Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

60S ribosomal protein L13a

Gene

RPL13A

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

Functioni

Associated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA.4 Publications

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB
  • structural constituent of ribosome Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Biological processi

Translation regulation

Enzyme and pathway databases

ReactomeiREACT_115902. SRP-dependent cotranslational protein targeting to membrane.
REACT_1404. Peptide chain elongation.
REACT_1797. Formation of a pool of free 40S subunits.
REACT_1986. Eukaryotic Translation Termination.
REACT_2085. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_79. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_9491. Viral mRNA Translation.

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L13a
Alternative name(s):
23 kDa highly basic protein
Gene namesi
Name:RPL13A
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:10304. RPL13A.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: Reactome
  • cytosolic large ribosomal subunit Source: UniProtKB
  • focal adhesion Source: UniProtKB
  • GAIT complex Source: UniProtKB
  • large ribosomal subunit Source: ProtInc
  • membrane Source: UniProtKB
  • nucleolus Source: UniProtKB
  • nucleus Source: UniProtKB
  • ribonucleoprotein complex Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi77 – 771S → A: Loss of interferon-gamma induced phosphorylation. 1 Publication

Organism-specific databases

PharmGKBiPA38122.

Polymorphism and mutation databases

BioMutaiRPL13A.
DMDMi730451.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed5 Publications
Chaini2 – 20320260S ribosomal protein L13aPRO_0000133769Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine5 Publications
Modified residuei59 – 591CitrullineBy similarity
Modified residuei77 – 771Phosphoserine; by ZIPK/DAPK31 Publication
Modified residuei140 – 1401CitrullineBy similarity
Modified residuei191 – 1911N6-acetyllysine1 Publication

Post-translational modificationi

Phosphorylation at Ser-77 upon interferon-gamma treatment in monocytes involves a DAPK1-DAPK3 kinase cascade and is causing release from the ribosome, association with the GAIT complex and subsequent involvement in transcript-selective translation inhibition.2 Publications
Citrullinated by PADI4.By similarity

Keywords - PTMi

Acetylation, Citrullination, Phosphoprotein

Proteomic databases

MaxQBiP40429.
PaxDbiP40429.
PRIDEiP40429.

PTM databases

PhosphoSiteiP40429.

Expressioni

Gene expression databases

BgeeiP40429.
CleanExiHS_RPL13A.
ExpressionAtlasiP40429. baseline.
GenevisibleiP40429. HS.

Organism-specific databases

HPAiHPA038751.

Interactioni

Subunit structurei

Component of the 60S ribosome. Component of the GAIT complex. Interacts with EIF4G1.3 Publications

Protein-protein interaction databases

BioGridi117068. 49 interactions.
IntActiP40429. 24 interactions.
MINTiMINT-1417412.
STRINGi9606.ENSP00000375730.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V6Xelectron microscopy5.00CO1-203[»]
ProteinModelPortaliP40429.
SMRiP40429. Positions 7-146.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L13P family.Curated

Phylogenomic databases

eggNOGiCOG0102.
GeneTreeiENSGT00390000010799.
HOGENOMiHOG000225289.
HOVERGENiHBG062176.
InParanoidiP40429.
KOiK02872.
OrthoDBiEOG7H1JMP.
PhylomeDBiP40429.
TreeFamiTF300159.

Family and domain databases

Gene3Di3.90.1180.10. 1 hit.
HAMAPiMF_01366. Ribosomal_L13.
InterProiIPR005822. Ribosomal_L13.
IPR023563. Ribosomal_L13_CS.
IPR023564. Ribosomal_L13_dom.
IPR005755. Ribosomal_L13_euk/arc.
[Graphical view]
PANTHERiPTHR11545. PTHR11545. 1 hit.
PTHR11545:SF3. PTHR11545:SF3. 1 hit.
PfamiPF00572. Ribosomal_L13. 1 hit.
[Graphical view]
SUPFAMiSSF52161. SSF52161. 1 hit.
TIGRFAMsiTIGR01077. L13_A_E. 1 hit.
PROSITEiPS00783. RIBOSOMAL_L13. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P40429-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEVQVLVLD GRGHLLGRLA AIVAKQVLLG RKVVVVRCEG INISGNFYRN
60 70 80 90 100
KLKYLAFLRK RMNTNPSRGP YHFRAPSRIF WRTVRGMLPH KTKRGQAALD
110 120 130 140 150
RLKVFDGIPP PYDKKKRMVV PAALKVVRLK PTRKFAYLGR LAHEVGWKYQ
160 170 180 190 200
AVTATLEEKR KEKAKIHYRK KKQLMRLRKQ AEKNVEKKID KYTEVLKTHG

LLV
Length:203
Mass (Da):23,577
Last modified:January 23, 2007 - v2
Checksum:i3E80D0AB77A0D406
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56932 mRNA. Translation: CAA40254.1.
AB028893 Genomic DNA. Translation: BAA88214.1.
AK291120 mRNA. Translation: BAF83809.1.
CH471177 Genomic DNA. Translation: EAW52495.1.
BC000514 mRNA. Translation: AAH00514.1.
BC001675 mRNA. Translation: AAH01675.1.
BC001836 mRNA. Translation: AAH01836.1.
BC062537 mRNA. Translation: AAH62537.1.
BC065236 mRNA. Translation: AAH65236.1.
BC070223 mRNA. Translation: AAH70223.1.
BC071929 mRNA. Translation: AAH71929.1.
CCDSiCCDS12768.1.
PIRiS29539.
RefSeqiNP_001257420.1. NM_001270491.1.
NP_036555.1. NM_012423.3.
UniGeneiHs.523185.

Genome annotation databases

EnsembliENST00000391857; ENSP00000375730; ENSG00000142541.
GeneIDi23521.
KEGGihsa:23521.
UCSCiuc002pny.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56932 mRNA. Translation: CAA40254.1.
AB028893 Genomic DNA. Translation: BAA88214.1.
AK291120 mRNA. Translation: BAF83809.1.
CH471177 Genomic DNA. Translation: EAW52495.1.
BC000514 mRNA. Translation: AAH00514.1.
BC001675 mRNA. Translation: AAH01675.1.
BC001836 mRNA. Translation: AAH01836.1.
BC062537 mRNA. Translation: AAH62537.1.
BC065236 mRNA. Translation: AAH65236.1.
BC070223 mRNA. Translation: AAH70223.1.
BC071929 mRNA. Translation: AAH71929.1.
CCDSiCCDS12768.1.
PIRiS29539.
RefSeqiNP_001257420.1. NM_001270491.1.
NP_036555.1. NM_012423.3.
UniGeneiHs.523185.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4V6Xelectron microscopy5.00CO1-203[»]
ProteinModelPortaliP40429.
SMRiP40429. Positions 7-146.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117068. 49 interactions.
IntActiP40429. 24 interactions.
MINTiMINT-1417412.
STRINGi9606.ENSP00000375730.

PTM databases

PhosphoSiteiP40429.

Polymorphism and mutation databases

BioMutaiRPL13A.
DMDMi730451.

Proteomic databases

MaxQBiP40429.
PaxDbiP40429.
PRIDEiP40429.

Protocols and materials databases

DNASUi23521.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000391857; ENSP00000375730; ENSG00000142541.
GeneIDi23521.
KEGGihsa:23521.
UCSCiuc002pny.4. human.

Organism-specific databases

CTDi23521.
GeneCardsiGC19P049991.
H-InvDBHIX0027968.
HIX0158081.
HGNCiHGNC:10304. RPL13A.
HPAiHPA038751.
neXtProtiNX_P40429.
PharmGKBiPA38122.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0102.
GeneTreeiENSGT00390000010799.
HOGENOMiHOG000225289.
HOVERGENiHBG062176.
InParanoidiP40429.
KOiK02872.
OrthoDBiEOG7H1JMP.
PhylomeDBiP40429.
TreeFamiTF300159.

Enzyme and pathway databases

ReactomeiREACT_115902. SRP-dependent cotranslational protein targeting to membrane.
REACT_1404. Peptide chain elongation.
REACT_1797. Formation of a pool of free 40S subunits.
REACT_1986. Eukaryotic Translation Termination.
REACT_2085. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_79. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_9491. Viral mRNA Translation.

Miscellaneous databases

ChiTaRSiRPL13A. human.
GeneWikiiRPL13A.
GenomeRNAii23521.
NextBioi45973.
PROiP40429.

Gene expression databases

BgeeiP40429.
CleanExiHS_RPL13A.
ExpressionAtlasiP40429. baseline.
GenevisibleiP40429. HS.

Family and domain databases

Gene3Di3.90.1180.10. 1 hit.
HAMAPiMF_01366. Ribosomal_L13.
InterProiIPR005822. Ribosomal_L13.
IPR023563. Ribosomal_L13_CS.
IPR023564. Ribosomal_L13_dom.
IPR005755. Ribosomal_L13_euk/arc.
[Graphical view]
PANTHERiPTHR11545. PTHR11545. 1 hit.
PTHR11545:SF3. PTHR11545:SF3. 1 hit.
PfamiPF00572. Ribosomal_L13. 1 hit.
[Graphical view]
SUPFAMiSSF52161. SSF52161. 1 hit.
TIGRFAMsiTIGR01077. L13_A_E. 1 hit.
PROSITEiPS00783. RIBOSOMAL_L13. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Conservation of a 23-kDa human transplantation antigen in mammalian species."
    Price S.R., Nightingale M.S., Bobak D.A., Tsuchiya M., Moss J., Vaughan M.
    Genomics 14:959-964(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome."
    Higa S., Yoshihama M., Tanaka T., Kenmochi N.
    Gene 240:371-377(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "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].
    Tissue: Lung, Lymph, Muscle, Pancreas and Skin.
  6. Bienvenut W.V., Waridel P., Quadroni M.
    Submitted (MAR-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 2-12; 38-49; 104-115 AND 135-159, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Cervix carcinoma.
  7. "Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control."
    Mazumder B., Sampath P., Seshadri V., Maitra R.K., DiCorleto P.E., Fox P.L.
    Cell 115:187-198(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, PHOSPHORYLATION.
  8. "Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing."
    Odintsova T.I., Muller E.C., Ivanov A.V., Egorov T.A., Bienert R., Vladimirov S.N., Kostka S., Otto A., Wittmann-Liebold B., Karpova G.G.
    J. Protein Chem. 22:249-258(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY.
  9. "Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation."
    Sampath P., Mazumder B., Seshadri V., Gerber C.A., Chavatte L., Kinter M., Ting S.M., Dignam J.D., Kim S., Driscoll D.M., Fox P.L.
    Cell 119:195-208(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE GAIT COMPLEX.
  10. "L13a blocks 48S assembly: role of a general initiation factor in mRNA-specific translational control."
    Kapasi P., Chaudhuri S., Vyas K., Baus D., Komar A.A., Fox P.L., Merrick W.C., Mazumder B.
    Mol. Cell 25:113-126(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH EIF4G1.
  11. "Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation."
    Chaudhuri S., Vyas K., Kapasi P., Komar A.A., Dinman J.D., Barik S., Mazumder B.
    RNA 13:2224-2237(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression."
    Mukhopadhyay R., Ray P.S., Arif A., Brady A.K., Kinter M., Fox P.L.
    Mol. Cell 32:371-382(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-77, MUTAGENESIS OF SER-77.
  13. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
    Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
    Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  14. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-191, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  16. "Heterotrimeric GAIT complex drives transcript-selective translation inhibition in murine macrophages."
    Arif A., Chatterjee P., Moodt R.A., Fox P.L.
    Mol. Cell. Biol. 32:5046-5055(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, RECONSTITUTION OF THE GAIT COMPLEX.
  17. "Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
    Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
    Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  18. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
  19. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (5.0 ANGSTROMS) OF 80S RIBOSOME.

Entry informationi

Entry nameiRL13A_HUMAN
AccessioniPrimary (citable) accession number: P40429
Secondary accession number(s): A8K505
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 145 of the entry and version 2 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 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.