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

Histone H2A type 1-A

Gene

HIST1H2AA

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

Functioni

Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-3214815. HDACs deacetylate histones.
R-HSA-3214847. HATs acetylate histones.
R-HSA-3214858. RMTs methylate histone arginines.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone H2A type 1-A
Alternative name(s):
Histone H2A/r
Gene namesi
Name:HIST1H2AA
Synonyms:H2AFR
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:18729. HIST1H2AA.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • nuclear chromatin Source: GO_Central
  • nuclear chromosome, telomeric region Source: BHF-UCL
  • nucleosome Source: UniProtKB-KW
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleosome core, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi2 – 21S → A: Blocks the inhibition of transcription by RPS6KA5/MSK1. 1 Publication

Organism-specific databases

PharmGKBiPA134988774.

Polymorphism and mutation databases

BioMutaiHIST1H2AA.
DMDMi74752099.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 131130Histone H2A type 1-APRO_0000230199Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication
Modified residuei2 – 21Phosphoserine; by RPS6KA51 Publication
Modified residuei4 – 41Citrulline; alternate1 Publication
Modified residuei4 – 41Symmetric dimethylarginine; by PRMT5; alternateBy similarity
Modified residuei6 – 61N6-acetyllysineBy similarity
Cross-linki14 – 14Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki16 – 16Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Modified residuei37 – 371N6-crotonyllysine1 Publication
Modified residuei105 – 1051N5-methylglutamine1 Publication
Modified residuei119 – 1191N6-crotonyllysine1 Publication
Modified residuei120 – 1201N6-crotonyllysine; alternate1 Publication
Cross-linki120 – 120Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate4 Publications
Modified residuei121 – 1211Phosphothreonine; by VPRBP2 Publications
Modified residuei123 – 1231PhosphoserineBy similarity
Modified residuei127 – 1271N6-crotonyllysine1 Publication

Post-translational modificationi

Deiminated on Arg-4 in granulocytes upon calcium entry.1 Publication
Monoubiquitination of Lys-120 (H2AK119Ub) by RING1, TRIM27 and RNF2/RING2 complex gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. It is involved in the initiation of both imprinted and random X inactivation. Ubiquitinated H2A is enriched in inactive X chromosome chromatin. Ubiquitination of H2A functions downstream of methylation of 'Lys-27' of histone H3 (H3K27me). H2AK119Ub by RNF2/RING2 can also be induced by ultraviolet and may be involved in DNA repair. Monoubiquitination of Lys-120 (H2AK119Ub) by TRIM27 may promote transformation of cells in a number of breast cancers (PubMed:25470042). Following DNA double-strand breaks (DSBs), it is ubiquitinated through 'Lys-63' linkage of ubiquitin moieties by the E2 ligase UBE2N and the E3 ligases RNF8 and RNF168, leading to the recruitment of repair proteins to sites of DNA damage. Ubiquitination at Lys-14 and Lys-16 (H2AK13Ub and H2AK15Ub, respectively) in response to DNA damage is initiated by RNF168 that mediates monoubiquitination at these 2 sites, and 'Lys-63'-linked ubiquitin are then conjugated to monoubiquitin; RNF8 is able to extend 'Lys-63'-linked ubiquitin chains in vitro. H2AK119Ub and ionizing radiation-induced 'Lys-63'-linked ubiquitination (H2AK13Ub and H2AK15Ub) are distinct events.11 Publications
Phosphorylation on Ser-2 (H2AS1ph) is enhanced during mitosis. Phosphorylation on Ser-2 by RPS6KA5/MSK1 directly represses transcription. Acetylation of H3 inhibits Ser-2 phosphorylation by RPS6KA5/MSK1. Phosphorylation at Thr-121 (H2AT120ph) by VPRBP is present in the regulatory region of many tumor suppresor genes and down-regulates their transcription.4 Publications
Glutamine methylation at Gln-105 (H2AQ104me) by FBL is specifically dedicated to polymerase I. It is present at 35S ribosomal DNA locus and impairs binding of the FACT complex (PubMed:24352239).1 Publication
Symmetric dimethylation on Arg-4 by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.By similarity
Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.1 Publication

Keywords - PTMi

Acetylation, Citrullination, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ96QV6.
PaxDbiQ96QV6.
PRIDEiQ96QV6.
TopDownProteomicsiQ96QV6.

PTM databases

iPTMnetiQ96QV6.
PhosphoSiteiQ96QV6.
SwissPalmiQ96QV6.

Expressioni

Gene expression databases

BgeeiQ96QV6.
CleanExiHS_HIST1H2AA.

Organism-specific databases

HPAiHPA041189.

Interactioni

Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

Protein-protein interaction databases

BioGridi128742. 18 interactions.
DIPiDIP-43896N.
IntActiQ96QV6. 9 interactions.
MINTiMINT-3057462.
STRINGi9606.ENSP00000297012.

Structurei

3D structure databases

ProteinModelPortaliQ96QV6.
SMRiQ96QV6. Positions 16-116.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the histone H2A family.Curated

Phylogenomic databases

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
GeneTreeiENSGT00760000118934.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiQ96QV6.
KOiK11251.
OMAiGHYSKRV.
OrthoDBiEOG7M0NTR.
PhylomeDBiQ96QV6.
TreeFamiTF300137.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q96QV6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGRGKQGGK ARAKSKSRSS RAGLQFPVGR IHRLLRKGNY AERIGAGAPV
60 70 80 90 100
YLAAVLEYLT AEILELAGNA SRDNKKTRII PRHLQLAIRN DEELNKLLGG
110 120 130
VTIAQGGVLP NIQAVLLPKK TESHHHKAQS K
Length:131
Mass (Da):14,234
Last modified:January 23, 2007 - v3
Checksum:iD7E5D3D43BD84D32
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY131982 Genomic DNA. Translation: AAN59963.1.
AL512384 Genomic DNA. Translation: CAC44614.1.
BC062211 mRNA. Translation: AAH62211.1.
CCDSiCCDS4562.1.
RefSeqiNP_734466.1. NM_170745.3.
UniGeneiHs.406739.

Genome annotation databases

EnsembliENST00000297012; ENSP00000297012; ENSG00000164508.
GeneIDi221613.
KEGGihsa:221613.
UCSCiuc003nfc.4. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY131982 Genomic DNA. Translation: AAN59963.1.
AL512384 Genomic DNA. Translation: CAC44614.1.
BC062211 mRNA. Translation: AAH62211.1.
CCDSiCCDS4562.1.
RefSeqiNP_734466.1. NM_170745.3.
UniGeneiHs.406739.

3D structure databases

ProteinModelPortaliQ96QV6.
SMRiQ96QV6. Positions 16-116.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128742. 18 interactions.
DIPiDIP-43896N.
IntActiQ96QV6. 9 interactions.
MINTiMINT-3057462.
STRINGi9606.ENSP00000297012.

PTM databases

iPTMnetiQ96QV6.
PhosphoSiteiQ96QV6.
SwissPalmiQ96QV6.

Polymorphism and mutation databases

BioMutaiHIST1H2AA.
DMDMi74752099.

Proteomic databases

EPDiQ96QV6.
PaxDbiQ96QV6.
PRIDEiQ96QV6.
TopDownProteomicsiQ96QV6.

Protocols and materials databases

DNASUi221613.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000297012; ENSP00000297012; ENSG00000164508.
GeneIDi221613.
KEGGihsa:221613.
UCSCiuc003nfc.4. human.

Organism-specific databases

CTDi221613.
GeneCardsiHIST1H2AA.
HGNCiHGNC:18729. HIST1H2AA.
HPAiHPA041189.
MIMi613499. gene.
neXtProtiNX_Q96QV6.
PharmGKBiPA134988774.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1756. Eukaryota.
COG5262. LUCA.
GeneTreeiENSGT00760000118934.
HOGENOMiHOG000234652.
HOVERGENiHBG009342.
InParanoidiQ96QV6.
KOiK11251.
OMAiGHYSKRV.
OrthoDBiEOG7M0NTR.
PhylomeDBiQ96QV6.
TreeFamiTF300137.

Enzyme and pathway databases

ReactomeiR-HSA-3214815. HDACs deacetylate histones.
R-HSA-3214847. HATs acetylate histones.
R-HSA-3214858. RMTs methylate histone arginines.

Miscellaneous databases

GeneWikiiHIST1H2AA.
GenomeRNAii221613.
NextBioi91401.
PROiQ96QV6.
SOURCEiSearch...

Gene expression databases

BgeeiQ96QV6.
CleanExiHS_HIST1H2AA.

Family and domain databases

Gene3Di1.10.20.10. 1 hit.
InterProiIPR009072. Histone-fold.
IPR002119. Histone_H2A.
IPR007125. Histone_H2A/H2B/H3.
IPR032454. Histone_H2A_C.
IPR032458. Histone_H2A_CS.
[Graphical view]
PfamiPF00125. Histone. 1 hit.
PF16211. Histone_H2A_C. 1 hit.
[Graphical view]
PRINTSiPR00620. HISTONEH2A.
SMARTiSM00414. H2A. 1 hit.
[Graphical view]
SUPFAMiSSF47113. SSF47113. 1 hit.
PROSITEiPS00046. HISTONE_H2A. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The human and mouse replication-dependent histone genes."
    Marzluff W.F., Gongidi P., Woods K.R., Jin J., Maltais L.J.
    Genomics 80:487-498(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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: Testis.
  4. "Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo."
    Aihara H., Nakagawa T., Yasui K., Ohta T., Hirose S., Dhomae N., Takio K., Kaneko M., Takeshima Y., Muramatsu M., Ito T.
    Genes Dev. 18:877-888(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-121.
  5. "Phosphorylation of histone H2A inhibits transcription on chromatin templates."
    Zhang Y., Griffin K., Mondal N., Parvin J.D.
    J. Biol. Chem. 279:21866-21872(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT SER-2, MUTAGENESIS OF SER-2.
  6. "Role of histone H2A ubiquitination in Polycomb silencing."
    Wang H., Wang L., Erdjument-Bromage H., Vidal M., Tempst P., Jones R.S., Zhang Y.
    Nature 431:873-878(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-120.
  7. "Deimination of histone H2A and H4 at arginine 3 in HL-60 granulocytes."
    Hagiwara T., Hidaka Y., Yamada M.
    Biochemistry 44:5827-5834(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION AT SER-2, CITRULLINATION AT ARG-4, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Role of Bmi-1 and Ring1A in H2A ubiquitylation and Hox gene silencing."
    Cao R., Tsukada Y., Zhang Y.
    Mol. Cell 20:845-854(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-120.
  9. Cited for: UBIQUITINATION AT LYS-120.
  10. "RNF8 ubiquitylates histones at DNA double-strand breaks and promotes assembly of repair proteins."
    Mailand N., Bekker-Jensen S., Faustrup H., Melander F., Bartek J., Lukas C., Lukas J.
    Cell 131:887-900(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  11. "RNF8 transduces the DNA-damage signal via histone ubiquitylation and checkpoint protein assembly."
    Huen M.S.Y., Grant R., Manke I., Minn K., Yu X., Yaffe M.B., Chen J.
    Cell 131:901-914(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  12. Cited for: UBIQUITINATION.
  13. "RNF168 binds and amplifies ubiquitin conjugates on damaged chromosomes to allow accumulation of repair proteins."
    Doil C., Mailand N., Bekker-Jensen S., Menard P., Larsen D.H., Pepperkok R., Ellenberg J., Panier S., Durocher D., Bartek J., Lukas J., Lukas C.
    Cell 136:435-446(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION.
  14. "Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification."
    Tan M., Luo H., Lee S., Jin F., Yang J.S., Montellier E., Buchou T., Cheng Z., Rousseaux S., Rajagopal N., Lu Z., Ye Z., Zhu Q., Wysocka J., Ye Y., Khochbin S., Ren B., Zhao Y.
    Cell 146:1016-1028(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: CROTONYLATION AT LYS-37; LYS-119; LYS-120 AND LYS-127.
  15. "RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA Damage signaling."
    Mattiroli F., Vissers J.H., van Dijk W.J., Ikpa P., Citterio E., Vermeulen W., Marteijn J.A., Sixma T.K.
    Cell 150:1182-1195(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-14 AND LYS-16 BY RNF168.
  16. "A novel ubiquitin mark at the N-terminal tail of histone H2As targeted by RNF168 ubiquitin ligase."
    Gatti M., Pinato S., Maspero E., Soffientini P., Polo S., Penengo L.
    Cell Cycle 11:2538-2544(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-14 AND LYS-16 BY RNF168.
  17. "VprBP has intrinsic kinase activity targeting histone H2A and represses gene transcription."
    Kim K., Kim J.M., Kim J.S., Choi J., Lee Y.S., Neamati N., Song J.S., Heo K., An W.
    Mol. Cell 52:459-467(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION AT THR-121.
  18. "Glutamine methylation in histone H2A is an RNA-polymerase-I-dedicated modification."
    Tessarz P., Santos-Rosa H., Robson S.C., Sylvestersen K.B., Nelson C.J., Nielsen M.L., Kouzarides T.
    Nature 505:564-568(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: METHYLATION AT GLN-105.
  19. "TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein."
    Bhatnagar S., Gazin C., Chamberlain L., Ou J., Zhu X., Tushir J.S., Virbasius C.M., Lin L., Zhu L.J., Wajapeyee N., Green M.R.
    Nature 516:116-120(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-120.

Entry informationi

Entry nameiH2A1A_HUMAN
AccessioniPrimary (citable) accession number: Q96QV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: January 23, 2007
Last modified: April 13, 2016
This is version 130 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) 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.