modified residuei1097Phosphotyrosine; by autocatalysisBy similarity1

Post-translational modificationi

Autophosphorylated on C-terminal tyrosine residues upon ligand stimulation. Dephosphorylated by PTPRJ on Tyr-906, Tyr-1016 and Tyr-1063 (By similarity).By similarity
Proteolytically cleaved by caspase-3. The soluble RET kinase fragment is able to induce cell death. The extracellular cell-membrane anchored RET cadherin fragment accelerates cell adhesion in sympathetic neurons (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei708 – 709Cleavage; by caspase-3By similarity2
Sitei1018 – 1019Cleavage; by caspase-3By similarity2

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

EPDiP35546.
MaxQBiP35546.
PaxDbiP35546.
PRIDEiP35546.

PTM databases

iPTMnetiP35546.
PhosphoSitePlusiP35546.

Expressioni

Tissue specificityi

Expressed in peripheral nerve cells, hematopoietic cells and podocytes.1 Publication

Gene expression databases

BgeeiENSMUSG00000030110.
CleanExiMM_RET.
GenevisibleiP35546. MM.

Interactioni

Subunit structurei

Phosphorylated form interacts with the PBT domain of DOK2, DOK4 and DOK5. The phosphorylated form interacts with PLCG1 and GRB7. Interacts (not phosphorylated) with PTK2/FAK1 (via FERM domain). Extracellular cell-membrane anchored RET cadherin fragments form complex in neurons with reduced trophic status, preferentially at the contact sites between somas. Interacts with AIP in the pituitary gland; this interaction prevents the formation of the AIP-survivin complex. Binds to ARTN. Interacts (inactive) with CBLC and CD2AP; dissociates upon activation by GDNF which increases CBLC:CD2AP interaction.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Epha5Q606295EBI-5548911,EBI-1267609

Protein-protein interaction databases

BioGridi202865. 2 interactors.
IntActiP35546. 10 interactors.
MINTiMINT-5313433.
STRINGi10090.ENSMUSP00000032201.

Chemistry databases

BindingDBiP35546.

Structurei

Secondary structure

11115
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1057 – 1059Combined sources3
Turni1061 – 1064Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UEFX-ray2.50C/D1055-1067[»]
ProteinModelPortaliP35546.
SMRiP35546.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP35546.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini168 – 273CadherinPROSITE-ProRule annotationAdd BLAST106
Domaini725 – 1017Protein kinasePROSITE-ProRule annotationAdd BLAST293

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni806 – 808Inhibitors bindingBy similarity3

Sequence similaritiesi

Belongs to the protein kinase superfamily. Tyr protein kinase family.PROSITE-ProRule annotation
Contains 1 cadherin domain.PROSITE-ProRule annotation
Contains 1 protein kinase domain.PROSITE-ProRule annotation

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG0200. Eukaryota.
COG0515. LUCA.
GeneTreeiENSGT00760000118923.
HOGENOMiHOG000010301.
HOVERGENiHBG002609.
InParanoidiP35546.
KOiK05126.
OMAiWRQGDGK.
OrthoDBiEOG091G0CQZ.
PhylomeDBiP35546.
TreeFamiTF317640.

Family and domain databases

Gene3Di2.60.40.60. 1 hit.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR001245. Ser-Thr/Tyr_kinase_cat_dom.
IPR008266. Tyr_kinase_AS.
IPR020635. Tyr_kinase_cat_dom.
IPR016249. Tyr_kinase_Ret_rcpt.
[Graphical view]
PfamiPF00028. Cadherin. 1 hit.
PF07714. Pkinase_Tyr. 1 hit.
[Graphical view]
PIRSFiPIRSF000631. TyrPK_receptor_Ret. 1 hit.
PRINTSiPR00109. TYRKINASE.
SMARTiSM00219. TyrKc. 1 hit.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 1 hit.
SSF56112. SSF56112. 1 hit.
PROSITEiPS50268. CADHERIN_2. 1 hit.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00109. PROTEIN_KINASE_TYR. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P35546-1) [UniParc]FASTAAdd to basket
Also known as: Ret51

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
MAKATSGAAG LGLKLILLLP LLGEAPLGLY FSRDAYWERL YVDQPAGTPL
60 70 80 90 100
LYVHALRDAP GEVPSFRLGQ HLYGVYRTRL HENDWIRINE TTGLLYLNQS
110 120 130 140 150
LDHSSWEQLS IRNGGFPLLT IFLQVFLGST AQREGECHWP GCTRVYFSFI
160 170 180 190 200
NDTFPNCSSF KAQDLCIPET AVSFRVRENR PPGTFYHFHM LPVQFLCPNI
210 220 230 240 250
SVKYSLLGGD SLPFRCDPDC LEVSTRWALD RELREKYVLE ALCIVAGPGA
260 270 280 290 300
NKETVTLSFP VTVYDEDDSA PTFSGGVGTA SAVVEFKRKE GTVVATLQVF
310 320 330 340 350
DADVVPASGE LVRRYTNTLL SGDSWAQQTF RVEHSPIETL VQVNNNSVRA
360 370 380 390 400
TMHNYKLILN RSLSISESRV LQLAVLVNDS DFQGPGAGGI LVLHFNVSVL
410 420 430 440 450
PVTLNLPRAY SFPVNKRARR YAQIGKVCVE NCQEFSGVSI QYKLQPSSIN
460 470 480 490 500
CTALGVVTSP EDTSGTLFVN DTEALRRPEC TKLQYTVVAT DRQTRRQTQA
510 520 530 540 550
SLVVTVEGTS ITEEVGCPKS CAVNKRRPEC EECGGLGSPT GRCEWRQGDG
560 570 580 590 600
KGITRNFSTC SPSTRTCPDG HCDAVESRDA NICPQDCLRA DIVGGHERGE
610 620 630 640 650
RQGIKAGYGI CNCFPDEKKC FCEPEDSQGP LCDALCRTII TAALFSLIIS
660 670 680 690 700
ILLSIFCVCH HHKHGHKPPI ASAEMTFCRP AQGFPISYSS SGTRRPSLDS
710 720 730 740 750
TENQVPVDSF KIPEDPKWEF PRKNLVLGKT LGEGEFGKVV KATAFRLKGR
760 770 780 790 800
AGYTTVAVKM LKENASQSEL RDLLSEFNLL KQVNHPHVIK LYGACSQDGP
810 820 830 840 850
LLLIVEYAKY GSLRGFLRDS RKIGPAYVSG GGSRNSSSLD HPDERVLTMG
860 870 880 890 900
DLISFAWQIS RGMQYLAEMK LVHRDLAARN ILVAEGRKMK ISDFGLSRDV
910 920 930 940 950
YEEDSYVKKS KGRIPVKWMA IESLFDHIYT TQSDVWSFGV LLWEIVTLGG
960 970 980 990 1000
NPYPGIPPER LFNLLKTGHR MERPDNCSEE MYRLMLQCWK QEPDKRPVFA
1010 1020 1030 1040 1050
DISKDLEKMM VKSRDYLDLA ASTPSDSLLY DDGLSEEETP LVDCNNAPLP
1060 1070 1080 1090 1100
RSLPSTWIEN KLYGMSDPNW PGESPVPLTR ADGTSTGFPR YANDSVYANW
1110
MVSPSAAKLM DTFDS
Length:1,115
Mass (Da):123,874
Last modified:August 16, 2004 - v2
Checksum:iA5CF1EF45A640413
GO
Isoform 2 (identifier: P35546-2) [UniParc]FASTAAdd to basket
Also known as: Ret9

The sequence of this isoform differs from the canonical sequence as follows:
     1065-1115: MSDPNWPGESPVPLTRADGTSTGFPRYANDSVYANWMVSPSAAKLMDTFDS → RISHAFTRF

Show »
Length:1,073
Mass (Da):119,469
Checksum:iDB582E8D490C4A62
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti174F → S in CAA48013 (PubMed:8455936).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0113041065 – 1115MSDPN…DTFDS → RISHAFTRF in isoform 2. 3 PublicationsAdd BLAST51

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X67812 mRNA. Translation: CAA48013.1.
AF209436 mRNA. Translation: AAF21033.1.
AY326397 mRNA. Translation: AAP88379.1.
AK051633 mRNA. Translation: BAC34699.1.
BC059012 mRNA. Translation: AAH59012.1.
CCDSiCCDS20470.1. [P35546-1]
CCDS39608.1. [P35546-2]
PIRiI48735. S29926.
RefSeqiNP_001074249.1. NM_001080780.1. [P35546-2]
NP_033076.2. NM_009050.2. [P35546-1]
UniGeneiMm.57199.

Genome annotation databases

EnsembliENSMUST00000032201; ENSMUSP00000032201; ENSMUSG00000030110. [P35546-1]
ENSMUST00000088790; ENSMUSP00000086169; ENSMUSG00000030110. [P35546-2]
GeneIDi19713.
KEGGimmu:19713.
UCSCiuc009dlm.1. mouse. [P35546-1]
uc009dln.1. mouse. [P35546-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X67812 mRNA. Translation: CAA48013.1.
AF209436 mRNA. Translation: AAF21033.1.
AY326397 mRNA. Translation: AAP88379.1.
AK051633 mRNA. Translation: BAC34699.1.
BC059012 mRNA. Translation: AAH59012.1.
CCDSiCCDS20470.1. [P35546-1]
CCDS39608.1. [P35546-2]
PIRiI48735. S29926.
RefSeqiNP_001074249.1. NM_001080780.1. [P35546-2]
NP_033076.2. NM_009050.2. [P35546-1]
UniGeneiMm.57199.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UEFX-ray2.50C/D1055-1067[»]
ProteinModelPortaliP35546.
SMRiP35546.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202865. 2 interactors.
IntActiP35546. 10 interactors.
MINTiMINT-5313433.
STRINGi10090.ENSMUSP00000032201.

Chemistry databases

BindingDBiP35546.
ChEMBLiCHEMBL2034799.

PTM databases

iPTMnetiP35546.
PhosphoSitePlusiP35546.

Proteomic databases

EPDiP35546.
MaxQBiP35546.
PaxDbiP35546.
PRIDEiP35546.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000032201; ENSMUSP00000032201; ENSMUSG00000030110. [P35546-1]
ENSMUST00000088790; ENSMUSP00000086169; ENSMUSG00000030110. [P35546-2]
GeneIDi19713.
KEGGimmu:19713.
UCSCiuc009dlm.1. mouse. [P35546-1]
uc009dln.1. mouse. [P35546-2]

Organism-specific databases

CTDi5979.
MGIiMGI:97902. Ret.

Phylogenomic databases

eggNOGiKOG0200. Eukaryota.
COG0515. LUCA.
GeneTreeiENSGT00760000118923.
HOGENOMiHOG000010301.
HOVERGENiHBG002609.
InParanoidiP35546.
KOiK05126.
OMAiWRQGDGK.
OrthoDBiEOG091G0CQZ.
PhylomeDBiP35546.
TreeFamiTF317640.

Enzyme and pathway databases

BRENDAi2.7.10.1. 3474.
ReactomeiR-MMU-5673001. RAF/MAP kinase cascade.
R-MMU-8853659. RET signaling.

Miscellaneous databases

EvolutionaryTraceiP35546.
PROiP35546.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000030110.
CleanExiMM_RET.
GenevisibleiP35546. MM.

Family and domain databases

Gene3Di2.60.40.60. 1 hit.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR011009. Kinase-like_dom.
IPR000719. Prot_kinase_dom.
IPR017441. Protein_kinase_ATP_BS.
IPR001245. Ser-Thr/Tyr_kinase_cat_dom.
IPR008266. Tyr_kinase_AS.
IPR020635. Tyr_kinase_cat_dom.
IPR016249. Tyr_kinase_Ret_rcpt.
[Graphical view]
PfamiPF00028. Cadherin. 1 hit.
PF07714. Pkinase_Tyr. 1 hit.
[Graphical view]
PIRSFiPIRSF000631. TyrPK_receptor_Ret. 1 hit.
PRINTSiPR00109. TYRKINASE.
SMARTiSM00219. TyrKc. 1 hit.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 1 hit.
SSF56112. SSF56112. 1 hit.
PROSITEiPS50268. CADHERIN_2. 1 hit.
PS00107. PROTEIN_KINASE_ATP. 1 hit.
PS50011. PROTEIN_KINASE_DOM. 1 hit.
PS00109. PROTEIN_KINASE_TYR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRET_MOUSE
AccessioniPrimary (citable) accession number: P35546
Secondary accession number(s): Q8BQ34, Q9QXH9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: August 16, 2004
Last modified: November 2, 2016
This is version 161 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

Treatment with withaferin A (WA) leads tumor regression in medullary thyroid carcinomas (MTC).

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Human and mouse protein kinases
    Human and mouse protein kinases: classification and index
  4. 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.