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Protein

Retinoic acid-induced protein 1

Gene

RAI1

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

Functioni

Transcriptional regulator of the circadian clock components: CLOCK, ARNTL/BMAL1, ARNTL2/BMAL2, PER1/3, CRY1/2, NR1D1/2 and RORA/C. Positively regulates the transcriptional activity of CLOCK a core component of the circadian clock. Regulates transcription through chromatin remodeling by interacting with other proteins in chromatin as well as proteins in the basic transcriptional machinery. May be important for embryonic and postnatal development. May be involved in neuronal differentiation.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1780 – 1835C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST56
Zinc fingeri1855 – 1903PHD-typePROSITE-ProRule annotationAdd BLAST49

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Biological rhythms

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-400253. Circadian Clock.

Names & Taxonomyi

Protein namesi
Recommended name:
Retinoic acid-induced protein 1
Gene namesi
Name:RAI1
Synonyms:KIAA1820
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:9834. RAI1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Involvement in diseasei

Smith-Magenis syndrome (SMS)2 Publications
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionCharacterized by congenital mental retardation associated with development and growth delays. Affected persons have characteristic behavioral abnormalities, including self-injurious behaviors and sleep disturbance, and distinct craniofacial and skeletal anomalies.
See also OMIM:182290

Organism-specific databases

DisGeNETi10743.
MalaCardsiRAI1.
MIMi182290. phenotype.
OpenTargetsiENSG00000108557.
Orphaneti1713. 17p11.2 microduplication syndrome.
819. Smith-Magenis syndrome.
PharmGKBiPA34188.

Polymorphism and mutation databases

BioMutaiRAI1.
DMDMi50400978.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000971591 – 1906Retinoic acid-induced protein 1Add BLAST1906

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei339PhosphoserineCombined sources1
Modified residuei345PhosphoserineCombined sources1
Modified residuei472PhosphothreonineCombined sources1
Modified residuei568PhosphoserineCombined sources1
Modified residuei683PhosphoserineCombined sources1
Modified residuei696PhosphothreonineCombined sources1
Modified residuei805PhosphoserineCombined sources1
Cross-linki819Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Modified residuei880PhosphoserineCombined sources1
Modified residuei892PhosphoserineCombined sources1
Cross-linki901Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)Combined sources
Cross-linki901Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei1064PhosphoserineCombined sources1
Modified residuei1068PhosphothreonineCombined sources1
Modified residuei1122PhosphoserineCombined sources1
Modified residuei1352PhosphoserineCombined sources1
Modified residuei1358PhosphoserineCombined sources1
Modified residuei1374PhosphoserineCombined sources1
Modified residuei1431PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ7Z5J4.
MaxQBiQ7Z5J4.
PaxDbiQ7Z5J4.
PeptideAtlasiQ7Z5J4.
PRIDEiQ7Z5J4.

PTM databases

iPTMnetiQ7Z5J4.
PhosphoSitePlusiQ7Z5J4.

Expressioni

Tissue specificityi

Expressed in all tissues examined with higher expression in the heart and brain. No expression was seen in the corpus callosum of the brain.1 Publication

Gene expression databases

BgeeiENSG00000108557.
CleanExiHS_RAI1.
ExpressionAtlasiQ7Z5J4. baseline and differential.
GenevisibleiQ7Z5J4. HS.

Organism-specific databases

HPAiHPA023898.
HPA054906.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
PIN1Q135264EBI-743815,EBI-714158

Protein-protein interaction databases

BioGridi115966. 25 interactors.
IntActiQ7Z5J4. 17 interactors.
MINTiMINT-1477867.
STRINGi9606.ENSP00000323074.

Structurei

3D structure databases

ProteinModelPortaliQ7Z5J4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1160 – 1177Nuclear localization signalSequence analysisAdd BLAST18
Motifi1223 – 1240Nuclear localization signalSequence analysisAdd BLAST18

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi124 – 135Poly-ProAdd BLAST12
Compositional biasi156 – 336Gln-richAdd BLAST181
Compositional biasi278 – 291Poly-GlnAdd BLAST14
Compositional biasi1243 – 1249Poly-Ser7
Compositional biasi1493 – 1496Poly-Gly4
Compositional biasi1628 – 1641Ser-richAdd BLAST14
Compositional biasi1746 – 1751Poly-Ala6

Sequence similaritiesi

Contains 1 C2HC pre-PHD-type zinc finger.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1780 – 1835C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST56
Zinc fingeri1855 – 1903PHD-typePROSITE-ProRule annotationAdd BLAST49

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410IJJX. Eukaryota.
ENOG410Z8S8. LUCA.
GeneTreeiENSGT00530000063684.
HOVERGENiHBG056862.
InParanoidiQ7Z5J4.
KOiK19749.
OMAiQNLHAYQ.
OrthoDBiEOG091G008I.
PhylomeDBiQ7Z5J4.
TreeFamiTF331317.

Family and domain databases

InterProiIPR001965. Znf_PHD.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
PROSITEiPS51805. EPHD. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q7Z5J4-1) [UniParc]FASTAAdd to basket

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
MQSFRERCGF HGKQQNYQQT SQETSRLENY RQPSQAGLSC DRQRLLAKDY
60 70 80 90 100
YNPQPYPSYE GGAGTPSGTA AAVAADKYHR GSKALPTQQG LQGRPAFPGY
110 120 130 140 150
GVQDSSPYPG RYAGEESLQA WGAPQPPPPQ PQPLPAGVAK YDENLMKKTA
160 170 180 190 200
VPPSRQYAEQ GAQVPFRTHS LHVQQPPPPQ QPLAYPKLQR QKLQNDIASP
210 220 230 240 250
LPFPQGTHFP QHSQSFPTSS TYSSSVQGGG QGAHSYKSCT APTAQPHDRP
260 270 280 290 300
LTASSSLAPG QRVQNLHAYQ SGRLSYDQQQ QQQQQQQQQQ QALQSRHHAQ
310 320 330 340 350
ETLHYQNLAK YQHYGQQGQG YCQPDAAVRT PEQYYQTFSP SSSHSPARSV
360 370 380 390 400
GRSPSYSSTP SPLMPNLENF PYSQQPLSTG AFPAGITDHS HFMPLLNPSP
410 420 430 440 450
TDATSSVDTQ AGNCKPLQKD KLPENLLSDL SLQSLTALTS QVENISNTVQ
460 470 480 490 500
QLLLSKAAVP QKKGVKNLVS RTPEQHKSQH CSPEGSGYSA EPAGTPLSEP
510 520 530 540 550
PSSTPQSTHA EPQEADYLSG SEDPLERSFL YCNQARGSPA RVNSNSKAKP
560 570 580 590 600
ESVSTCSVTS PDDMSTKSDD SFQSLHGSLP LDSFSKFVAG ERDCPRLLLS
610 620 630 640 650
ALAQEDLASE ILGLQEAIGE KADKAWAEAP SLVKDSSKPP FSLENHSACL
660 670 680 690 700
DSVAKSAWPR PGEPEALPDS LQLDKGGNAK DFSPGLFEDP SVAFATPDPK
710 720 730 740 750
KTTGPLSFGT KPTLGVPAPD PTTAAFDCFP DTTAASSADS ANPFAWPEEN
760 770 780 790 800
LGDACPRWGL HPGELTKGLE QGGKASDGIS KGDTHEASAC LGFQEEDPPG
810 820 830 840 850
EKVASLPGDF KQEEVGGVKE EAGGLLQCPE VAKADRWLED SRHCCSTADF
860 870 880 890 900
GDLPLLPPTS RKEDLEAEEE YSSLCELLGS PEQRPGMQDP LSPKAPLICT
910 920 930 940 950
KEEVEEVLDS KAGWGSPCHL SGESVILLGP TVGTESKVQS WFESSLSHMK
960 970 980 990 1000
PGEEGPDGER APGDSTTSDA SLAQKPNKPA VPEAPIAKKE PVPRGKSLRS
1010 1020 1030 1040 1050
RRVHRGLPEA EDSPCRAPVL PKDLLLPESC TGPPQGQMEG AGAPGRGASE
1060 1070 1080 1090 1100
GLPRMCTRSL TALSEPRTPG PPGLTTTPAP PDKLGGKQRA AFKSGKRVGK
1110 1120 1130 1140 1150
PSPKAASSPS NPAALPVASD SSPMGSKTKE TDSPSTPGKD QRSMILRSRT
1160 1170 1180 1190 1200
KTQEIFHSKR RRPSEGRLPN CRATKKLLDN SHLPATFKVS SSPQKEGRVS
1210 1220 1230 1240 1250
QRARVPKPGA GSKLSDRPLH ALKRKSAFMA PVPTKKRNLV LRSRSSSSSN
1260 1270 1280 1290 1300
ASGNGGDGKE ERPEGSPTLF KRMSSPKKAK PTKGNGEPAT KLPPPETPDA
1310 1320 1330 1340 1350
CLKLASRAAF QGAMKTKVLP PRKGRGLKLE AIVQKITSPS LKKFACKAPG
1360 1370 1380 1390 1400
ASPGNPLSPS LSDKDRGLKG AGGSPVGVEE GLVNVGTGQK LPTSGADPLC
1410 1420 1430 1440 1450
RNPTNRSLKG KLMNSKKLSS TDCFKTEAFT SPEALQPGGT ALAPKKRSRK
1460 1470 1480 1490 1500
GRAGAHGLSK GPLEKRPYLG PALLLTPRDR ASGTQGASED NSGGGGKKPK
1510 1520 1530 1540 1550
MEELGLASQP PEGRPCQPQT RAQKQPGHTN YSSYSKRKRL TRGRAKNTTS
1560 1570 1580 1590 1600
SPCKGRAKRR RQQQVLPLDP AEPEIRLKYI SSCKRLRSDS RTPAFSPFVR
1610 1620 1630 1640 1650
VEKRDAFTTI CTVVNSPGDA PKPHRKPSSS ASSSSSSSSF SLDAAGASLA
1660 1670 1680 1690 1700
TLPGGSILQP RPSLPLSSTM HLGPVVSKAL STSCLVCCLC QNPANFKDLG
1710 1720 1730 1740 1750
DLCGPYYPEH CLPKKKPKLK EKVRPEGTCE EASLPLERTL KGPECAAAAT
1760 1770 1780 1790 1800
AGKPPRPDGP ADPAKQGPLR TSARGLSRRL QSCYCCDGRE DGGEEAAPAD
1810 1820 1830 1840 1850
KGRKHECSKE APAEPGGEAQ EHWVHEACAV WTGGVYLVAG KLFGLQEAMK
1860 1870 1880 1890 1900
VAVDMMCSSC QEAGATIGCC HKGCLHTYHY PCASDAGCIF IEENFSLKCP

KHKRLP
Length:1,906
Mass (Da):203,352
Last modified:July 19, 2004 - v2
Checksum:i8D33A56C33BFE888
GO
Isoform 2 (identifier: Q7Z5J4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     207-233: THFPQHSQSFPTSSTYSSSVQGGGQGA → WWAGG
     407-434: VDTQAGNCKPLQKDKLPENLLSDLSLQS → PAD
     1415-1479: Missing.
     1803-1821: Missing.
     1856-1906: MCSSCQEAGA...LKCPKHKRLP → HGGTVALAPG...LCWAMPGTWK

Show »
Length:1,862
Mass (Da):198,392
Checksum:i9C4D9E4EF917A911
GO
Isoform 3 (identifier: Q7Z5J4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1598-1640: FVRVEKRDAF...ASSSSSSSSF → LEPSLGAQNP...AYSAREQGQR
     1641-1906: Missing.

Note: No experimental confirmation available.
Show »
Length:1,640
Mass (Da):175,343
Checksum:iA178ECCDECEDA431
GO
Isoform 4 (identifier: Q7Z5J4-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     947-966: SHMKPGEEGPDGERAPGDST → YSVYICIHIHIYNIYEDCKC
     967-1906: Missing.

Note: No experimental confirmation available.
Show »
Length:966
Mass (Da):104,319
Checksum:iEBD2A4453EADBA58
GO

Sequence cautioni

The sequence BAB47449 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti440S → L in AAO31738 (PubMed:12837267).Curated1
Sequence conflicti1302L → F in AAO31738 (PubMed:12837267).Curated1
Sequence conflicti1513G → A in AAO31738 (PubMed:12837267).Curated1
Sequence conflicti1682T → A in CAD39144 (PubMed:17974005).Curated1

Polymorphismi

The poly-Gln tract is polymorphic and the number of Gln varies from 12 to 14 (PubMed:11404004). The size of the poly-Gln region may influence the age at onset of spinocerebellar ataxia type 2 (SCA2) (PubMed:10915763).2 Publications

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_05130090G → A.Corresponds to variant rs3803763dbSNPEnsembl.1
Natural variantiVAR_024344165P → T.Corresponds to variant rs11649804dbSNPEnsembl.1
Natural variantiVAR_051301939Q → P.Corresponds to variant rs1759075dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_010995207 – 233THFPQ…GGQGA → WWAGG in isoform 2. 1 PublicationAdd BLAST27
Alternative sequenceiVSP_010996407 – 434VDTQA…LSLQS → PAD in isoform 2. 1 PublicationAdd BLAST28
Alternative sequenceiVSP_010997947 – 966SHMKP…PGDST → YSVYICIHIHIYNIYEDCKC in isoform 4. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_010998967 – 1906Missing in isoform 4. 1 PublicationAdd BLAST940
Alternative sequenceiVSP_0109991415 – 1479Missing in isoform 2. 1 PublicationAdd BLAST65
Alternative sequenceiVSP_0110001598 – 1640FVRVE…SSSSF → LEPSLGAQNPRSGQNAPPAP ADARPLCTTRDRRAYSAREQ GQR in isoform 3. 1 PublicationAdd BLAST43
Alternative sequenceiVSP_0110011641 – 1906Missing in isoform 3. 1 PublicationAdd BLAST266
Alternative sequenceiVSP_0110021803 – 1821Missing in isoform 2. 1 PublicationAdd BLAST19
Alternative sequenceiVSP_0110031856 – 1906MCSSC…HKRLP → HGGTVALAPGDFSLPGLRFA SLFQGPSWCDCPVLATSTPS SWSRCVPAAKKPGPPLGAAT KDASTPTTTRVPAMQVRARP GTGGHWSPSKQSRGTLPGHS SPNPGPISLFSFPPLLPQQF FYPSVCLDLCWAMPGTWK in isoform 2. 1 PublicationAdd BLAST51

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ271790 mRNA. Translation: CAC20423.1.
AJ271791 Genomic DNA. Translation: CAC20424.1.
AY172136 mRNA. Translation: AAO31738.1.
AB058723 mRNA. Translation: BAB47449.1. Different initiation.
BC021209 mRNA. Translation: AAH21209.1.
AL133649 mRNA. Translation: CAB63768.1.
AL834468 mRNA. Translation: CAD39127.1.
AL834486 mRNA. Translation: CAD39144.1.
CCDSiCCDS11188.1. [Q7Z5J4-1]
PIRiT43490.
RefSeqiNP_109590.3. NM_030665.3. [Q7Z5J4-1]
UniGeneiHs.655395.
Hs.727059.

Genome annotation databases

EnsembliENST00000353383; ENSP00000323074; ENSG00000108557. [Q7Z5J4-1]
GeneIDi10743.
KEGGihsa:10743.
UCSCiuc002grm.4. human. [Q7Z5J4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism, Triplet repeat expansion

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ271790 mRNA. Translation: CAC20423.1.
AJ271791 Genomic DNA. Translation: CAC20424.1.
AY172136 mRNA. Translation: AAO31738.1.
AB058723 mRNA. Translation: BAB47449.1. Different initiation.
BC021209 mRNA. Translation: AAH21209.1.
AL133649 mRNA. Translation: CAB63768.1.
AL834468 mRNA. Translation: CAD39127.1.
AL834486 mRNA. Translation: CAD39144.1.
CCDSiCCDS11188.1. [Q7Z5J4-1]
PIRiT43490.
RefSeqiNP_109590.3. NM_030665.3. [Q7Z5J4-1]
UniGeneiHs.655395.
Hs.727059.

3D structure databases

ProteinModelPortaliQ7Z5J4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi115966. 25 interactors.
IntActiQ7Z5J4. 17 interactors.
MINTiMINT-1477867.
STRINGi9606.ENSP00000323074.

PTM databases

iPTMnetiQ7Z5J4.
PhosphoSitePlusiQ7Z5J4.

Polymorphism and mutation databases

BioMutaiRAI1.
DMDMi50400978.

Proteomic databases

EPDiQ7Z5J4.
MaxQBiQ7Z5J4.
PaxDbiQ7Z5J4.
PeptideAtlasiQ7Z5J4.
PRIDEiQ7Z5J4.

Protocols and materials databases

DNASUi10743.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000353383; ENSP00000323074; ENSG00000108557. [Q7Z5J4-1]
GeneIDi10743.
KEGGihsa:10743.
UCSCiuc002grm.4. human. [Q7Z5J4-1]

Organism-specific databases

CTDi10743.
DisGeNETi10743.
GeneCardsiRAI1.
GeneReviewsiRAI1.
H-InvDBHIX0013588.
HGNCiHGNC:9834. RAI1.
HPAiHPA023898.
HPA054906.
MalaCardsiRAI1.
MIMi182290. phenotype.
607642. gene.
neXtProtiNX_Q7Z5J4.
OpenTargetsiENSG00000108557.
Orphaneti1713. 17p11.2 microduplication syndrome.
819. Smith-Magenis syndrome.
PharmGKBiPA34188.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IJJX. Eukaryota.
ENOG410Z8S8. LUCA.
GeneTreeiENSGT00530000063684.
HOVERGENiHBG056862.
InParanoidiQ7Z5J4.
KOiK19749.
OMAiQNLHAYQ.
OrthoDBiEOG091G008I.
PhylomeDBiQ7Z5J4.
TreeFamiTF331317.

Enzyme and pathway databases

ReactomeiR-HSA-400253. Circadian Clock.

Miscellaneous databases

ChiTaRSiRAI1. human.
GenomeRNAii10743.
PROiQ7Z5J4.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000108557.
CleanExiHS_RAI1.
ExpressionAtlasiQ7Z5J4. baseline and differential.
GenevisibleiQ7Z5J4. HS.

Family and domain databases

InterProiIPR001965. Znf_PHD.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
PROSITEiPS51805. EPHD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRAI1_HUMAN
AccessioniPrimary (citable) accession number: Q7Z5J4
Secondary accession number(s): Q8N3B4
, Q8ND08, Q8WU64, Q96JK5, Q9H1C1, Q9H1C2, Q9UF69
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: November 2, 2016
This is version 117 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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: 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. 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.