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.5KG680100.3.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 MIKC_MADS
Protein Properties Length: 252aa    MW: 27919.5 Da    PI: 9.4562
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5KG680100.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF978.1e-31959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krien++nrqvtf+kRrng+lKKA+ELS+LCdae+a++ifss+g+lyeys+
  Pavir.5KG680100.3.p  9 KRIENTTNRQVTFCKRRNGLLKKAYELSILCDAEIALVIFSSRGRLYEYST 59
                         79***********************************************96 PP
2K-box90.23.8e-3083168994
                K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaL 94 
                           + + +++ qqe+akL ++i++Lq++++hl+Ge++++++ keL+++e++Le+++ +iRskK+e+ll++ie++qk+  e+++++++ 
  Pavir.5KG680100.3.p  83 IDVNSHQYFQQEAAKLHQQIQTLQNSNKHLMGESIGNMTAKELRSIESRLERGIGRIRSKKHEMLLAEIEYMQKRVAEAERAQQEA 168
                          566889*************************************************************************9998875 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004329.7E-42160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.894161IPR002100Transcription factor, MADS-box
CDDcd002654.32E-46275No hitNo description
SuperFamilySSF554552.35E-32274IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004042.2E-32323IPR002100Transcription factor, MADS-box
PfamPF003194.1E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004042.2E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004042.2E-323859IPR002100Transcription factor, MADS-box
PfamPF014862.2E-2285166IPR002487Transcription factor, K-box
PROSITE profilePS5129712.71588193IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 252 aa     Download sequence    Send to blast
MGRGKIEIKR IENTTNRQVT FCKRRNGLLK KAYELSILCD AEIALVIFSS RGRLYEYSTN  60
SVRSTIERYK KASASTSGTA PVIDVNSHQY FQQEAAKLHQ QIQTLQNSNK HLMGESIGNM  120
TAKELRSIES RLERGIGRIR SKKHEMLLAE IEYMQKRVAE AERAQQEAAE DQMTPPPDGA  180
EATTTELQAL PPSLDPRGYY LQAAQATMLA AASTASSSSS SQHQQEHHLQ TALHLGYHIK  240
VDSAAASKGF L*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P3e-21173173Myocyte-specific enhancer factor 2B
1tqe_Q3e-21173173Myocyte-specific enhancer factor 2B
1tqe_R3e-21173173Myocyte-specific enhancer factor 2B
1tqe_S3e-21173173Myocyte-specific enhancer factor 2B
6c9l_A3e-21173173Myocyte-specific enhancer factor 2B
6c9l_B3e-21173173Myocyte-specific enhancer factor 2B
6c9l_C3e-21173173Myocyte-specific enhancer factor 2B
6c9l_D3e-21173173Myocyte-specific enhancer factor 2B
6c9l_E3e-21173173Myocyte-specific enhancer factor 2B
6c9l_F3e-21173173Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in developing seeds. {ECO:0000269|PubMed:14701936}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.5KG680100.3.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
GenBankBT0621101e-162BT062110.1 Zea mays full-length cDNA clone ZM_BFb0215E12 mRNA, complete cds.
GenBankKJ7269311e-162KJ726931.1 Zea mays clone pUT3477 MADS transcription factor (MADS41) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025817347.11e-149MADS-box transcription factor 21-like
SwissprotQ8RU311e-117MAD21_ORYSJ; MADS-box transcription factor 21
TrEMBLA0A3L6SJC71e-157A0A3L6SJC7_PANMI; MADS-box transcription factor 21
STRINGPavir.Ea03607.1.p1e-147(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G18960.15e-82MIKC_MADS 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. Dreni L, et al.
    The D-lineage MADS-box gene OsMADS13 controls ovule identity in rice.
    Plant J., 2007. 52(4): p. 690-9
    [PMID:17877710]