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.3KG213300.2.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: 318aa    MW: 34489 Da    PI: 6.7785
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG213300.2.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-15244268226
                          -S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   2 ktelCrffartGtCkyGdrCkFaHg 26 
                          ktelC+ + +tG C+yGd+C+FaHg
  Pavir.3KG213300.2.p 244 KTELCNKWEETGACPYGDQCQFAHG 268
                          9***********************8 PP
2zf-CCCH21.34.7e-07281306126
                          --S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHg 26 
                          ykte Cr  +++  C+yG rC+F H+
  Pavir.3KG213300.2.p 281 YKTEVCRMVLAGAVCPYGHRCHFRHS 306
                          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-18238275IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.7E-10239274IPR000571Zinc finger, CCCH-type
SMARTSM003561.1E-8242269IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.488242270IPR000571Zinc finger, CCCH-type
PfamPF006422.5E-12244268IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.105.3E-12276307IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.83E-8276309IPR000571Zinc finger, CCCH-type
SMARTSM003562.7E-4280307IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.394280308IPR000571Zinc finger, CCCH-type
PfamPF006423.0E-4281306IPR000571Zinc 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: 318 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 TKLGSRVFVG MDGGVNGEGE LKGGEEQQPN SGLEFEVYNQ  240
GMLKTELCNK WEETGACPYG DQCQFAHGIA ELRPVIRHPR YKTEVCRMVL AGAVCPYGHR  300
CHFRHSINPT DLFPLHP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1rgo_A2e-21244308569Butyrate 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.3KG213300.2.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-110C3H39_ORYSJ; Zinc finger CCCH domain-containing protein 39
TrEMBLA0A2S3H9Q30.0A0A2S3H9Q3_9POAL; Uncharacterized protein
STRINGPavir.J13968.1.p0.0(Panicum virgatum)
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]