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.2NG419400.1.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: 262aa    MW: 30277.5 Da    PI: 9.1477
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2NG419400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF99.71.2e-31959151
                         S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
               SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                         krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s
  Pavir.2NG419400.1.p  9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 59
                         79***********************************************96 PP
2K-box981.4e-32861779100
                K-box   9 leeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkl 98 
                          +e++  +s+++e+ kLk+++enLqr+qR+llGedL++L +keL+qLe+qL++sl++iRs++++++l+q+++lq++e++l e+nk+Lr+kl
  Pavir.2NG419400.1.p  86 KENELVQSSRNEYLKLKARVENLQRTQRNLLGEDLGTLGIKELEQLEKQLDSSLRHIRSTRTQHMLDQLNDLQRREHMLCEANKCLRRKL 175
                          45667899*********************************************************************************9 PP

                K-box  99 ee 100
                          ee
  Pavir.2NG419400.1.p 176 EE 177
                          87 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004321.4E-40160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.137161IPR002100Transcription factor, MADS-box
CDDcd002659.20E-44278No hitNo description
SuperFamilySSF554551.83E-32289IPR002100Transcription factor, MADS-box
PRINTSPR004041.0E-32323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.5E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004041.0E-322338IPR002100Transcription factor, MADS-box
PRINTSPR004041.0E-323859IPR002100Transcription factor, MADS-box
PfamPF014864.9E-2688175IPR002487Transcription factor, K-box
PROSITE profilePS5129715.42691181IPR002487Transcription 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: 262 aa     Download sequence    Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSN RGKLYEFCSG  60
QSSITKTLER YQKSSYGGPD TAIQNKENEL VQSSRNEYLK LKARVENLQR TQRNLLGEDL  120
GTLGIKELEQ LEKQLDSSLR HIRSTRTQHM LDQLNDLQRR EHMLCEANKC LRRKLEETSS  180
QVHGQVWEHG GNLLGYERQS PQQGPSHVRN GFFHPLEVAP EPTLQIGYDA VYLQLASCLR  240
YEYCLRFAPE HMNNFMPTWL P*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ox0_A2e-33761771103Developmental protein SEPALLATA 3
4ox0_B2e-33761771103Developmental protein SEPALLATA 3
4ox0_C2e-33761771103Developmental protein SEPALLATA 3
4ox0_D2e-33761771103Developmental protein SEPALLATA 3
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed at early stage of flower development in the spikelet (rice flower) primordia and later in stamen and pistil primordia. Expressed during ovule development in the inner and outer integuments. {ECO:0000269|PubMed:12395189, ECO:0000269|PubMed:9065695}.
UniprotTISSUE SPECIFICITY: Expressed in lodicules, stamens and carpels. {ECO:0000269|PubMed:12395189, ECO:0000269|PubMed:9065695, ECO:0000269|PubMed:9339904}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. May be involved in the control of flowering time. {ECO:0000269|PubMed:9339904, ECO:0000269|Ref.9}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.2NG419400.1.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
GenBankAJ4306940.0AJ430694.1 Zea mays mRNA for putative MADS-domain transcription factor (m27 gene).
GenBankBT0333980.0BT033398.1 Zea mays full-length cDNA clone ZM_BFb0100K01 mRNA, complete cds.
GenBankBT0879420.0BT087942.1 Zea mays full-length cDNA clone ZM_BFb0323H23 mRNA, complete cds.
GenBankKJ7283370.0KJ728337.1 Zea mays clone pUT6618 MADS transcription factor (MADS49) mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025803090.11e-171MADS-box transcription factor 8 isoform X1
SwissprotQ9SAR11e-151MADS8_ORYSJ; MADS-box transcription factor 8
TrEMBLA0A3L6T9X91e-172A0A3L6T9X9_PANMI; MADS-box transcription factor 8 isoform X1
STRINGPavir.Ba01535.1.p1e-178(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP34833469
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.11e-90MIKC_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. Jang YH, et al.
    Survey of rice proteins interacting with OsFCA and OsFY proteins which are homologous to the Arabidopsis flowering time proteins, FCA and FY.
    Plant Cell Physiol., 2009. 50(8): p. 1479-92
    [PMID:19561057]
  3. Cui R, et al.
    Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa).
    Plant J., 2010. 61(5): p. 767-81
    [PMID:20003164]
  4. Bai X, et al.
    Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice.
    Sci Rep, 2016. 6: p. 19022
    [PMID:26744119]