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.6NG358100.2.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 C2H2
Protein Properties Length: 529aa    MW: 54593 Da    PI: 9.7011
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG358100.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.41.3e-056385123
                         EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                         ++C+ C+k F r  nL+ H r H
  Pavir.6NG358100.2.p 63 FVCEVCNKGFQREQNLQLHRRGH 85
                         89*******************88 PP
2zf-C2H213.20.00026139161123
                          EEETTTTEEESSHHHHHHHHHHT CS
              zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                          +kC +C+k++  +s+ k H +t+
  Pavir.6NG358100.2.p 139 WKCDKCNKRYAVQSDWKAHSKTC 161
                          58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.73E-76285No hitNo description
Gene3DG3DSA:3.30.160.607.2E-66285IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.0946385IPR007087Zinc finger, C2H2
SMARTSM003550.00416385IPR015880Zinc finger, C2H2-like
PfamPF121713.4E-56385IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002806585IPR007087Zinc finger, C2H2
SMARTSM00355300104134IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.603.9E-5127160IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.73E-7134159No hitNo description
SMARTSM00355110139159IPR015880Zinc 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: 529 aa     Download sequence    Send to blast
MAAAHLFGLG DAQMQPPLPQ QAAPPPPAAA PAPKKKRNQP GNPNPDAEVI ALSPKSLLAT  60
NRFVCEVCNK GFQREQNLQL HRRGHNLPWK LKQKNPKETR RRVYLCPEPT CVHHDPSRAL  120
GDLTGIKKHY CRKHGEKKWK CDKCNKRYAV QSDWKAHSKT CGTREYRCDC GTLFSRRDSF  180
ITHRAFCDAM AQESARAPPI GAGMYGSGGM ALGLSGLAAS QLHSFQDQAH SSAATAIGGN  240
PAAQFEHLMP SSAGSPAFRG AQPASSSSSP FYLGGAEDGH QSQPGHTSLL HGKPAFHGLM  300
QLPEQHGQPG SNGLLNLGFF SGASSGQDAR LVFPNQFNGA TGGNGRGDGS EHGNSGANTG  360
SAAIFSGNLM GNQMAGGGGG FSSSLYNSTE TVAPPQMSAT ALLQKAAQMG ATTSGGGGGS  420
VNSLLRGLGS GGALNGRPSG AAGFMAGESS SSRSTSQAEN ESQFRDLMNS LAASGSGGFP  480
GMDDGKLSTR DFLGVSGGVV RSMGGAAGLP LRHGAAGIGM GSLDPEMK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-34135196364Zinc finger protein JACKDAW
5b3h_F9e-34135196364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.45240.0callus| leaf| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269|PubMed:22898356, ECO:0000269|PubMed:24821766}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00255DAPTransfer from AT2G02070Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG358100.2.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0539560.0BT053956.1 Zea mays full-length cDNA clone ZM_BFc0072P10 mRNA, complete cds.
GenBankEU9759570.0EU975957.1 Zea mays clone 506559 INDETERMINATE-related protein 1 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025821061.10.0protein indeterminate-domain 5, chloroplastic-like isoform X1
SwissprotQ9ZUL31e-123IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A3L6PM370.0A0A3L6PM37_PANMI; INDETERMINATE-related protein 1
STRINGPavir.Fb02381.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02080.11e-112indeterminate(ID)-domain 4
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]