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 Sobic.003G394900.1.p
Common NameSb03g043210, SORBIDRAFT_03g043210
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family C2H2
Protein Properties Length: 1346aa    MW: 149029 Da    PI: 8.7311
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.003G394900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2140.0001513071333123
                            EEET..TTTEEESSHHHHHHHHHH..T CS
               zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                            y+Cp   Cg++F+  s++ rH r+  H
  Sobic.003G394900.1.p 1307 YVCPepECGQTFRFVSDFSRHKRRtgH 1333
                            99********************98666 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005457.7E-151859IPR003349JmjN domain
PROSITE profilePS5118313.4811960IPR003349JmjN domain
PfamPF023759.9E-132053IPR003349JmjN domain
SMARTSM005582.3E-48184353IPR003347JmjC domain
PROSITE profilePS5118435.433187353IPR003347JmjC domain
SuperFamilySSF511971.35E-25200350No hitNo description
PfamPF023732.2E-38217336IPR003347JmjC domain
SMARTSM003553412241246IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.09412471276IPR007087Zinc finger, C2H2
SMARTSM003551312471271IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012491271IPR007087Zinc finger, C2H2
SuperFamilySSF576673.68E-1512581318No hitNo description
Gene3DG3DSA:3.30.160.602.0E-912751301IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.63512771306IPR007087Zinc finger, C2H2
SMARTSM003557.8E-412771301IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028012791301IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.4E-1013021329IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.7413071333IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.32313071338IPR007087Zinc finger, C2H2
PROSITE patternPS00028013091333IPR007087Zinc 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:0033169Biological Processhistone H3-K9 demethylation
GO:0035067Biological Processnegative regulation of histone acetylation
GO:0040010Biological Processpositive regulation of growth rate
GO:0045815Biological Processpositive regulation of gene expression, epigenetic
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
GO:0071558Molecular Functionhistone demethylase activity (H3-K27 specific)
Sequence ? help Back to Top
Protein Sequence    Length: 1346 aa     Download sequence    Send to blast
MASSQGEPVP PWLKSLPLAP EFRPTAAEFV DPIAYLLKIE PAAAPFGICK IVPPLPPPPK  60
RATLGNLSRS FAALHPDDPT PTFPTRHQQL GLCPRRPRPA LKPVWLSSHR YTLPKFEAKA  120
GASRKALLAR LSVPATKQLS PLDVEALFWR SSADRPVVVE YASDMPGSGF APCAARPTQL  180
PAANVGETAW NMRGVARSPA SLLRFVREEV PGVTSPMLYV GMMFSWFAWH VEDHDLHSLN  240
YMHYGAPKTW YAVPRDAALA FEEVVRVHGY GGEVNSLETF AMLGDKTTVM SPQVLVDSGI  300
PCCRLVQNAG EFVVTFPRAY HSGFSHGFNC GEASNIATPE WLRVAKEAAV RRASINRPPM  360
VSHYQLLYEL ALSLCLRDPS NGTMEPRSCR LKEKKKSEGD QLIKKIFVQN VIEDNKLLGH  420
FLSDGSSCII LPVNYSDGSP LSTLLSKFQS TTDSRISHDQ CSKTEAPKDS RCLPKDQADK  480
NWELSSSNKI SLSVCSGKTV PPTTCIYDCA NMSASSYTHN TENNKGGMNS AAGLLDQGLL  540
SCVACGILSF SCVAVIKPRE CAAKWLMTAD SSLINDRLAS SGEHHMIDGL QGGRTTGGIL  600
RSDSEMNGNS IISDADDVPL NGCSALDLLA SAYGDPSDSD EDVMNKKIQI PNVSNELINH  660
TVESQPNTSN NGDCDGTKVS SSSKESQQGP TSQNSKCIGN SNTLNGPKGV RTRNKDLLKM  720
VLSEGFQPKD IYSETHKKVQ CEPSSSNKTS TESPCSTEYH VSHNSATICM DNNRGSMTMV  780
NNLVTSVVKP DKDSSRMHVF CLEHAIEVEK QLQAIGGADI FLLCRPEYPR IEVEARLLAE  840
EMEFVYDWKD ILFKEATIED REKIQEVVQD EEAIPTNSDW AVKLGINLYY SANLAKSPLY  900
NKQVPYNRVI YEAFGYGSPN DSPVKLKTYS RRQGRAKKIV LAGRWCGKVW MSNQVHPYLA  960
DRIKIHEPEE TDETFPSDQK SNAEPVEDSS RQAASTRKSS SRAIEGKISK REKESLEKAN  1020
AKKPKITEED NSKSLEGTAE ASTQSRTALE KTSRKEKEHV EKANTKKLKH TEKVSEAIKG  1080
PSEASYPAPA GMVVRSSSRI ANRKSMLKSR MDEEDIGSTN RPKSKVEDDK DNPAGRSTAK  1140
SLRQKTKLDA KKKTKETRVE KRKAPSPASQ KDEEEQSYEG CSITKQRLSL RKKGAKIEEK  1200
QQQMEKSRYR GRAPPSSPKS KEEYACDVEG CSMSFGTEEA LSLHKNDICP EKGCCRKFFS  1260
HKYLLQHRKV HTDDRPLKCP WKGCSMAFKW PWARTEHMRV HTGDRPYVCP EPECGQTFRF  1320
VSDFSRHKRR TGHAGMPAKK AKAKK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-76123748353Transcription factor jumonji (Jmj) family protein
6ip4_A2e-76123748353Arabidopsis JMJ13
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaves and flag leaves. Expressed at low levels in roots, shoots, stems and panicles. {ECO:0000269|PubMed:24280387}.
Functional Description ? help Back to Top
Source Description
UniProtHistone demethylase that demethylates 'Lys-27' (H3K27me) of histone H3 with a specific activity for H3K27me3 and H3K27me2. No activity on H3K4me3, H3K9me3, H3K27me1 and H3K36me3. Involved in biotic stress response. May demethylate H3K27me3-marked defense-related genes and increase their basal and induced expression levels during pathogen infection. {ECO:0000269|PubMed:24280387}.
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
PlantRegMapSobic.003G394900.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By salt stress, abscisic acid (ABA), jasmonic acid (JA), the ethylene precursor ACC and infection by the bacterial pathogen Xanthomonas oryzae pv. oryzae. {ECO:0000269|PubMed:24280387}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9490540.0EU949054.1 Zea mays clone 394823 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021310712.10.0lysine-specific demethylase JMJ705
SwissprotQ5N7120.0JM705_ORYSJ; Lysine-specific demethylase JMJ705
TrEMBLA0A1B6Q7Q40.0A0A1B6Q7Q4_SORBI; Uncharacterized protein
STRINGSb03g043210.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP53463246
Representative plantOGRP44011217
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. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]