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Entry version 55 (16 Oct 2019)
Sequence version 1 (28 Jun 2011)
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Protein

Protein PAF1 homolog

Gene

VIP2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score:

Annotation score:5 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>
-Experimental evidence at protein leveli <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

Component of the PAF1 complex (PAF1C) which is involved in histone modifications such as methylation on histone H3 'Lys-4' (H3K4me3) (PubMed:20363855). Involved in regulation of flowering time. Required for the expression of the flowering repressors and MAD-box genes FLC, AGL27/FLM and AGL31/MAF2. Required for histone H3 trimethylation on 'Lys-4' H3K4me3 at the FLC and AGL27/FLM loci (PubMed:15520273). Involved in the control of seed dormancy and germination (PubMed:21799800).3 Publications

<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

Biological processFlowering, Transcription, Transcription regulation

<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_and_taxonomy_section">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:
Protein PAF1 homologCurated
Alternative name(s):
Protein EARLY FLOWERING 71 Publication
Protein VERNALIZATION INDEPENDENCE 21 Publication
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:VIP21 Publication
Synonyms:ELF71 Publication
Ordered Locus Names:At1g79730Imported
ORF Names:F19K16.29Imported, F20B17.16Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiArabidopsis thaliana (Mouse-ear cress)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri3702 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000006548 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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 1

Organism-specific databases

Arabidopsis Information Portal

More...
Araporti
AT1G79730

The Arabidopsis Information Resource

More...
TAIRi
locus:2017879 AT1G79730

<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

Keywords - Cellular componenti

Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Early flowering, reduced plant size and defects in floral morphology in whorls 1-3, but fully fertile flowers (PubMed:12750345). Reduced seed dormancy and increased germination rate of freshly harvested seeds (PubMed:21799800).2 Publications

<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

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004327581 – 589Protein PAF1 homologAdd BLAST589

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
F4HQA1

PRoteomics IDEntifications database

More...
PRIDEi
F4HQA1

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
F4HQA1

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the ‘Expression’ section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms. By default, the information is derived from experiments at the mRNA level, unless specified ‘at protein level’. <br></br>Examples: <a href="http://www.uniprot.org/uniprot/P92958#expression">P92958</a>, <a href="http://www.uniprot.org/uniprot/Q8TDN4#expression">Q8TDN4</a>, <a href="http://www.uniprot.org/uniprot/O14734#expression">O14734</a><p><a href='/help/tissue_specificity' target='_top'>More...</a></p>Tissue specificityi

Expressed in roots, leaves and shoot apex.1 Publication

Gene expression databases

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
F4HQA1 baseline and differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
F4HQA1 AT

<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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Component of the nuclear PAF1 complex (PAF1C), which consists of VIP2/ELF7/PAF1, VIP3/SKI8/WDR61, VIP4/LEO1, VIP5/RTF1, VIP6/ELF8/CTR9 and CDC73.

1 Publication

GO - Molecular functioni

Protein-protein interaction databases

Protein interaction database and analysis system

More...
IntActi
F4HQA1, 3 interactors

STRING: functional protein association networks

More...
STRINGi
3702.AT1G79730.1

<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

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 coili126 – 159Sequence analysisAdd BLAST34

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 biasi6 – 94Pro-richPROSITE-ProRule annotationAdd BLAST89

<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 PAF1 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG2478 Eukaryota
ENOG410YZXE LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000084593

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
F4HQA1

KEGG Orthology (KO)

More...
KOi
K15174

Identification of Orthologs from Complete Genome Data

More...
OMAi
DRKNQQM

Database of Orthologous Groups

More...
OrthoDBi
599989at2759

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR007133 RNA_pol_II-assoc_Paf1

The PANTHER Classification System

More...
PANTHERi
PTHR23188 PTHR23188, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03985 Paf1, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

F4HQA1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASYRPPYPP LPQPPSQNSL APPPPPPSLP PPVPPPPPSH QPYSYPPPPP
60 70 80 90 100
PPPHAYYQQG PHYPQFNQLQ APPPPPPPSA PPPLVPDPPR HQGPNDHEKG
110 120 130 140 150
ASKQVGRRER AKPDPSKHHH RSHLPHSKKI ETEEERRLRK KRELEKQRQD
160 170 180 190 200
EKHRQQMKNS HKSQMPKGHT EEKKPTPLLT TDRVENRLKK PTTFICKLKF
210 220 230 240 250
RNELPDPSAQ LKLMTIKRDK DQFTKYTITS LEKLWKPKIF VEPDLGIPLD
260 270 280 290 300
LLDLSVYNPP KVKAPLAPED EELLRDDDAV TPIKKDGIRR KERPTDKGMS
310 320 330 340 350
WLVKTQYISS INNESARQSL TEKQAKELRE MKGGINILHN LNNRERQIKD
360 370 380 390 400
IEASFEACKS RPVHATNKNL QPVEVLPLLP YFDRYDEQFV VANFDGAPIA
410 420 430 440 450
DSEFFGKLDP SIRDAHESRA ILKSYVVAGS DTANPEKFLA YMVPSLDELS
460 470 480 490 500
KDIHDENEEI SYTWVREYLW DVQPNANDPG TYLVSFDNGT ASYLPLPMRL
510 520 530 540 550
NLRKKRAREG RSSDEIEHFP VPSRVTVRRR STVSVIEHKD SGVYSSRVGA
560 570 580
SSSKMRRLED EGGLGRSWKH EPEQDANQYS DGNEDDYSE
Length:589
Mass (Da):67,338
Last modified:June 28, 2011 - 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:i8909E557DED725A0
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAF68118 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence AAG52243 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti185E → Q in AAM10397 (PubMed:14593172).Curated1
Sequence conflicti185E → Q in AAO11627 (PubMed:14593172).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AC010793 Genomic DNA Translation: AAF68118.1 Sequence problems.
AC011717 Genomic DNA Translation: AAG52243.1 Sequence problems.
CP002684 Genomic DNA Translation: AEE36292.1
AY093780 mRNA Translation: AAM10397.1
BT002711 mRNA Translation: AAO11627.1

Protein sequence database of the Protein Information Resource

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PIRi
C96828

NCBI Reference Sequences

More...
RefSeqi
NP_178091.2, NM_106622.5

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
AT1G79730.1; AT1G79730.1; AT1G79730

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
844312

Gramene; a comparative resource for plants

More...
Gramenei
AT1G79730.1; AT1G79730.1; AT1G79730

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ath:AT1G79730

<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
AC010793 Genomic DNA Translation: AAF68118.1 Sequence problems.
AC011717 Genomic DNA Translation: AAG52243.1 Sequence problems.
CP002684 Genomic DNA Translation: AEE36292.1
AY093780 mRNA Translation: AAM10397.1
BT002711 mRNA Translation: AAO11627.1
PIRiC96828
RefSeqiNP_178091.2, NM_106622.5

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

IntActiF4HQA1, 3 interactors
STRINGi3702.AT1G79730.1

PTM databases

iPTMnetiF4HQA1

Proteomic databases

PaxDbiF4HQA1
PRIDEiF4HQA1

Genome annotation databases

EnsemblPlantsiAT1G79730.1; AT1G79730.1; AT1G79730
GeneIDi844312
GrameneiAT1G79730.1; AT1G79730.1; AT1G79730
KEGGiath:AT1G79730

Organism-specific databases

AraportiAT1G79730
TAIRilocus:2017879 AT1G79730

Phylogenomic databases

eggNOGiKOG2478 Eukaryota
ENOG410YZXE LUCA
HOGENOMiHOG000084593
InParanoidiF4HQA1
KOiK15174
OMAiDRKNQQM
OrthoDBi599989at2759

Miscellaneous databases

Protein Ontology

More...
PROi
PR:F4HQA1

Gene expression databases

ExpressionAtlasiF4HQA1 baseline and differential
GenevisibleiF4HQA1 AT

Family and domain databases

InterProiView protein in InterPro
IPR007133 RNA_pol_II-assoc_Paf1
PANTHERiPTHR23188 PTHR23188, 1 hit
PfamiView protein in Pfam
PF03985 Paf1, 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 nameiPAF1_ARATH
<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: F4HQA1
Secondary accession number(s): Q8RW91, Q9CA82, Q9MA04
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 29, 2015
Last sequence update: June 28, 2011
Last modified: October 16, 2019
This is version 55 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 statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
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