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.4NG131700.1.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 MIKC_MADS
Protein Properties Length: 226aa    MW: 24865.9 Da    PI: 6.4065
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4NG131700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF81.17.2e-261059251
                         ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         rien   rqvtfskRr g++KKAeEL vLCda+va+i++s tgkl  ++s
  Pavir.4NG131700.1.p 10 RIENAAARQVTFSKRRRGLFKKAEELAVLCDADVALIVISATGKLSQFAS 59
                         8*********************************************9986 PP
2K-box59.31.6e-20891711698
                K-box  16 slqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                            q +++ L++++ +  r +R++ Ge+Le Ls++eL+q+e++Le +l ++ s+K++l+++qi+elq+k  +l++en+ L+k++
  Pavir.4NG131700.1.p  89 VEQSKYSGLNEQLTEASRGLRQMRGEELEGLSVEELHQMERKLEAGLHRVLSTKDQLFMQQISELQQKGAQLEDENRLLKKQV 171
                          45778888899999999***************************************************************987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006627.375161IPR002100Transcription factor, MADS-box
SMARTSM004321.0E-33160IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-22323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.83E-28375IPR002100Transcription factor, MADS-box
PfamPF003191.5E-241057IPR002100Transcription factor, MADS-box
CDDcd002654.45E-321375No hitNo description
PRINTSPR004041.2E-222338IPR002100Transcription factor, MADS-box
PRINTSPR004041.2E-223859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129712.8687177IPR002487Transcription factor, K-box
PfamPF014861.1E-1991171IPR002487Transcription factor, K-box
Gene3DG3DSA:1.20.5.4908.7E-4148171No hitNo description
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: 226 aa     Download sequence    Send to blast
MARERRAIRR IENAAARQVT FSKRRRGLFK KAEELAVLCD ADVALIVISA TGKLSQFASS  60
SMNDIIDKYS THSKNLGKSH QQPSIDLNVE QSKYSGLNEQ LTEASRGLRQ MRGEELEGLS  120
VEELHQMERK LEAGLHRVLS TKDQLFMQQI SELQQKGAQL EDENRLLKKQ VPHVITAGAA  180
VVAADTENVL TEDGQSSESV MTALHSGSSH DNDDGSDISL KLSLP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A3e-18173173MEF2C
5f28_B3e-18173173MEF2C
5f28_C3e-18173173MEF2C
5f28_D3e-18173173MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.123140.0leaf| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in the L1 cell layer of the embryo 2 days after pollination. {ECO:0000269|PubMed:15682279}.
UniprotTISSUE SPECIFICITY: Expressed in palea and stamen primordia. {ECO:0000269|PubMed:15682279}.
UniprotTISSUE SPECIFICITY: Expressed in roots, shoots and developing panicles. {ECO:0000269|PubMed:14701936, ECO:0000269|PubMed:15682279}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
UniProtProbable transcription factor. May be required for spikelet (rice flower) development. {ECO:0000269|PubMed:15682279}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4NG131700.1.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
GenBankAJ4306350.0AJ430635.1 Zea mays partial mRNA for putative MADS-domain transcription factor (m21 gene).
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025812968.11e-149MADS-box transcription factor 55-like
SwissprotQ69TG51e-112MAD55_ORYSJ; MADS-box transcription factor 55
SwissprotQ9XJ661e-112MAD22_ORYSJ; MADS-box transcription factor 22
TrEMBLA0A2T8JDX21e-147A0A2T8JDX2_9POAL; Uncharacterized protein
STRINGPavir.Db01833.1.p1e-163(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP12213697
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G22540.15e-51MIKC_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. Lee S,Choi SC,An G
    Rice SVP-group MADS-box proteins, OsMADS22 and OsMADS55, are negative regulators of brassinosteroid responses.
    Plant J., 2008. 54(1): p. 93-105
    [PMID:18182025]
  3. Lee S,Jeong DH,An G
    A possible working mechanism for rice SVP-group MADS-box proteins as negative regulators of brassinosteroid responses.
    Plant Signal Behav, 2008. 3(7): p. 471-4
    [PMID:19704489]
  4. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]