PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID ORGLA10G0088000.1
Organism
Oryza glaberrima
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family C2H2
Protein Properties Length: 409aa    MW: 44267.4 Da    PI: 8.0487
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ORGLA10G0088000.1genomeAGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.81.9e-053961123
                       EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                       ++C+ C+k F r  nL+ H r H
  ORGLA10G0088000.1 39 FVCEVCNKGFQRDQNLQLHRRGH 61
                       89*******************88 PP
2zf-C2H213.30.00026124146123
                        EEETTTTEEESSHHHHHHHHHHT CS
            zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                        ++C+ Cgk++  +s+ k H +++
  ORGLA10G0088000.1 124 WRCERCGKRYAVHSDWKAHVKNC 146
                        58******************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.42E-73861No hitNo description
Gene3DG3DSA:3.30.160.608.3E-63861IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.973961IPR007087Zinc finger, C2H2
PfamPF121717.5E-53961IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.0213961IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002804161IPR007087Zinc finger, C2H2
SMARTSM003558989119IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.2E-4112144IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.42E-7119144No hitNo description
SMARTSM0035599124144IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 409 aa     Download sequence    Send to blast
MAAAQEPRAK KKRSLPGNPD PEAEVIALSP RALVATNRFV CEVCNKGFQR DQNLQLHRRG  60
HNLPWKLRHR AAAVSAVTTA APAPRKRVYV CPEPTCVHHD PARALGDLTG IKKHFSRKHG  120
EKRWRCERCG KRYAVHSDWK AHVKNCGTRE YRCDCGILFS RKDSLLTHRA FCDALAEESA  180
RLLAAANNSS SITTTTCNNS NISSNNNNNN INSISNSNNL LITSSSSSPP LFLPFSTTPA  240
ENPNPNQLLF LQQHQAAHHQ LLLPQFQQPP SSPPAYFDHL AFGGGGGVIT GSSCNDDNSS  300
IAGDVMVAAG GDSVSFGLTS EGSVTMHAGD VGRRRLTRDF LGVDHDAGEV DELELDELPA  360
DLSTTAAACQ GCNFAAATTA ACCATDFTTG SRQYLGRLPP VNETWSHNF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-33120188371Zinc finger protein JACKDAW
5b3h_F6e-33120188371Zinc finger protein JACKDAW
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that acts as a flowering master switch in both long and short days, independently of the circadian clock (PubMed:18790997, PubMed:18725639, PubMed:18774969, PubMed:19304997, PubMed:24280027). Promotes flowering upstream of HD1 by up-regulating FTL1, FTL4, FTL5, FTL6, EHD1, HD3A and RFT1 (PubMed:18790997, PubMed:18725639, PubMed:18774969). Seems to repress FTL11 expression (PubMed:18725639). May recognize the consensus motif 5'-TTTGTCGTAAT-3' in target gene promoters (PubMed:18725639). {ECO:0000269|PubMed:18725639, ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997, ECO:0000269|PubMed:24280027, ECO:0000303|PubMed:19304997}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00673SELEXTransfer from GRMZM2G011357Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapORGLA10G0088000.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by FKF1 (PubMed:25850808). Down-regulated by DLF1 (PubMed:25036785). During the basic vegetative growth phase (BVP, photoperiod-insensitive phase), suppressed via phytochrome-mediated light signals involving the phytochromobilin synthase HY2 (PubMed:25573482). {ECO:0000269|PubMed:25036785, ECO:0000269|PubMed:25573482, ECO:0000269|PubMed:25850808}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB3591960.0AB359196.1 Oryza sativa Japonica Group Ehd2 mRNA for early heading date 2, complete cds, cultivar: Tohoku IL9.
GenBankFJ0095780.0FJ009578.1 Oryza sativa Japonica Group cultivar Zhonghua 11 Cys2/His2-type zinc finger transcription factor (RID1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015614407.10.0protein indeterminate-domain 12
SwissprotB1B5340.0EHD2_ORYSJ; Protein EARLY HEADING DATE 2
TrEMBLA0A0E0QZ670.0A0A0E0QZ67_ORYRU; Uncharacterized protein
STRINGORUFI10G10700.10.0(Oryza rufipogon)
STRINGOS10T0419200-000.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP130962832
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G03840.13e-91C2H2 family protein
Publications ? help Back to Top
  1. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  2. Park SJ, et al.
    Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod.
    Plant J., 2008. 56(6): p. 1018-29
    [PMID:18774969]
  3. Song Y,Gao Z,Luan W
    Interaction between temperature and photoperiod in regulation of flowering time in rice.
    Sci China Life Sci, 2012. 55(3): p. 241-9
    [PMID:22527521]
  4. Hu S, et al.
    A point mutation in the zinc finger motif of RID1/EHD2/OsID1 protein leads to outstanding yield-related traits in japonica rice variety Wuyunjing 7.
    Rice (N Y), 2013. 6(1): p. 24
    [PMID:24280027]
  5. Cai Y, et al.
    Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice.
    PLoS ONE, 2014. 9(7): p. e102529
    [PMID:25036785]
  6. Yoshitake Y, et al.
    The effects of phytochrome-mediated light signals on the developmental acquisition of photoperiod sensitivity in rice.
    Sci Rep, 2015. 5: p. 7709
    [PMID:25573482]
  7. Han SH,Yoo SC,Lee BD,An G,Paek NC
    Rice FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (OsFKF1) promotes flowering independent of photoperiod.
    Plant Cell Environ., 2015. 38(12): p. 2527-40
    [PMID:25850808]
  8. Jin J, et al.
    MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice.
    Plant Physiol., 2015. 168(4): p. 1275-85
    [PMID:25855537]
  9. Brambilla V,Gomez-Ariza J,Cerise M,Fornara F
    The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals.
    Front Plant Sci, 2017. 8: p. 665
    [PMID:28491078]