PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Medtr3g075210.1
Common NameMTR_3g075210
Organism
Medicago truncatula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago
Family C2H2
Protein Properties Length: 1573aa    MW: 177196 Da    PI: 8.0987
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Medtr3g075210.1genomeMtView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2156.9e-0514561481123
                       EEET..TTTEEESSHHHHHHHHHH.T CS
          zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                       y+C    C++sF +k++L++H r+ +
  Medtr3g075210.1 1456 YQCDieGCTMSFESKDELVHHKRNiC 1481
                       99********************9877 PP
2zf-C2H212.80.0003514811503323
                       ET..TTTEEESSHHHHHHHHHHT CS
          zf-C2H2    3 Cp..dCgksFsrksnLkrHirtH 23  
                       Cp   Cgk F ++ +L++H r+H
  Medtr3g075210.1 1481 CPvkGCGKKFFSHKYLVQHRRVH 1503
                       9999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005453.1E-141758IPR003349JmjN domain
PROSITE profilePS5118313.3841859IPR003349JmjN domain
PfamPF023751.3E-121952IPR003349JmjN domain
SuperFamilySSF511977.14E-27150337No hitNo description
SMARTSM005581.7E-49172341IPR003347JmjC domain
PROSITE profilePS5118434.79172341IPR003347JmjC domain
PfamPF023735.9E-36205324IPR003347JmjC domain
Gene3DG3DSA:3.30.160.601.6E-414471478IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003555.414561478IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.50814791508IPR007087Zinc finger, C2H2
SMARTSM003550.004514791503IPR015880Zinc finger, C2H2-like
SuperFamilySSF576676.8E-614791515No hitNo description
Gene3DG3DSA:3.30.160.601.4E-514801507IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014811503IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.9E-815081533IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.82415091538IPR007087Zinc finger, C2H2
SMARTSM003550.001615091533IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015111533IPR007087Zinc finger, C2H2
SuperFamilySSF576675.2E-915191561No hitNo description
Gene3DG3DSA:3.30.160.603.8E-915341561IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003551.215391565IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.76215391570IPR007087Zinc finger, C2H2
PROSITE patternPS00028015411565IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0032259Biological Processmethylation
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0008168Molecular Functionmethyltransferase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1573 aa     Download sequence    Send to blast
MAESNGDVFP WLKSMPVAPE YRPTPAEFED PIAYIFKIEN EASKFGICKI IPPFPPSSKK  60
TTISNLNRSF PNSTFTTRQQ QIGFCPRKPR PVKRPVWQSG DHYTFSEFEA KAKWFERSYM  120
NKKKKNSNSA LEIETLFWKA TVDKPFSVEY ANDMPGSAFA DTVENNNKPF SSVANSTWNM  180
RRVSRAKGSL LRFMKEEIPG VTSPMVYLAM LFSWFAWHVE DHDLHSLNYL HMGASKTWYG  240
VPRDAAVAFE DVVRVHGYGG EINPLVTFSI LGEKTTVMSP EVFISAGVPC CRLVQNAGEF  300
VVTFPRAYHT GFSHGFNCAE AANIATPEWL RVAKDAAIRR ASINYSPMVS HLQLLYDLAL  360
ALCSRIPGGI SAAPRSSRLK DKKKGEGEAV IKELFVQDVL QNNDLLHVLG NESSVVLLPR  420
NSVDISSCSK LRVGCRPPKV NPGFSFDVCN SEGLSSSKGF VSDDLVFDRN RGIAQEKNLC  480
SVNDELTLLS EGKGIPSLDA NGNKSPSSSK QLQRDSESET SQGDGLSEQR LFSCVTCGLL  540
NFSCVAIVQP REPAARYLMS ADCSFFNDWV AASGLPGSNK YTAPHEDAHI PEPNMYAGWT  600
KKNAQEEALH SEGENGNTAA TALALLASAY GSSSDSEEDA VDGHESNAIN FTSESLPSNF  660
CDSNDNPMTI LDKDDTLSES ASYEAHRNEC NLSHHPRDQS FEEQDYKITS GAAFENTRAM  720
PYSTTYSSRD TNDAEKSLSI EAIVPVNHKN VLLVPQCDEE SSRMHVFCLE HAVEAEQQLR  780
PIGGAHILLL CHPDYPKIEA EAQLVAEDLG IDCTWKNIAY RHGTKEDEKR IQSALDSEEA  840
SLGNGDWTVK LGINLFYSAS LSRSPLYSKQ MPYNSVIYYA FGRSSPASSP IEPKVYQRRA  900
DKQKKVVAGK WCGKVWMSNQ VHPLLAIRDS EYVEDERSLR GLVLPDVKIE RSGSTPKTAT  960
AITKSGRKRK TTSESRRRIR KGNFDDKDVV LDNSAEDEPS PRPRRFLRSK QAKGVEKDGA  1020
ALQRNCSPYH HRKPISKQTN CTESDVVSDD SIDDDYMQNR WSFNVKKAKF AGNEVVSDDA  1080
EDYDSDCHQM EELRSNQDEG TERDSVSEDS LDVGSLPLHR KTSRSKHADY IGEDAISDDQ  1140
MESGCQKQKK RIAKSWQGKY LAEKDSVISD DQLELNKLKQ QRGNPKSRKA RNLANEDAVS  1200
DDQTNVYRRK YQRRAVKVRQ AKCVAEEDVM SDDQLEVSYQ RHKTGISRRK NKGIDRVKNE  1260
MSDDQLDDHF QKQQRKNPRS RHIKQTDEED IDDSADNNAH LLHRNPKRKK AKCKDEDHMI  1320
LDNEMEDDSL QQRKRTLPSK QSKRKTLKQM KQSKTLQMKN QTPQPVKRGA QKNAKQVKQP  1380
SHLRSNLSDN SREPSIDMEE DEEGGPSTRL RKRVLKAQES EVKSKDRETK RKRANGVAAA  1440
KVSACNPKSE DEEAEYQCDI EGCTMSFESK DELVHHKRNI CPVKGCGKKF FSHKYLVQHR  1500
RVHEDDRPLK CPWKGCKMSF KWAWARTEHI RVHTGARPYA CAEPGCGQTF RFVSDFSRHK  1560
RKTGHLAKKI RQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-7943621353Transcription factor jumonji (Jmj) family protein
6ip4_A5e-7943621353Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
114101432RKRVLKAQESEVKSKDRETKRKR
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in the shoot apical meristem and primary and secondary root tips, and lower expression in cotyledons, leaves and root axis along vascular tissues. Detected in inflorescences, stems and siliques. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3. Demethylates both tri- (H3K27me3) and di-methylated (H3K27me2) H3K27me (PubMed:21642989, PubMed:27111035). Demethylates also H3K4me3/2 and H3K36me3/2 in an in vitro assay (PubMed:20711170). Involved in the transcriptional regulation of hundreds of genes regulating developmental patterning and responses to various stimuli (PubMed:18467490). Binds DNA via its four zinc fingers in a sequence-specific manner, 5'-CTCTGYTY-3', to promote the demethylation of H3K27me3 and the regulation of organ boundary formation (PubMed:27111034, PubMed:27111035). Involved in the regulation of flowering time by repressing FLOWERING LOCUS C (FLC) expression (PubMed:15377760). Interacts with the NF-Y complexe to regulate SOC1 (PubMed:25105952). Mediates the recruitment of BRM to its target loci (PubMed:27111034). {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:20711170, ECO:0000269|PubMed:21642989, ECO:0000269|PubMed:25105952, ECO:0000269|PubMed:27111034, ECO:0000269|PubMed:27111035}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00608ChIP-seqTransfer from AT3G48430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapMedtr3g075210.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2357530.0AC235753.2 Medicago truncatula clone mth2-128c9, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013460954.10.0lysine-specific demethylase REF6 isoform X2
SwissprotQ9STM30.0REF6_ARATH; Lysine-specific demethylase REF6
TrEMBLA0A072V0U60.0A0A072V0U6_MEDTR; Lysine-specific demethylase REF6-like protein, putative
STRINGAES856630.0(Medicago truncatula)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF56483250
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G48430.10.0relative of early flowering 6
Publications ? help Back to Top
  1. Young ND, et al.
    The Medicago genome provides insight into the evolution of rhizobial symbioses.
    Nature, 2011. 480(7378): p. 520-4
    [PMID:22089132]
  2. Li C, et al.
    Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 687-93
    [PMID:27111034]
  3. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  4. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
    [PMID:27134142]
  5. Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE
    Research progress on the autonomous flowering time pathway in Arabidopsis.
    Physiol Mol Biol Plants, 2017. 23(3): p. 477-485
    [PMID:28878488]
  6. Li C, et al.
    Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis.
    Plant Biotechnol. J., 2018. 16(8): p. 1446-1451
    [PMID:29331085]
  7. Wang X, et al.
    The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis.
    PLoS Genet., 2019. 15(4): p. e1008068
    [PMID:30969965]
  8. Qiu Q, et al.
    DNA methylation repels targeting of Arabidopsis REF6.
    Nat Commun, 2019. 10(1): p. 2063
    [PMID:31048693]