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Protein

Probable lysine-specific demethylase ELF6

Gene

ELF6

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Acts probably as a histone 'Lys-4' (H3K4me) demethylase. Involved in transcriptional gene regulation. Acts as a repressor of the photoperiodic flowering pathway and of FT. Binds around the transcription start site of the FT locus.3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi305 – 3051Iron; catalyticPROSITE-ProRule annotation
Metal bindingi307 – 3071Iron; catalyticPROSITE-ProRule annotation
Metal bindingi396 – 3961Iron; catalyticPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1251 – 127525C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1281 – 130525C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1311 – 133727C2H2-type 3PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • histone H3-K9 demethylation Source: TAIR
  • negative regulation of long-day photoperiodism, flowering Source: TAIR
  • negative regulation of short-day photoperiodism, flowering Source: TAIR
  • regulation of transcription, DNA-templated Source: TAIR
  • response to brassinosteroid Source: TAIR
  • transcription, DNA-templated Source: UniProtKB-KW
  • unidimensional cell growth Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Probable lysine-specific demethylase ELF6 (EC:1.14.11.-)
Alternative name(s):
Early flowering 6
Jumonji domain-containing protein 11
Probable lysine-specific histone demethylase ELF6
Gene namesi
Name:ELF6
Synonyms:JMJ11, PKDM9B
Ordered Locus Names:At5g04240
ORF Names:F21E1.160
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G04240.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Early flowering, but normal development of all organs. Partially redundant with JMJ14. Brassinosteroid-insensitive phenotype.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 13401340Probable lysine-specific demethylase ELF6PRO_0000412632Add
BLAST

Proteomic databases

PaxDbiQ6BDA0.
PRIDEiQ6BDA0.
ProMEXiQ6BDA0.

Expressioni

Tissue specificityi

Expressed at low levels in cotyledons and leaves. Detected in inflorescences, stems, roots and siliques but not in shoot apical meristems or root tips.2 Publications

Gene expression databases

GenevisibleiQ6BDA0. AT.

Interactioni

Subunit structurei

Interacts with BZR2 (via N-terminus).1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
BZR2Q9LN632EBI-1798417,EBI-617078

Protein-protein interaction databases

BioGridi15583. 1 interaction.
DIPiDIP-46102N.
IntActiQ6BDA0. 1 interaction.
STRINGi3702.AT5G04240.1.

Structurei

3D structure databases

ProteinModelPortaliQ6BDA0.
SMRiQ6BDA0. Positions 14-442, 1216-1336.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini16 – 5742JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini262 – 428167JmjCPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi573 – 5764Poly-Asp

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated
Contains 3 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1251 – 127525C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1281 – 130525C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri1311 – 133727C2H2-type 3PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
KOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000239739.
InParanoidiQ6BDA0.
OMAiKARTPYK.
PhylomeDBiQ6BDA0.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6BDA0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGNVEIPNWL KALPLAPVFR PTDTEFADPI AYISKIEKEA SAFGICKIIP
60 70 80 90 100
PLPKPSKKYV FYNLNKSLLK CPELVSDVDI SKVCKEDRAV FTTRQQELGQ
110 120 130 140 150
TVKKNKGEKG KSNSQRSGVK QVWQSGGVYT LDQFEAKSKA FYKTQLGTVK
160 170 180 190 200
ELAPVVIEAL FWKAALEKPI YIEYANDVPG SAFGEPEDHF RHFRQRKRRG
210 220 230 240 250
RGFYQRKTEN NDPSGKNGEK SSPEVEKAPL ASTSLSSQDS SKQKNMDIVD
260 270 280 290 300
EMEGTAGWKL SNSSWNLQMI ARSPGSVTRF MPDDIPGVTS PMVYIGMLFS
310 320 330 340 350
WFAWHVEDHE LHSMNYLHTG SPKTWYAVPC DYALDFEEVI RKNSYGRNID
360 370 380 390 400
QLAALTQLGE KTTLVSPEMI VASGIPCCRL VQNPGEFVVT FPRSYHVGFS
410 420 430 440 450
HGFNCGEAAN FGTPQWLNVA KEAAVRRAAM NYLPMLSHQQ LLYLLTMSFV
460 470 480 490 500
SRVPRSLLPG GRSSRLRDRQ REEREFLVKR AFVEDILNEN KNLSVLLREP
510 520 530 540 550
GSRLVMWDPD LLPRHSALAL AAAGVAGASA VSPPAVAKKE LEEGHSELQN
560 570 580 590 600
KEKTSLLEEL SLFMEKLNDV YYDDDDGLLN DFQVDTGTLP CVACGVLGFP
610 620 630 640 650
FMSVVQPSEK ALKDLSERQG ETDAQEIMTL SSEKSDCEWK TSSRYIRPRI
660 670 680 690 700
FCLEHTIELQ RLLQSRGGLK FLVICHKDFQ KFKAHAAIVA EEVKVPFSYD
710 720 730 740 750
DVLLESASQE ELSLIDLAIE DEEKYEHSVD WTSELGINLR YCVKVRKNSP
760 770 780 790 800
TKKIQHALSL GGLFSDTSQM LDFTTIRWLQ RKSRSKAKPS STSSFTPCEH
810 820 830 840 850
LEVKADGKLR DNLDSQTGKK EEKIIQYSRK KKLNPKPSAE QVQELATLAK
860 870 880 890 900
SKDFDKTCKN FSSRSHLDSA IRSEMNSEIG DSGRVIGVSF SINPCSSSFT
910 920 930 940 950
VGHGQEHPEI TVKFGSDLDG NVTNSLSMVN GDSADLTLTS ISREQHQGHS
960 970 980 990 1000
MTSNNNGSNS GSHVVASQTI LVSTGDNHDG PRKLSGDYVC SDVSVRGIQE
1010 1020 1030 1040 1050
AVEMSDQEFG EPRSTVTNIE DEQQSQIVKP TQREAVFGDH EQVEGAEAVS
1060 1070 1080 1090 1100
TRENLCSEII LHTEHSSAHV GMEIPDINTA SENLVVDMTH DGEPLESSDI
1110 1120 1130 1140 1150
LSSSNGDEAS SNGLQVLNDE LSMESEVSSS ENTEVIEAPN SMGEAKKKRK
1160 1170 1180 1190 1200
IESESETNDN PESSIGFIRS PCEGLRSRGK RKATCETSLK HTETSDEEKK
1210 1220 1230 1240 1250
PIAKRLKKTP KACSGSRQQE VPTTTHPNRC YLEGCKMTFE SKAKLQTHKR
1260 1270 1280 1290 1300
NRCTHEGCGK KFRAHKYLVL HQRVHKDERP FECSWKGCSM TFKWQWARTE
1310 1320 1330 1340
HLRLHTGERP YICKVDGCGL SFRFVSDYSR HRRKTMHYVT
Length:1,340
Mass (Da):150,072
Last modified:September 13, 2004 - v1
Checksum:i40CB360D273989DC
GO

Sequence cautioni

The sequence BAD94870.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAC05506.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY664500 mRNA. Translation: AAT77780.1.
AL391716 Genomic DNA. Translation: CAC05506.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED90717.1.
AK222064 mRNA. Translation: BAD94870.1. Different initiation.
RefSeqiNP_196044.2. NM_120506.4.
UniGeneiAt.10092.
At.72547.

Genome annotation databases

EnsemblPlantsiAT5G04240.1; AT5G04240.1; AT5G04240.
GeneIDi830303.
GrameneiAT5G04240.1; AT5G04240.1; AT5G04240.
KEGGiath:AT5G04240.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY664500 mRNA. Translation: AAT77780.1.
AL391716 Genomic DNA. Translation: CAC05506.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED90717.1.
AK222064 mRNA. Translation: BAD94870.1. Different initiation.
RefSeqiNP_196044.2. NM_120506.4.
UniGeneiAt.10092.
At.72547.

3D structure databases

ProteinModelPortaliQ6BDA0.
SMRiQ6BDA0. Positions 14-442, 1216-1336.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15583. 1 interaction.
DIPiDIP-46102N.
IntActiQ6BDA0. 1 interaction.
STRINGi3702.AT5G04240.1.

Proteomic databases

PaxDbiQ6BDA0.
PRIDEiQ6BDA0.
ProMEXiQ6BDA0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G04240.1; AT5G04240.1; AT5G04240.
GeneIDi830303.
GrameneiAT5G04240.1; AT5G04240.1; AT5G04240.
KEGGiath:AT5G04240.

Organism-specific databases

TAIRiAT5G04240.

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
KOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000239739.
InParanoidiQ6BDA0.
OMAiKARTPYK.
PhylomeDBiQ6BDA0.

Miscellaneous databases

PROiQ6BDA0.

Gene expression databases

GenevisibleiQ6BDA0. AT.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time."
    Noh B., Lee S.H., Kim H.J., Yi G., Shin E.A., Lee M., Jung K.J., Doyle M.R., Amasino R.M., Noh Y.S.
    Plant Cell 16:2601-2613(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY.
  2. "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana."
    Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E., Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.
    , Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A., Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I., Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T., Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U., Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.
    Nature 408:823-826(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
    Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
    , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
    Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 858-1340.
    Strain: cv. Columbia.
  5. "Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence."
    Zhou X., Ma H.
    BMC Evol. Biol. 8:294-294(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE.
  6. "Comparative analysis of JmjC domain-containing proteins reveals the potential histone demethylases in Arabidopsis and rice."
    Lu F., Li G., Cui X., Liu C., Wang X.J., Cao X.
    J. Integr. Plant Biol. 50:886-896(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY, NOMENCLATURE, TISSUE SPECIFICITY.
  7. "Modulation of brassinosteroid-regulated gene expression by Jumonji domain-containing proteins ELF6 and REF6 in Arabidopsis."
    Yu X., Li L., Li L., Guo M., Chory J., Yin Y.
    Proc. Natl. Acad. Sci. U.S.A. 105:7618-7623(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH BZR2, DISRUPTION PHENOTYPE.
  8. "Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis."
    Jeong J.H., Song H.R., Ko J.H., Jeong Y.M., Kwon Y.E., Seol J.H., Amasino R.M., Noh B., Noh Y.S.
    PLoS ONE 4:E8033-E8033(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiELF6_ARATH
AccessioniPrimary (citable) accession number: Q6BDA0
Secondary accession number(s): Q56WH6, Q9FYD7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 21, 2011
Last sequence update: September 13, 2004
Last modified: May 11, 2016
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.