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 Pavir.9KG207900.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family C2H2
Protein Properties Length: 399aa    MW: 42696.2 Da    PI: 9.3754
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG207900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.61.1e-0585107123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C++C+k F r  nL+ H r H
  Pavir.9KG207900.1.p  85 FVCEICNKGFQRDQNLQLHRRGH 107
                          89*******************88 PP
2zf-C2H2140.00014159181123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          ++C+ Cgk++  +s+ k H + +
  Pavir.9KG207900.1.p 159 WRCERCGKRYAVQSDWKAHVKGC 181
                          58*****************9866 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.09E-884107No hitNo description
Gene3DG3DSA:3.30.160.601.2E-584107IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.01785107IPR015880Zinc finger, C2H2-like
PfamPF121716.0E-585107IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.94985107IPR007087Zinc finger, C2H2
PROSITE patternPS00028087107IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.607.3E-4148179IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.09E-8154179No hitNo description
SMARTSM0035595159179IPR015880Zinc 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: 399 aa     Download sequence    Send to blast
MMLSDLSSDH EATGSSSHGG DIAISYALSP LFLAPAASAT APPPRPEAPP RAAGAKRKRS  60
QPGNPEPGAE VIALSPRTLV ATNRFVCEIC NKGFQRDQNL QLHRRGHNLP WKLRQRTSLP  120
SSGGGRQGDA AAAPPRKRVY VCPEPTCKHF SRKHGEKRWR CERCGKRYAV QSDWKAHVKG  180
CGTREYRCDC GILFTRKDSL LTHRAFCDAL AEESARLLAA AAASNGGSAI TTTNRSNGGN  240
TSSDLLFSSS IATPLFLPFP NPPPPPAAAA AQNPNAFYFL HQGQQPQQLA RPFLQPRMMV  300
QPSPYLIDLH ADATAGGGDT VNFGGLPPDS SVALRGGGHR RLTRDFLGVD GGGQVEELQL  360
PPPLYAATTA AASCATDLTR QCLGERLPPV NETWSHNF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-32155217365Zinc finger protein JACKDAW
5b3h_F3e-32155217365Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.316052e-51root
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Detected in young expanded leaves emerging from the culms (PubMed:18774969). In young panicles, accumulates in spikelets and panicle branches (PubMed:18774969). Under short days (SD), observed in leaves by 1 week after germination and reaches a peak by 2 weeks. Subsequently, the level gradually decreases, but maintains at low levels even after flowering (about 9 weeks) (PubMed:18790997). Under long days (LD), present in leaves at low levels during all developmental stages from at least 1 week after germination (PubMed:18790997). {ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997}.
UniprotTISSUE SPECIFICITY: Mostly expressed in developing leaves (more in sheaths than in blades, especially in the outer epidermal cell of immature leaves and in the region immediately beneath the meristem where internodes are visible) and panicles, and, at very low levels, around the shoot apex and in roots. {ECO:0000269|PubMed:18725639, ECO:0000269|PubMed:18774969, ECO:0000269|PubMed:18790997, ECO:0000269|PubMed:24280027}.
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG207900.1.p
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0587577e-97AF058757.1 Zea mays zinc finger protein ID1 (id1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004983079.11e-179protein indeterminate-domain 12
SwissprotB1B5341e-122EHD2_ORYSJ; Protein EARLY HEADING DATE 2
TrEMBLA0A2T7C6N30.0A0A2T7C6N3_9POAL; Uncharacterized protein
STRINGSi036003m1e-161(Setaria italica)
STRINGGRMZM2G011357_P011e-161(Zea mays)
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
AT1G03840.12e-74C2H2 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]