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Protein

Protein argonaute-2

Gene

Ago2

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

Functioni

Required for RNA-mediated gene silencing (RNAi) by the RNA-induced silencing complex (RISC). The 'minimal RISC' appears to include AGO2 bound to a short guide RNA such as a microRNA (miRNA) or short interfering RNA (siRNA). These guide RNAs direct RISC to complementary mRNAs that are targets for RISC-mediated gene silencing. The precise mechanism of gene silencing depends on the degree of complementarity between the miRNA or siRNA and its target. Binding of RISC to a perfectly complementary mRNA generally results in silencing due to endonucleolytic cleavage of the mRNA specifically by AGO2. Binding of RISC to a partially complementary mRNA results in silencing through inhibition of translation, and this is independent of endonuclease activity. May inhibit translation initiation by binding to the 7-methylguanosine cap, thereby preventing the recruitment of the translation initiation factor eIF4-E. May also inhibit translation initiation via interaction with EIF6, which itself binds to the 60S ribosomal subunit and prevents its association with the 40S ribosomal subunit. The inhibition of translational initiation leads to the accumulation of the affected mRNA in cytoplasmic processing bodies (P-bodies), where mRNA degradation may subsequently occur. In some cases RISC-mediated translational repression is also observed for miRNAs that perfectly match the 3' untranslated region (3'-UTR). Can also up-regulate the translation of specific mRNAs under certain growth conditions. Binds to the AU element of the 3'-UTR of the TNF (TNF-alpha) mRNA and up-regulates translation under conditions of serum starvation. Also required for transcriptional gene silencing (TGS), in which short RNAs known as antigene RNAs or agRNAs direct the transcriptional repression of complementary promoter regions. Regulates lymphoid and erythroid development and function, and this is independent of endonuclease activity.3 Publications

Catalytic activityi

Endonucleolytic cleavage to 5'-phosphomonoester.UniRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi598 – 5981Divalent metal cationUniRule annotation
Metal bindingi670 – 6701Divalent metal cationUniRule annotation
Metal bindingi808 – 8081Divalent metal cationUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein, Endonuclease, Hydrolase, Nuclease, Repressor, Ribonucleoprotein

Keywords - Biological processi

Differentiation, RNA-mediated gene silencing, Transcription, Transcription regulation, Translation regulation

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-MMU-203927. MicroRNA (miRNA) biogenesis.
R-MMU-426486. Small interfering RNA (siRNA) biogenesis.
R-MMU-426496. Post-transcriptional silencing by small RNAs.
R-MMU-5578749. Transcriptional regulation by small RNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein argonaute-2UniRule annotation (EC:3.1.26.n2UniRule annotation)
Short name:
Argonaute2UniRule annotation
Short name:
mAgo2
Alternative name(s):
Argonaute RISC catalytic component 2
Eukaryotic translation initiation factor 2C 2UniRule annotation
Short name:
eIF-2C 2UniRule annotation
Short name:
eIF2C 2UniRule annotation
Piwi/argonaute family protein meIF2C2
Protein slicerUniRule annotation
Gene namesi
Name:Ago2
Synonyms:Eif2c2, Kiaa4215
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:2446632. Ago2.

Subcellular locationi

  • CytoplasmP-body UniRule annotation
  • Nucleus UniRule annotation

  • Note: Translational repression of mRNAs results in their recruitment to P-bodies. Translocation to the nucleus requires IMP8.UniRule annotation

GO - Cellular componenti

  • cytoplasm Source: MGI
  • cytoplasmic mRNA processing body Source: MGI
  • cytosol Source: MGI
  • dendrite Source: MGI
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • membrane Source: MGI
  • micro-ribonucleoprotein complex Source: UniProtKB
  • mRNA cap binding complex Source: UniProtKB
  • nucleus Source: MGI
  • polysome Source: UniProtKB
  • RISC complex Source: BHF-UCL
  • RISC-loading complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Embryonic death with a strong defect in neural tube closure and apparent cardiac failure.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 860860Protein argonaute-2PRO_0000194058Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21Nitrated tyrosineCombined sources
Modified residuei701 – 70114-hydroxyprolineUniRule annotation

Post-translational modificationi

Hydroxylated. 4-hydroxylation appears to enhance protein stability but is not required for miRNA-binding or endonuclease activity.UniRule annotation

Keywords - PTMi

Hydroxylation, Nitration

Proteomic databases

EPDiQ8CJG0.
MaxQBiQ8CJG0.
PaxDbiQ8CJG0.
PRIDEiQ8CJG0.

PTM databases

iPTMnetiQ8CJG0.
PhosphoSiteiQ8CJG0.

Expressioni

Tissue specificityi

Ubiquitous expression in 9.5 day embryos with highest levels in forebrain, heart, limb buds, and branchial arches.1 Publication

Gene expression databases

BgeeiQ8CJG0.
CleanExiMM_EIF2C2.
GenevisibleiQ8CJG0. MM.

Interactioni

Subunit structurei

Interacts with AGO1. Also interacts with DDB1, DDX5, DDX6, DDX20, DHX30, DHX36, DDX47, DHX9, EIF6, ELAVL, FXR1, GEMIN4, HNRNPF, IGF2BP1, ILF3, IMP8, MATR3, MOV10, PABPC1, PRMT5, P4HA1, P4HB, RBM4, SART3, TNRC6A, TNRC6B, UPF1 and YBX1. Interacts with the P-body components DCP1A and XRN1. Associates with polysomes and messenger ribonucleoproteins (mNRPs). Interacts with RBM4; the interaction is modulated under stress-induced conditions, occurs under both cell proliferation and differentiation conditions and in an RNA- and phosphorylation-independent manner (By similarity). Interacts with DICER1 through its Piwi domain and with TARBP2 during assembly of the RNA-induced silencing complex (RISC). Together, DICER1, AGO2 and TARBP2 constitute the trimeric RISC loading complex (RLC), or micro-RNA (miRNA) loading complex (miRLC). Within the RLC/miRLC, DICER1 and TARBP2 are required to process precursor miRNAs (pre-miRNAs) to mature miRNAs and then load them onto AGO2. AGO2 bound to the mature miRNA constitutes the minimal RISC and may subsequently dissociate from DICER1 and TARBP2. Note however that the term RISC has also been used to describe the trimeric RLC/miRLC. The formation of RISC complexes containing siRNAs rather than miRNAs appears to occur independently of DICER1. Interacts with LIMD1, WTIP and AJUBA (By similarity). Interacts with TRIM71. Interacts with APOBEC3G in an RNA-dependent manner. Interacts with APOBEC3A, APOBEC3C, APOBEC3F and APOBEC3H (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
DICER1Q9UPY32EBI-528299,EBI-395506From a different organism.
Rc3h1Q4VGL62EBI-528299,EBI-2366263

GO - Molecular functioni

Protein-protein interaction databases

BioGridi232092. 7 interactions.
DIPiDIP-35014N.
IntActiQ8CJG0. 51 interactions.
STRINGi10090.ENSMUSP00000042207.

Structurei

3D structure databases

ProteinModelPortaliQ8CJG0.
SMRiQ8CJG0. Positions 23-860.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini236 – 349114PAZUniRule annotationAdd
BLAST
Domaini518 – 819302PiwiUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni312 – 3176Interaction with guide RNABy similarity
Regioni525 – 56743Interaction with guide RNABy similarityAdd
BLAST
Regioni588 – 5914Interaction with GW182 family membersSequence analysis
Regioni651 – 66111Interaction with GW182 family membersSequence analysisAdd
BLAST
Regioni710 – 7112Interaction with guide RNABy similarity
Regioni754 – 7629Interaction with guide RNABy similarity
Regioni791 – 81323Interaction with guide RNABy similarityAdd
BLAST

Domaini

The Piwi domain may perform RNA cleavage by a mechanism similar to that of RNase H. However, while RNase H utilizes a triad of Asp-Asp-Glu (DDE) for metal ion coordination, this protein appears to utilize a triad of Asp-Asp-His (DDH).UniRule annotation

Sequence similaritiesi

Belongs to the argonaute family. Ago subfamily.UniRule annotation
Contains 1 PAZ domain.UniRule annotation
Contains 1 Piwi domain.UniRule annotation

Phylogenomic databases

eggNOGiKOG1041. Eukaryota.
ENOG410XP07. LUCA.
GeneTreeiENSGT00760000119148.
HOGENOMiHOG000116043.
HOVERGENiHBG006101.
InParanoidiQ8CJG0.
KOiK11593.
OMAiANFFEME.
OrthoDBiEOG7HHWRC.
TreeFamiTF101510.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_03031. AGO2.
InterProiIPR028602. AGO2.
IPR014811. ArgoL1.
IPR032472. ArgoL2.
IPR032473. Argonaute_Mid_dom.
IPR032474. Argonaute_N.
IPR003100. PAZ_dom.
IPR003165. Piwi.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF08699. ArgoL1. 1 hit.
PF16488. ArgoL2. 1 hit.
PF16487. ArgoMid. 1 hit.
PF16486. ArgoN. 1 hit.
PF02170. PAZ. 1 hit.
PF02171. Piwi. 1 hit.
[Graphical view]
SMARTiSM01163. DUF1785. 1 hit.
SM00949. PAZ. 1 hit.
SM00950. Piwi. 1 hit.
[Graphical view]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEiPS50821. PAZ. 1 hit.
PS50822. PIWI. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8CJG0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYSGAGPVLA SPAPTTSPIP GYAFKPPPRP DFGTTGRTIK LQANFFEMDI
60 70 80 90 100
PKIDIYHYEL DIKPEKCPRR VNREIVEHMV QHFKTQIFGD RKPVFDGRKN
110 120 130 140 150
LYTAMPLPIG RDKVELEVTL PGEGKDRIFK VSIKWVSCVS LQALHDALSG
160 170 180 190 200
RLPSVPFETI QALDVVMRHL PSMRYTPVGR SFFTASEGCS NPLGGGREVW
210 220 230 240 250
FGFHQSVRPS LWKMMLNIDV SATAFYKAQP VIEFVCEVLD FKSIEEQQKP
260 270 280 290 300
LTDSQRVKFT KEIKGLKVEI THCGQMKRKY RVCNVTRRPA SHQTFPLQQE
310 320 330 340 350
SGQTVECTVA QYFKDRHKLV LRYPHLPCLQ VGQEQKHTYL PLEVCNIVAG
360 370 380 390 400
QRCIKKLTDN QTSTMIRATA RSAPDRQEEI SKLMRSASFN TDPYVREFGI
410 420 430 440 450
MVKDEMTDVT GRVLQPPSIL YGGRNKAIAT PVQGVWDMRN KQFHTGIEIK
460 470 480 490 500
VWAIACFAPQ RQCTEVHLKS FTEQLRKISR DAGMPIQGQP CFCKYAQGAD
510 520 530 540 550
SVEPMFRHLK NTYAGLQLVV VILPGKTPVY AEVKRVGDTV LGMATQCVQM
560 570 580 590 600
KNVQRTTPQT LSNLCLKINV KLGGVNNILL PQGRPPVFQQ PVIFLGADVT
610 620 630 640 650
HPPAGDGKKP SIAAVVGSMD AHPNRYCATV RVQQHRQEII QDLAAMVREL
660 670 680 690 700
LIQFYKSTRF KPTRIIFYRD GVSEGQFQQV LHHELLAIRE ACIKLEKDYQ
710 720 730 740 750
PGITFIVVQK RHHTRLFCTD KNERVGKSGN IPAGTTVDTK ITHPTEFDFY
760 770 780 790 800
LCSHAGIQGT SRPSHYHVLW DDNRFSSDEL QILTYQLCHT YVRCTRSVSI
810 820 830 840 850
PAPAYYAHLV AFRARYHLVD KEHDSAEGSH TSGQSNGRDH QALAKAVQVH
860
QDTLRTMYFA
Length:860
Mass (Da):97,304
Last modified:July 27, 2011 - v3
Checksum:iA4E13C633846062C
GO

Sequence cautioni

The sequence AAH96465.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti65 – 651E → G in AAH96465 (PubMed:15489334).Curated
Sequence conflicti67 – 671C → R in BAC15767 (PubMed:12526743).Curated
Sequence conflicti129 – 1291F → L in BAC15767 (PubMed:12526743).Curated
Sequence conflicti360 – 3601N → D in BAC15767 (PubMed:12526743).Curated
Sequence conflicti563 – 5631N → D in AAH96465 (PubMed:15489334).Curated
Sequence conflicti711 – 7111R → P in AAH96465 (PubMed:15489334).Curated
Sequence conflicti761 – 7611S → G in BAC15767 (PubMed:12526743).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB081472 mRNA. Translation: BAC15767.1.
BC096465 mRNA. Translation: AAH96465.1. Different initiation.
BC128379 mRNA. Translation: AAI28380.1.
BC129922 mRNA. Translation: AAI29923.1.
AK220193 mRNA. Translation: BAD90378.1.
CCDSiCCDS37098.1.
RefSeqiNP_694818.3. NM_153178.4.
UniGeneiMm.23095.
Mm.391971.
Mm.440409.
Mm.476931.
Mm.486474.
Mm.490340.

Genome annotation databases

EnsembliENSMUST00000044113; ENSMUSP00000042207; ENSMUSG00000036698.
GeneIDi239528.
KEGGimmu:239528.
UCSCiuc007wbu.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB081472 mRNA. Translation: BAC15767.1.
BC096465 mRNA. Translation: AAH96465.1. Different initiation.
BC128379 mRNA. Translation: AAI28380.1.
BC129922 mRNA. Translation: AAI29923.1.
AK220193 mRNA. Translation: BAD90378.1.
CCDSiCCDS37098.1.
RefSeqiNP_694818.3. NM_153178.4.
UniGeneiMm.23095.
Mm.391971.
Mm.440409.
Mm.476931.
Mm.486474.
Mm.490340.

3D structure databases

ProteinModelPortaliQ8CJG0.
SMRiQ8CJG0. Positions 23-860.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi232092. 7 interactions.
DIPiDIP-35014N.
IntActiQ8CJG0. 51 interactions.
STRINGi10090.ENSMUSP00000042207.

PTM databases

iPTMnetiQ8CJG0.
PhosphoSiteiQ8CJG0.

Proteomic databases

EPDiQ8CJG0.
MaxQBiQ8CJG0.
PaxDbiQ8CJG0.
PRIDEiQ8CJG0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000044113; ENSMUSP00000042207; ENSMUSG00000036698.
GeneIDi239528.
KEGGimmu:239528.
UCSCiuc007wbu.2. mouse.

Organism-specific databases

CTDi27161.
MGIiMGI:2446632. Ago2.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1041. Eukaryota.
ENOG410XP07. LUCA.
GeneTreeiENSGT00760000119148.
HOGENOMiHOG000116043.
HOVERGENiHBG006101.
InParanoidiQ8CJG0.
KOiK11593.
OMAiANFFEME.
OrthoDBiEOG7HHWRC.
TreeFamiTF101510.

Enzyme and pathway databases

ReactomeiR-MMU-203927. MicroRNA (miRNA) biogenesis.
R-MMU-426486. Small interfering RNA (siRNA) biogenesis.
R-MMU-426496. Post-transcriptional silencing by small RNAs.
R-MMU-5578749. Transcriptional regulation by small RNAs.

Miscellaneous databases

PROiQ8CJG0.
SOURCEiSearch...

Gene expression databases

BgeeiQ8CJG0.
CleanExiMM_EIF2C2.
GenevisibleiQ8CJG0. MM.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_03031. AGO2.
InterProiIPR028602. AGO2.
IPR014811. ArgoL1.
IPR032472. ArgoL2.
IPR032473. Argonaute_Mid_dom.
IPR032474. Argonaute_N.
IPR003100. PAZ_dom.
IPR003165. Piwi.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF08699. ArgoL1. 1 hit.
PF16488. ArgoL2. 1 hit.
PF16487. ArgoMid. 1 hit.
PF16486. ArgoN. 1 hit.
PF02170. PAZ. 1 hit.
PF02171. Piwi. 1 hit.
[Graphical view]
SMARTiSM01163. DUF1785. 1 hit.
SM00949. PAZ. 1 hit.
SM00950. Piwi. 1 hit.
[Graphical view]
SUPFAMiSSF101690. SSF101690. 1 hit.
SSF53098. SSF53098. 1 hit.
PROSITEiPS50821. PAZ. 1 hit.
PS50822. PIWI. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Short-interfering-RNA-mediated gene silencing in mammalian cells requires Dicer and eIF2C translation initiation factors."
    Doi N., Zenno S., Ueda R., Ohki-Hamazaki H., Ui-Tei K., Saigo K.
    Curr. Biol. 13:41-46(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: B5/EGFP.
    Tissue: Trophoblast stem cell.
  3. "Prediction of the coding sequences of mouse homologues of KIAA gene. The complete nucleotide sequences of mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R.F., Ohara R., Inamoto S., Nagase T., Ohara O., Koga H.
    Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 158-860.
    Tissue: Embryonic tail.
  4. Cited for: FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
  5. "A human, ATP-independent, RISC assembly machine fueled by pre-miRNA."
    Maniataki E., Mourelatos Z.
    Genes Dev. 19:2979-2990(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DICER1 AND TARBP2.
  6. Cited for: NITRATION [LARGE SCALE ANALYSIS] AT TYR-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain.
  7. "A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway."
    O'Carroll D., Mecklenbrauker I., Das P.P., Santana A., Koenig U., Enright A.J., Miska E.A., Tarakhovsky A.
    Genes Dev. 21:1999-2004(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. "Essential and overlapping functions for mammalian Argonautes in microRNA silencing."
    Su H., Trombly M.I., Chen J., Wang X.
    Genes Dev. 23:304-317(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "The let-7 target gene mouse lin-41 is a stem cell specific E3 ubiquitin ligase for the miRNA pathway protein Ago2."
    Rybak A., Fuchs H., Hadian K., Smirnova L., Wulczyn E.A., Michel G., Nitsch R., Krappmann D., Wulczyn F.G.
    Nat. Cell Biol. 11:1411-1420(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRIM71.
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas and Spleen.
  11. "The ubiquitin ligase mLin41 temporally promotes neural progenitor cell maintenance through FGF signaling."
    Chen J., Lai F., Niswander L.
    Genes Dev. 26:803-815(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRIM71.
  12. "Trim71 cooperates with microRNAs to repress Cdkn1a expression and promote embryonic stem cell proliferation."
    Chang H.M., Martinez N.J., Thornton J.E., Hagan J.P., Nguyen K.D., Gregory R.I.
    Nat. Commun. 3:923-923(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRIM71.

Entry informationi

Entry nameiAGO2_MOUSE
AccessioniPrimary (citable) accession number: Q8CJG0
Secondary accession number(s): A1A563, Q4VAB3, Q571J6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 14, 2003
Last sequence update: July 27, 2011
Last modified: June 8, 2016
This is version 123 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Translation initiation factors
    List of translation initiation factor entries
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  3. 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.