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Protein

Neuroplastin

Gene

NPTN

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

Functioni

Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity (By similarity).By similarity

GO - Molecular functioni

  1. ATP binding Source: InterPro
  2. cell adhesion molecule binding Source: HGNC
  3. transmembrane receptor protein tyrosine kinase activity Source: InterPro
  4. type 1 fibroblast growth factor receptor binding Source: UniProtKB

GO - Biological processi

  1. homophilic cell adhesion via plasma membrane adhesion molecules Source: HGNC
  2. long-term synaptic potentiation Source: UniProtKB
  3. positive regulation of cytosolic calcium ion concentration Source: UniProtKB
  4. positive regulation of fibroblast growth factor receptor signaling pathway Source: UniProtKB
  5. positive regulation of long-term neuronal synaptic plasticity Source: HGNC
  6. positive regulation of neuron projection development Source: UniProtKB
  7. positive regulation of protein phosphorylation Source: UniProtKB
  8. transmembrane receptor protein tyrosine kinase signaling pathway Source: InterPro
Complete GO annotation...

Keywords - Biological processi

Cell adhesion, Neurogenesis

Names & Taxonomyi

Protein namesi
Recommended name:
Neuroplastin
Alternative name(s):
Stromal cell-derived receptor 1
Short name:
SDR-1
Gene namesi
Name:NPTN
Synonyms:SDFR1, SDR1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 15

Organism-specific databases

HGNCiHGNC:17867. NPTN.

Subcellular locationi

Cell membrane Curated; Single-pass type I membrane protein Curated
Note: Enriched at postsynaptic density.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini29 – 339311ExtracellularSequence AnalysisAdd
BLAST
Transmembranei340 – 36021HelicalSequence AnalysisAdd
BLAST
Topological domaini361 – 39838CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. cell surface Source: UniProtKB
  2. integral component of membrane Source: UniProtKB-KW
  3. presynaptic membrane Source: HGNC
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134927704.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828Add
BLAST
Chaini29 – 398370NeuroplastinPRO_0000394470Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi52 ↔ 116PROSITE-ProRule annotation
Disulfide bondi170 ↔ 218PROSITE-ProRule annotation
Glycosylationi171 – 1711N-linked (GlcNAc...)Sequence Analysis
Glycosylationi197 – 1971N-linked (GlcNAc...)Sequence Analysis
Glycosylationi229 – 2291N-linked (GlcNAc...)1 Publication
Disulfide bondi259 ↔ 316PROSITE-ProRule annotation
Glycosylationi284 – 2841N-linked (GlcNAc...)1 Publication
Glycosylationi296 – 2961N-linked (GlcNAc...)1 Publication
Glycosylationi317 – 3171N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiQ9Y639.
PaxDbiQ9Y639.
PRIDEiQ9Y639.

PTM databases

PhosphoSiteiQ9Y639.

Expressioni

Tissue specificityi

Isoform 1 is ubiquitously expressed. Isoform 2 is expressed in brain cortex and cerebellum (at protein level).2 Publications

Gene expression databases

BgeeiQ9Y639.
CleanExiHS_NPTN.
ExpressionAtlasiQ9Y639. baseline and differential.
GenevestigatoriQ9Y639.

Organism-specific databases

HPAiHPA051497.

Interactioni

Protein-protein interaction databases

BioGridi117958. 10 interactions.
IntActiQ9Y639. 3 interactions.
MINTiMINT-4542281.
STRINGi9606.ENSP00000290401.

Structurei

3D structure databases

SMRiQ9Y639. Positions 31-335.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini29 – 134106Ig-like 1Add
BLAST
Domaini148 – 23588Ig-like 2Add
BLAST
Domaini238 – 32992Ig-like 3Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni149 – 16113Narpin; mediates binding with FGFR1 and has antidepressant-like activityBy similarityAdd
BLAST

Domaini

Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1 (By similarity).By similarity

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG149118.
GeneTreeiENSGT00390000010516.
HOVERGENiHBG008120.
InParanoidiQ9Y639.
OMAiLQKPRIN.
OrthoDBiEOG7V1FQN.
PhylomeDBiQ9Y639.
TreeFamiTF326759.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR027112. Neuroplastin.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
[Graphical view]
PANTHERiPTHR10075:SF5. PTHR10075:SF5. 1 hit.
PfamiPF07679. I-set. 2 hits.
[Graphical view]
PIRSFiPIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 2 hits.
[Graphical view]
PROSITEiPS50835. IG_LIKE. 3 hits.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

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

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 2 (identifier: Q9Y639-2) [UniParc]FASTAAdd to basket

Also known as: SDR-1-beta

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
MSGSSLPSAL ALSLLLVSGS LLPGPGAAQN AGFVKSPMSE TKLTGDAFEL
60 70 80 90 100
YCDVVGSPTP EIQWWYAEVN RAESFRQLWD GARKRRVTVN TAYGSNGVSV
110 120 130 140 150
LRITRLTLED SGTYECRASN DPKRNDLRQN PSITWIRAQA TISVLQKPRI
160 170 180 190 200
VTSEEVIIRD SPVLPVTLQC NLTSSSHTLT YSYWTKNGVE LSATRKNASN
210 220 230 240 250
MEYRINKPRA EDSGEYHCVY HFVSAPKANA TIEVKAAPDI TGHKRSENKN
260 270 280 290 300
EGQDATMYCK SVGYPHPDWI WRKKENGMPM DIVNTSGRFF IINKENYTEL
310 320 330 340 350
NIVNLQITED PGEYECNATN AIGSASVVTV LRVRSHLAPL WPFLGILAEI
360 370 380 390
IILVVIIVVY EKRKRPDEVP DDDEPAGPMK TNSTNNHKDK NLRQRNTN
Length:398
Mass (Da):44,387
Last modified:June 14, 2010 - v2
Checksum:i5109E3C03B4967EA
GO
Isoform 1 (identifier: Q9Y639-1) [UniParc]FASTAAdd to basket

Also known as: SDR-1-alpha

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E

Show »
Length:282
Mass (Da):31,291
Checksum:iB3E48A23984A6C4A
GO
Isoform 3 (identifier: Q9Y639-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     31-147: AGFVKSPMSE...AQATISVLQK → E
     372-375: Missing.

Show »
Length:278
Mass (Da):30,835
Checksum:i458E026CC87DD657
GO
Isoform 4 (identifier: Q9Y639-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     320-398: NAIGSASVVT...DKNLRQRNTN → WPHSGLSWEFWLKLSSLW

Note: No experimental confirmation available.

Show »
Length:337
Mass (Da):37,792
Checksum:i8C043513B3BCD50C
GO
Isoform 5 (identifier: Q9Y639-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     372-375: Missing.

Show »
Length:394
Mass (Da):43,931
Checksum:iC68D09CC61FB4B49
GO

Sequence cautioni

The sequence BAD93049.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti299 – 2991E → K in BAH12519 (PubMed:14702039).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei31 – 147117AGFVK…SVLQK → E in isoform 1 and isoform 3. 3 PublicationsVSP_039251Add
BLAST
Alternative sequencei320 – 39879NAIGS…QRNTN → WPHSGLSWEFWLKLSSLW in isoform 4. 1 PublicationVSP_039252Add
BLAST
Alternative sequencei372 – 3754Missing in isoform 3 and isoform 5. 3 PublicationsVSP_039253

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF109126 mRNA. Translation: AAD43217.1.
AF109127 mRNA. Translation: AAD43218.1.
AK297184 mRNA. Translation: BAH12519.1.
AK314248 mRNA. Translation: BAG36914.1.
AB209812 mRNA. Translation: BAD93049.1. Different initiation.
CH471082 Genomic DNA. Translation: EAW77931.1.
BC105979 mRNA. Translation: AAI05980.1.
BC117462 mRNA. Translation: AAI17463.1.
BC143880 mRNA. Translation: AAI43881.1.
BC143881 mRNA. Translation: AAI43882.1.
CCDSiCCDS10249.1. [Q9Y639-2]
CCDS10250.1. [Q9Y639-1]
CCDS58379.1. [Q9Y639-3]
CCDS58380.1. [Q9Y639-5]
PIRiT17219.
RefSeqiNP_001154835.1. NM_001161363.1. [Q9Y639-5]
NP_001154836.1. NM_001161364.1. [Q9Y639-3]
NP_036560.1. NM_012428.3. [Q9Y639-2]
NP_059429.1. NM_017455.3. [Q9Y639-1]
UniGeneiHs.744867.

Genome annotation databases

EnsembliENST00000345330; ENSP00000290401; ENSG00000156642. [Q9Y639-2]
ENST00000351217; ENSP00000342958; ENSG00000156642. [Q9Y639-1]
ENST00000562924; ENSP00000456349; ENSG00000156642. [Q9Y639-3]
ENST00000563691; ENSP00000457028; ENSG00000156642. [Q9Y639-5]
GeneIDi27020.
KEGGihsa:27020.
UCSCiuc002avr.3. human. [Q9Y639-3]
uc002avs.3. human. [Q9Y639-2]
uc002avt.3. human. [Q9Y639-1]
uc010bjc.3. human. [Q9Y639-5]

Polymorphism databases

DMDMi298286871.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF109126 mRNA. Translation: AAD43217.1.
AF109127 mRNA. Translation: AAD43218.1.
AK297184 mRNA. Translation: BAH12519.1.
AK314248 mRNA. Translation: BAG36914.1.
AB209812 mRNA. Translation: BAD93049.1. Different initiation.
CH471082 Genomic DNA. Translation: EAW77931.1.
BC105979 mRNA. Translation: AAI05980.1.
BC117462 mRNA. Translation: AAI17463.1.
BC143880 mRNA. Translation: AAI43881.1.
BC143881 mRNA. Translation: AAI43882.1.
CCDSiCCDS10249.1. [Q9Y639-2]
CCDS10250.1. [Q9Y639-1]
CCDS58379.1. [Q9Y639-3]
CCDS58380.1. [Q9Y639-5]
PIRiT17219.
RefSeqiNP_001154835.1. NM_001161363.1. [Q9Y639-5]
NP_001154836.1. NM_001161364.1. [Q9Y639-3]
NP_036560.1. NM_012428.3. [Q9Y639-2]
NP_059429.1. NM_017455.3. [Q9Y639-1]
UniGeneiHs.744867.

3D structure databases

SMRiQ9Y639. Positions 31-335.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117958. 10 interactions.
IntActiQ9Y639. 3 interactions.
MINTiMINT-4542281.
STRINGi9606.ENSP00000290401.

PTM databases

PhosphoSiteiQ9Y639.

Polymorphism databases

DMDMi298286871.

Proteomic databases

MaxQBiQ9Y639.
PaxDbiQ9Y639.
PRIDEiQ9Y639.

Protocols and materials databases

DNASUi27020.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000345330; ENSP00000290401; ENSG00000156642. [Q9Y639-2]
ENST00000351217; ENSP00000342958; ENSG00000156642. [Q9Y639-1]
ENST00000562924; ENSP00000456349; ENSG00000156642. [Q9Y639-3]
ENST00000563691; ENSP00000457028; ENSG00000156642. [Q9Y639-5]
GeneIDi27020.
KEGGihsa:27020.
UCSCiuc002avr.3. human. [Q9Y639-3]
uc002avs.3. human. [Q9Y639-2]
uc002avt.3. human. [Q9Y639-1]
uc010bjc.3. human. [Q9Y639-5]

Organism-specific databases

CTDi27020.
GeneCardsiGC15M073852.
HGNCiHGNC:17867. NPTN.
HPAiHPA051497.
MIMi612820. gene.
neXtProtiNX_Q9Y639.
PharmGKBiPA134927704.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG149118.
GeneTreeiENSGT00390000010516.
HOVERGENiHBG008120.
InParanoidiQ9Y639.
OMAiLQKPRIN.
OrthoDBiEOG7V1FQN.
PhylomeDBiQ9Y639.
TreeFamiTF326759.

Miscellaneous databases

ChiTaRSiNPTN. human.
GeneWikiiNPTN.
GenomeRNAii27020.
NextBioi49544.
PROiQ9Y639.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y639.
CleanExiHS_NPTN.
ExpressionAtlasiQ9Y639. baseline and differential.
GenevestigatoriQ9Y639.

Family and domain databases

Gene3Di2.60.40.10. 3 hits.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013098. Ig_I-set.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR027112. Neuroplastin.
IPR016243. Tyr_kinase_CSF1/PDGF_rcpt.
[Graphical view]
PANTHERiPTHR10075:SF5. PTHR10075:SF5. 1 hit.
PfamiPF07679. I-set. 2 hits.
[Graphical view]
PIRSFiPIRSF000615. TyrPK_CSF1-R. 1 hit.
SMARTiSM00409. IG. 1 hit.
SM00408. IGc2. 2 hits.
[Graphical view]
PROSITEiPS50835. IG_LIKE. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isoform specific expression of the SDR-1 protein, alpha and beta in subregions of adult rodent brain."
    Lopez N.D., Kinoshita A., Taniwaki M., Tada H., Shirozu M., Nakano T., Tashiro K., Honjo T.
    Biomed. Res. 20:43-49(1998)
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), TISSUE SPECIFICITY.
  2. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 5).
    Tissue: Brain and Stomach.
  3. Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S., Ohara O., Nagase T., Kikuno R.F.
    Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 4).
    Tissue: Brain.
  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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Tissue: Brain and Skin.
  6. "Signal peptide prediction based on analysis of experimentally verified cleavage sites."
    Zhang Z., Henzel W.J.
    Protein Sci. 13:2819-2824(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 29-43 (ISOFORM 1).
  7. "The immunolocalization of the synaptic glycoprotein neuroplastin differs substantially between the human and the rodent brain."
    Bernstein H.G., Smalla K.H., Bogerts B., Gordon-Weeks P.R., Beesley P.W., Gundelfinger E.D., Kreutz M.R.
    Brain Res. 1134:107-112(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.
  8. "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
    Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
    J. Proteome Res. 8:651-661(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-284 AND ASN-296.
    Tissue: Liver.
  9. "Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins."
    Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D.
    Nat. Biotechnol. 27:378-386(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-229.
    Tissue: Leukemic T-cell.
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiNPTN_HUMAN
AccessioniPrimary (citable) accession number: Q9Y639
Secondary accession number(s): B2RAL7
, B7Z4D3, B7ZLL2, Q17R52, Q59EJ9, Q6NVX7, Q9Y640
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2006
Last sequence update: June 14, 2010
Last modified: March 31, 2015
This is version 119 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: 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

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.