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 Pavir.3KG216500.1.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 C3H
Protein Properties Length: 329aa    MW: 35631.3 Da    PI: 6.776
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG216500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH47.43e-15255279226
                          -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                          ktelC+ + +tG C+yGd+C+FaHg
  Pavir.3KG216500.1.p 255 KTELCNKWEETGACPYGDQCQFAHG 279
                          9***********************8 PP
2zf-CCCH19.71.5e-06292317126
                          --S---SGGGGTS.--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartG.tCkyGdrCkFaHg 26 
                          ykte Cr  ++ G  C+yG rC+F H+
  Pavir.3KG216500.1.p 292 YKTEVCRMVLA-GvVCPYGHRCHFRHS 317
                          9**********.66**********997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.103.5E-18249286IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.7E-10250285IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-8253280IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.488253281IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-12255279IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.32E-8287320IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.2E-11287318IPR000571Zinc finger, CCCH-type
SMARTSM003564.8E-4291318IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.188291319IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 329 aa     Download sequence    Send to blast
MEVVLAPDQP DGLHAAFGPK EPCGFGDRRF STPSLLNGGD LFYGYPSPSS PFGLGRVLSS  60
PSPRAASLSR GSSDSGSVVD EGNDAAAAAA AAAERRQRLA RLALQYQEVV TCFEVCLSYL  120
ADTSNEAATL RRENDELRIA NEDLARRIKM VGGRLVDEFS GLSLTEEHPI PLLPLTPLPA  180
PPAIPKSISV RSPVYLKMNQ NGKHRPSKPT KLGSPQRVSV GMESGVNGEG ELKGGEEQQP  240
NSGLEFEVYN QGMLKTELCN KWEETGACPY GDQCQFAHGI AELRPVIRHP RYKTEVCRMV  300
LAGVVCPYGH RCHFRHSINP TDLFPLHP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A5e-22255317567Butyrate response factor 2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.227191e-154root
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG216500.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0985716e-94AC098571.2 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1126_B10, complete sequence.
GenBankAC0988326e-94AC098832.3 Oryza sativa Japonica Group cultivar Nipponbare chromosome 5 clone OJ1268_B08, complete sequence.
GenBankAK1063546e-94AK106354.1 Oryza sativa Japonica Group cDNA clone:002-102-A03, full insert sequence.
GenBankAP0149616e-94AP014961.1 Oryza sativa Japonica Group DNA, chromosome 5, cultivar: Nipponbare, complete sequence.
GenBankCP0126136e-94CP012613.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 5 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808834.10.0zinc finger CCCH domain-containing protein 39-like
SwissprotQ6L5G11e-107C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLA0A2T7EA080.0A0A2T7EA08_9POAL; Uncharacterized protein
STRINGPavir.J13968.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP27753784
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G66810.13e-52C3H family protein
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]
  2. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]