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Entry version 113 (07 Oct 2020)
Sequence version 1 (12 Jun 2007)
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Protein

Phytochrome

Gene

PHYA

Organism
Vitis vinifera (Grape)
Status
Unreviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Protein inferred from homologyi <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei322Phytochromobilin chromophore (covalent; via 1 link)UniRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionPhotoreceptor proteinUniRule annotationARBA annotation, Receptor
Biological processSensory transduction, Transcription, Transcription regulationUniRule annotationARBA annotation
LigandChromophore

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
PhytochromeUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PHYAImported
Ordered Locus Names:VIT_14s0060g00100Imported
ORF Names:VITISV_020287Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiVitis vinifera (Grape)Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri29760 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsVitalesVitaceaeViteaeVitis
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000009183 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 14

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.UniRule annotation

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
A5B9C2

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

UniRule annotationARBA annotation

GO - Molecular functioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
29760.VIT_14s0060g00100.t01

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini217 – 390PHYTOCHROME_2InterPro annotationAdd BLAST174
Domaini616 – 686PASInterPro annotationAdd BLAST71
Domaini689 – 745PACInterPro annotationAdd BLAST57
Domaini749 – 801PASInterPro annotationAdd BLAST53
Domaini900 – 1117Histidine kinaseInterPro annotationAdd BLAST218

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 24DisorderedSequence analysisAdd BLAST24

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili397 – 417Sequence analysisAdd BLAST21

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi1 – 23PolarSequence analysisAdd BLAST23

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the phytochrome family.UniRule annotationARBA annotation

Keywords - Domaini

Coiled coilSequence analysis, RepeatARBA annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG502QRSA, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_010418_0_0_1

KEGG Orthology (KO)

More...
KOi
K12120

Identification of Orthologs from Complete Genome Data

More...
OMAi
YLHHIQR

Database of Orthologous Groups

More...
OrthoDBi
77253at2759

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00082, HisKA, 1 hit
cd00130, PAS, 2 hits

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.450.270, 1 hit
3.30.450.40, 1 hit
3.30.565.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003018, GAF
IPR029016, GAF-like_dom_sf
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR005467, His_kinase_dom
IPR003661, HisK_dim/P
IPR000014, PAS
IPR000700, PAS-assoc_C
IPR035965, PAS-like_dom_sf
IPR013654, PAS_2
IPR013767, PAS_fold
IPR016132, Phyto_chromo_attachment
IPR013516, Phyto_chromo_BS
IPR001294, Phytochrome
IPR012129, Phytochrome_A-E
IPR013515, Phytochrome_cen-reg
IPR043150, Phytochrome_PHY

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01590, GAF, 1 hit
PF02518, HATPase_c, 1 hit
PF00512, HisKA, 1 hit
PF00989, PAS, 2 hits
PF08446, PAS_2, 1 hit
PF00360, PHY, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF000084, Phytochrome, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01033, PHYTOCHROME

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00065, GAF, 1 hit
SM00387, HATPase_c, 1 hit
SM00388, HisKA, 1 hit
SM00091, PAS, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF55785, SSF55785, 3 hits
SSF55874, SSF55874, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00229, sensory_box, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50109, HIS_KIN, 1 hit
PS50113, PAC, 1 hit
PS50112, PAS, 2 hits
PS00245, PHYTOCHROME_1, 1 hit
PS50046, PHYTOCHROME_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

A5B9C2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSSRPTQSS STSGRSKHSA RIIAQTTVDA KLHADFEESG SSFDYSSSVR
60 70 80 90 100
FTPAGGDQQP RSDKVTTAYL HHIQKGKLIQ PFGSLLALDE KTFKVIAYSE
110 120 130 140 150
NAPEMLTMVS HAVPSVGEHP VLGIGTDVRT IFSGPSASAL HKALGFGEVS
160 170 180 190 200
LLNPILVHCK TSGKPFYAII HRVTGSLIID FEPVKPYEVP MTAAGALQSY
210 220 230 240 250
KLAAKAITRL QSLPSGSLER LCDTMVQEVF ELTGYDRVMA YKFHDDDHGE
260 270 280 290 300
VVSEITKPGL EPYLGLHYPA TDIPQAARFL FMKNKVRMIC DCRAKHIQVL
310 320 330 340 350
QDEKLPFDLT LCGSTLRAPH SCHVQYMENM NSIASLVMAV VVNDGDEEGE
360 370 380 390 400
SSNSGQPQKR KRLWGLVVCH HTTPRFVPFP LRYACEFLAQ VFAIHVNKEL
410 420 430 440 450
ELESQILEKN ILRTQTLLCD MLMRDAPLGI VSQSPNVMDL VKCDGAALLY
460 470 480 490 500
KNKVWRLGIT PSDFQLHDIC SWLSEYHMDS TGLSTDSLYD AGYPGALALG
510 520 530 540 550
DAVCGMAAVK ITSKDTLFWF RSHTAAEVRW GGAKHEPGEK DDGRKMHPRS
560 570 580 590 600
SFKAFLEVVK TRSLPWKDYE MDAIHSLQLI LRNAFKDSEA MDVNTNAIHT
610 620 630 640 650
KLNDLKIEGM QELEAVTSEM VRLIETASVP ILAVDVDGLV NGWNTKISEL
660 670 680 690 700
TSLPVDKAIG MHLLTLVEDS SADTVKKMLH LALQGQEEQN VQFEIKTHGS
710 720 730 740 750
KRDSGPISLV VNACASRDLH ENVVGVCFVA QDITSQKTVM DKFTRIEGDY
760 770 780 790 800
KAIVQNPNPL IPPIFGTDEF GWCSEWNPAM VKLSGWNREE VMDKMLLGEV
810 820 830 840 850
FGTHMACCRL KNREAFVGLG IVLNSVMTGR ESEKVSFGFF SKSGKYVECL
860 870 880 890 900
LSVSKKLDRE GAVTGVFCFL QLASQELQQA LHIQRLSEQT ALKRLKALAY
910 920 930 940 950
IKRQIKNPLS GIIFSRKMME DTDLGEEQQQ ILHTSAQCQR QLSKILDDHD
960 970 980 990 1000
LDSIIEGYLD LEMVEFTLRE VLVASISQVM IKSNGKGIQI VNDAEEGIMT
1010 1020 1030 1040 1050
ETLYGDGLRL QQVLADFLLI SVNFTPGGGQ LSVAASLIKD RLGESVHLVH
1060 1070 1080 1090 1100
LELRITHAGN GVPEQLLNQM FGNNGDASEE GISLLISRKL VKLMNGDVQY
1110 1120
LREAGKSTFI ISIELAAARK KPQA
Length:1,124
Mass (Da):124,347
Last modified:June 12, 2007 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iD1E5091A6BBB3EC0
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
EU436649 Genomic DNA Translation: ACC60965.1
AM451152 Genomic DNA Translation: CAN76586.1
FN596746 Genomic DNA Translation: CBI39690.3

NCBI Reference Sequences

More...
RefSeqi
XP_002278610.1, XM_002278574.4
XP_010659783.1, XM_010661481.2

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
VIT_14s0060g00100.t01; VIT_14s0060g00100.t01; VIT_14s0060g00100

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100240824

Gramene; a comparative resource for plants

More...
Gramenei
VIT_14s0060g00100.t01; VIT_14s0060g00100.t01; VIT_14s0060g00100

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vvi:100240824

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU436649 Genomic DNA Translation: ACC60965.1
AM451152 Genomic DNA Translation: CAN76586.1
FN596746 Genomic DNA Translation: CBI39690.3
RefSeqiXP_002278610.1, XM_002278574.4
XP_010659783.1, XM_010661481.2

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Protein-protein interaction databases

STRINGi29760.VIT_14s0060g00100.t01

Proteomic databases

PRIDEiA5B9C2

Genome annotation databases

EnsemblPlantsiVIT_14s0060g00100.t01; VIT_14s0060g00100.t01; VIT_14s0060g00100
GeneIDi100240824
GrameneiVIT_14s0060g00100.t01; VIT_14s0060g00100.t01; VIT_14s0060g00100
KEGGivvi:100240824

Phylogenomic databases

eggNOGiENOG502QRSA, Eukaryota
HOGENOMiCLU_010418_0_0_1
KOiK12120
OMAiYLHHIQR
OrthoDBi77253at2759

Family and domain databases

CDDicd00082, HisKA, 1 hit
cd00130, PAS, 2 hits
Gene3Di3.30.450.270, 1 hit
3.30.450.40, 1 hit
3.30.565.10, 1 hit
InterProiView protein in InterPro
IPR003018, GAF
IPR029016, GAF-like_dom_sf
IPR003594, HATPase_C
IPR036890, HATPase_C_sf
IPR005467, His_kinase_dom
IPR003661, HisK_dim/P
IPR000014, PAS
IPR000700, PAS-assoc_C
IPR035965, PAS-like_dom_sf
IPR013654, PAS_2
IPR013767, PAS_fold
IPR016132, Phyto_chromo_attachment
IPR013516, Phyto_chromo_BS
IPR001294, Phytochrome
IPR012129, Phytochrome_A-E
IPR013515, Phytochrome_cen-reg
IPR043150, Phytochrome_PHY
PfamiView protein in Pfam
PF01590, GAF, 1 hit
PF02518, HATPase_c, 1 hit
PF00512, HisKA, 1 hit
PF00989, PAS, 2 hits
PF08446, PAS_2, 1 hit
PF00360, PHY, 1 hit
PIRSFiPIRSF000084, Phytochrome, 1 hit
PRINTSiPR01033, PHYTOCHROME
SMARTiView protein in SMART
SM00065, GAF, 1 hit
SM00387, HATPase_c, 1 hit
SM00388, HisKA, 1 hit
SM00091, PAS, 2 hits
SUPFAMiSSF55785, SSF55785, 3 hits
SSF55874, SSF55874, 1 hit
TIGRFAMsiTIGR00229, sensory_box, 1 hit
PROSITEiView protein in PROSITE
PS50109, HIS_KIN, 1 hit
PS50113, PAC, 1 hit
PS50112, PAS, 2 hits
PS00245, PHYTOCHROME_1, 1 hit
PS50046, PHYTOCHROME_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiA5B9C2_VITVI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A5B9C2
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/TrEMBL: June 12, 2007
Last sequence update: June 12, 2007
Last modified: October 7, 2020
This is version 113 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiUnreviewed (UniProtKB/TrEMBL)

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteomeImported
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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