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Protein

Exosome complex component RRP46

Gene

EXOSC5

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

Functioni

Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes.2 Publications

GO - Molecular functioni

  1. 3'-5'-exoribonuclease activity Source: UniProtKB
  2. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. defense response to virus Source: MGI
  2. DNA deamination Source: UniProtKB
  3. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: UniProtKB
  4. gene expression Source: Reactome
  5. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
  6. RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
  7. rRNA processing Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_18355. ATF4 activates genes.
REACT_20619. mRNA decay by 3' to 5' exoribonuclease.
REACT_24915. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_25042. KSRP destabilizes mRNA.
REACT_25064. Tristetraprolin (TTP) destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP46
Alternative name(s):
Chronic myelogenous leukemia tumor antigen 28
Exosome component 5
Ribosomal RNA-processing protein 46
p12B
Gene namesi
Name:EXOSC5
Synonyms:CML28, RRP46
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 19

Organism-specific databases

HGNCiHGNC:24662. EXOSC5.

Subcellular locationi

Nucleusnucleolus 1 Publication. Cytoplasm 1 Publication. Nucleus 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. cytosol Source: Reactome
  3. exosome (RNase complex) Source: UniProtKB
  4. nucleolus Source: UniProtKB
  5. nucleus Source: HPA
  6. transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134890468.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 235235Exosome complex component RRP46PRO_0000139975Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei20 – 201Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ9NQT4.
PaxDbiQ9NQT4.
PRIDEiQ9NQT4.

PTM databases

PhosphoSiteiQ9NQT4.

Expressioni

Tissue specificityi

Highly expressed in a variety of hematopoietic and epithelial tumor cell lines, but not in normal hematopoietic tissues or other normal tissue, with the exception of testis.

Gene expression databases

BgeeiQ9NQT4.
CleanExiHS_EXOSC5.
ExpressionAtlasiQ9NQT4. baseline and differential.
GenevestigatoriQ9NQT4.

Organism-specific databases

HPAiHPA053150.
HPA055677.

Interactioni

Subunit structurei

Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts with EXOSC1. Interacts with GTPBP1. Interacts with ZC3HAV1. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner.6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
EXOSC1Q9Y3B210EBI-371876,EBI-371892
EXOSC3Q9NQT57EBI-371876,EBI-371866
EXOSC8Q96B264EBI-371876,EBI-371922

Protein-protein interaction databases

BioGridi121243. 39 interactions.
DIPiDIP-29846N.
IntActiQ9NQT4. 21 interactions.
MINTiMINT-1479651.
STRINGi9606.ENSP00000221233.

Structurei

Secondary structure

1
235
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi31 – 366Combined sources
Beta strandi39 – 4911Combined sources
Beta strandi52 – 6312Combined sources
Beta strandi74 – 818Combined sources
Beta strandi83 – 853Combined sources
Helixi89 – 10517Combined sources
Helixi107 – 1093Combined sources
Beta strandi111 – 12414Combined sources
Helixi129 – 14315Combined sources
Beta strandi152 – 1598Combined sources
Beta strandi165 – 1684Combined sources
Helixi171 – 1766Combined sources
Beta strandi178 – 1869Combined sources
Turni187 – 1893Combined sources
Beta strandi194 – 2007Combined sources
Helixi203 – 23129Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35D1-235[»]
ProteinModelPortaliQ9NQT4.
SMRiQ9NQT4. Positions 25-234.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NQT4.

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiCOG0689.
GeneTreeiENSGT00550000075002.
HOGENOMiHOG000229515.
HOVERGENiHBG051520.
InParanoidiQ9NQT4.
KOiK12590.
OMAiKIFQFYR.
PhylomeDBiQ9NQT4.
TreeFamiTF315920.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Q9NQT4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEETHTDAK IRAENGTGSS PRGPGCSLRH FACEQNLLSR PDGSASFLQG
60 70 80 90 100
DTSVLAGVYG PAEVKVSKEI FNKATLEVIL RPKIGLPGVA EKSRERLIRN
110 120 130 140 150
TCEAVVLGTL HPRTSITVVL QVVSDAGSLL ACCLNAACMA LVDAGVPMRA
160 170 180 190 200
LFCGVACALD SDGTLVLDPT SKQEKEARAV LTFALDSVER KLLMSSTKGL
210 220 230
YSDTELQQCL AAAQAASQHV FRFYRESLQR RYSKS
Length:235
Mass (Da):25,249
Last modified:October 1, 2000 - v1
Checksum:iC3C1FCB39D85B1EE
GO

Sequence cautioni

The sequence AAM75154.1 differs from that shown. Reason: Erroneous initiation. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti5 – 51T → M.1 Publication
Corresponds to variant rs10853751 [ dbSNP | Ensembl ].
VAR_030788
Natural varianti33 – 331C → W.
Corresponds to variant rs34500671 [ dbSNP | Ensembl ].
VAR_051868

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281134 mRNA. Translation: AAF82135.1.
AF285785 mRNA. Translation: AAM75154.1. Different initiation.
AC011462 Genomic DNA. No translation available.
BC007742 mRNA. Translation: AAH07742.1.
BC107696 mRNA. Translation: AAI07697.1.
CCDSiCCDS12580.1.
RefSeqiNP_064543.3. NM_020158.3.
UniGeneiHs.283741.

Genome annotation databases

EnsembliENST00000221233; ENSP00000221233; ENSG00000077348.
GeneIDi56915.
KEGGihsa:56915.
UCSCiuc002oqo.3. human.

Polymorphism databases

DMDMi14285757.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF281134 mRNA. Translation: AAF82135.1.
AF285785 mRNA. Translation: AAM75154.1. Different initiation.
AC011462 Genomic DNA. No translation available.
BC007742 mRNA. Translation: AAH07742.1.
BC107696 mRNA. Translation: AAI07697.1.
CCDSiCCDS12580.1.
RefSeqiNP_064543.3. NM_020158.3.
UniGeneiHs.283741.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2NN6X-ray3.35D1-235[»]
ProteinModelPortaliQ9NQT4.
SMRiQ9NQT4. Positions 25-234.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121243. 39 interactions.
DIPiDIP-29846N.
IntActiQ9NQT4. 21 interactions.
MINTiMINT-1479651.
STRINGi9606.ENSP00000221233.

PTM databases

PhosphoSiteiQ9NQT4.

Polymorphism databases

DMDMi14285757.

Proteomic databases

MaxQBiQ9NQT4.
PaxDbiQ9NQT4.
PRIDEiQ9NQT4.

Protocols and materials databases

DNASUi56915.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000221233; ENSP00000221233; ENSG00000077348.
GeneIDi56915.
KEGGihsa:56915.
UCSCiuc002oqo.3. human.

Organism-specific databases

CTDi56915.
GeneCardsiGC19M041892.
HGNCiHGNC:24662. EXOSC5.
HPAiHPA053150.
HPA055677.
MIMi606492. gene.
neXtProtiNX_Q9NQT4.
PharmGKBiPA134890468.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0689.
GeneTreeiENSGT00550000075002.
HOGENOMiHOG000229515.
HOVERGENiHBG051520.
InParanoidiQ9NQT4.
KOiK12590.
OMAiKIFQFYR.
PhylomeDBiQ9NQT4.
TreeFamiTF315920.

Enzyme and pathway databases

ReactomeiREACT_18355. ATF4 activates genes.
REACT_20619. mRNA decay by 3' to 5' exoribonuclease.
REACT_24915. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_25042. KSRP destabilizes mRNA.
REACT_25064. Tristetraprolin (TTP) destabilizes mRNA.

Miscellaneous databases

EvolutionaryTraceiQ9NQT4.
GeneWikiiExosome_component_5.
GenomeRNAii56915.
NextBioi62403.
PROiQ9NQT4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NQT4.
CleanExiHS_EXOSC5.
ExpressionAtlasiQ9NQT4. baseline and differential.
GenevestigatoriQ9NQT4.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA], CHARACTERIZATION.
  2. "CML28 is a broadly immunogenic antigen, which is overexpressed in tumor cells."
    Yang X.-F., Wu C.J., Chen L., Alyea E.P., Canning C., Kantoff P., Soiffer R.J., Dranoff G., Ritz J.
    Cancer Res. 62:5517-5522(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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], VARIANT MET-5.
    Tissue: B-cell.
  5. "The yeast exosome and human PM-Scl are related complexes of 3'-->5' exonucleases."
    Allmang C., Petfalski E., Podtelejnikov A., Mann M., Tollervey D., Mitchell P.
    Genes Dev. 13:2148-2158(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "AU binding proteins recruit the exosome to degrade ARE-containing mRNAs."
    Chen C.-Y., Gherzi R., Ong S.-E., Chan E.L., Raijmakers R., Pruijn G.J.M., Stoecklin G., Moroni C., Mann M., Karin M.
    Cell 107:451-464(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE RNA EXOSOME CORE COMPLEX.
  7. "The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements."
    Mukherjee D., Gao M., O'Connor J.P., Raijmakers R., Pruijn G., Lutz C.S., Wilusz J.
    EMBO J. 21:165-174(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN CYTOPLASMIC MRNA DEGRADATION.
  8. "Protein-protein interactions of hCsl4p with other human exosome subunits."
    Raijmakers R., Noordman Y.E., van Venrooij W.J., Pruijn G.J.M.
    J. Mol. Biol. 315:809-818(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, INTERACTION WITH EXOSC1.
  9. "The zinc-finger antiviral protein recruits the RNA processing exosome to degrade the target mRNA."
    Guo X., Ma J., Sun J., Gao G.
    Proc. Natl. Acad. Sci. U.S.A. 104:151-156(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ZC3HAV1.
  10. "p72 DEAD box RNA helicase is required for optimal function of the zinc-finger antiviral protein."
    Chen G., Guo X., Lv F., Xu Y., Gao G.
    Proc. Natl. Acad. Sci. U.S.A. 105:4352-4357(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH DDX17.
  11. "Dis3-like 1: a novel exoribonuclease associated with the human exosome."
    Staals R.H., Bronkhorst A.W., Schilders G., Slomovic S., Schuster G., Heck A.J., Raijmakers R., Pruijn G.J.
    EMBO J. 29:2358-2367(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA EXOSOME COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  12. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-20, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  13. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates."
    Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J., Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K., Gregory R.I., Deng H., Lima C.D., Alt F.W.
    Cell 144:353-363(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DEAMINATION OF TRANSCRIBED DNA SUBSTRATE.
  15. "Modulation of exosome-mediated mRNA turnover by interaction of GTP-binding protein 1 (GTPBP1) with its target mRNAs."
    Woo K.C., Kim T.D., Lee K.H., Kim D.Y., Kim S., Lee H.R., Kang H.J., Chung S.J., Senju S., Nishimura Y., Kim K.T.
    FASEB J. 25:2757-2769(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH GTPBP1.
  16. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  17. "Reconstitution, activities, and structure of the eukaryotic RNA exosome."
    Liu Q., Greimann J.C., Lima C.D.
    Cell 127:1223-1237(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS), LACK OF CATALYTIC ACTIVITY, RECONSTITUTION OF THE RNA EXOSOME CORE COMPLEX.
  18. Erratum
    Liu Q., Greimann J.C., Lima C.D.
    Cell 131:188-189(2007)

Entry informationi

Entry nameiEXOS5_HUMAN
AccessioniPrimary (citable) accession number: Q9NQT4
Secondary accession number(s): Q32Q81, Q8NG16, Q96I89
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: October 1, 2000
Last modified: March 4, 2015
This is version 135 of the entry and version 1 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

Caution

The six exosome core subunits containing a RNase PH-domain are not phosphorolytically active.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: 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

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.