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.3KG213300.1.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: 319aa    MW: 34617.1 Da    PI: 6.7785
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG213300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH47.52.9e-15245269226
                          -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                          ktelC+ + +tG C+yGd+C+FaHg
  Pavir.3KG213300.1.p 245 KTELCNKWEETGACPYGDQCQFAHG 269
                          9***********************8 PP
2zf-CCCH21.34.8e-07282307126
                          --S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                          ykte Cr  +++  C+yG rC+F H+
  Pavir.3KG213300.1.p 282 YKTEVCRMVLAGAVCPYGHRCHFRHS 307
                          9**********88**********997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1000.103.4E-18239276IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.7E-10240275IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.488243271IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-8243270IPR000571Zinc finger, CCCH-type
PfamPF006422.5E-12245269IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.3E-12277308IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.83E-8277310IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.394281309IPR000571Zinc finger, CCCH-type
SMARTSM003562.7E-4281308IPR000571Zinc finger, CCCH-type
PfamPF006423.0E-4282307IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0051511Biological Processnegative regulation of unidimensional cell growth
GO:1901347Biological Processnegative regulation of secondary cell wall biogenesis
GO:0003729Molecular FunctionmRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 319 aa     Download sequence    Send to blast
MEMVLAPAQP DGLHAAFGPK KPCGFGDPRF SSPNLLPNGG DLFYGYPSPS SPFGLGRALF  60
TPSPRAASLS RGSSDSGSIV DDGNDAATAA AAERRQRLAR IALQYQEVVT RFEFCLSYLA  120
DTSNEAAALR RENDELRIAN EDLAKLVDEF SSLSLTEEHP IPLSPLTPLP AAPAIPKSIS  180
VRSPVYLKMN QNGKHRPSKP TKLGSQRVFV GMDGGVNGEG ELKGGEEQQP NSGLEFEVYN  240
QGMLKTELCN KWEETGACPY GDQCQFAHGI AELRPVIRHP RYKTEVCRMV LAGAVCPYGH  300
RCHFRHSINP TDLFPLHP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A2e-21245309569Butyrate response factor 2
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.227191e-142root
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG213300.1.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
GenBankEU9592351e-88EU959235.1 Zea mays clone 212775 nucleic acid binding f mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808834.10.0zinc finger CCCH domain-containing protein 39-like
SwissprotQ6L5G11e-112C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLA0A2S3H9C90.0A0A2S3H9C9_9POAL; Uncharacterized protein
TrEMBLA0A3L6R9Y50.0A0A3L6R9Y5_PANMI; Zinc finger CCCH domain-containing protein 39-like
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
AT1G66810.12e-53C3H 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]