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 Potri.013G104900.1
Common NamePOPTR_0013s09980g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family MIKC_MADS
Protein Properties Length: 226aa    MW: 25901.6 Da    PI: 9.8829
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.013G104900.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF98.82.1e-31958150
                        S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE CS
              SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeys 50
                        krien++nrqvtf+kRrng+lKKA+ELSvLCdaev++i+fss+g+lyey+
  Potri.013G104900.1  9 KRIENTTNRQVTFCKRRNGLLKKAYELSVLCDAEVSLIVFSSRGRLYEYA 58
                        79***********************************************8 PP
2K-box103.23.5e-34771743100
               K-box   3 kssgksleeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenka 93 
                         +s++ s +e +a+++qqe+ak++++i+ Lq+++Rhl+Ge +++Ls+keL+qLe++Le+++++iRskK+elll++ie++qk+e el++e  +
  Potri.013G104900.1  77 SSNTASITEINAQYYQQESAKMRQQIQLLQNSNRHLMGEAVSNLSVKELKQLENRLERGMTRIRSKKHELLLAEIEYMQKREIELENESAC 167
                         4455559999********************************************************************************* PP

               K-box  94 Lrkklee 100
                         Lr+k++e
  Potri.013G104900.1 168 LRTKIAE 174
                         ****986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004323.8E-42160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006633.992161IPR002100Transcription factor, MADS-box
CDDcd002652.14E-42279No hitNo description
SuperFamilySSF554551.06E-32278IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-33323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003194.8E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-332338IPR002100Transcription factor, MADS-box
PRINTSPR004047.0E-333859IPR002100Transcription factor, MADS-box
PfamPF014862.8E-2687172IPR002487Transcription factor, K-box
PROSITE profilePS5129715.61588178IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
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
MGRGKIEIKR IENTTNRQVT FCKRRNGLLK KAYELSVLCD AEVSLIVFSS RGRLYEYANN  60
NSIRSTIDRY KKVSSDSSNT ASITEINAQY YQQESAKMRQ QIQLLQNSNR HLMGEAVSNL  120
SVKELKQLEN RLERGMTRIR SKKHELLLAE IEYMQKREIE LENESACLRT KIAEVERLQQ  180
ANMVTGEELN AIQALAASRN FFAPHFLEGG TAYPHTYNKK ILHLG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1tqe_P2e-20164164Myocyte-specific enhancer factor 2B
1tqe_Q2e-20164164Myocyte-specific enhancer factor 2B
1tqe_R2e-20164164Myocyte-specific enhancer factor 2B
1tqe_S2e-20164164Myocyte-specific enhancer factor 2B
6c9l_A2e-20164164Myocyte-specific enhancer factor 2B
6c9l_B2e-20164164Myocyte-specific enhancer factor 2B
6c9l_C2e-20164164Myocyte-specific enhancer factor 2B
6c9l_D2e-20164164Myocyte-specific enhancer factor 2B
6c9l_E2e-20164164Myocyte-specific enhancer factor 2B
6c9l_F2e-20164164Myocyte-specific enhancer factor 2B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.128820.0bud| catkin
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in flowers and seeds (Ref.1). Expressed in endotesta cell layer of developing seeds (PubMed:28369525). {ECO:0000269|PubMed:28369525, ECO:0000269|Ref.1}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in seed development (PubMed:21447172, Ref.1, PubMed:29853599). Plays a role in seed morphogenesis by promoting the correct development of endotesta cell layer, which directs the further development of the seed coat, the endosperm, and consequently the embryo (Ref.1, PubMed:29853599). {ECO:0000269|PubMed:21447172, ECO:0000269|PubMed:29853599, ECO:0000269|Ref.1}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.013G104900.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024439317.11e-165agamous-like MADS-box protein AGL11 isoform X1
SwissprotF6I4571e-130AG11C_VITVI; Agamous-like MADS-box protein AGL11
TrEMBLA0A2K1Y3W71e-163A0A2K1Y3W7_POPTR; Uncharacterized protein
TrEMBLA0A3N7FWC41e-163A0A3N7FWC4_POPTR; Uncharacterized protein
STRINGcassava4.1_021818m1e-139(Manihot esculenta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF68429102
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G09960.11e-114MIKC_MADS family protein
Publications ? help Back to Top
  1. Jaillon O, et al.
    The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Nature, 2007. 449(7161): p. 463-7
    [PMID:17721507]
  2. Díaz-Riquelme J,Lijavetzky D,Martínez-Zapater JM,Carmona MJ
    Genome-wide analysis of MIKCC-type MADS box genes in grapevine.
    Plant Physiol., 2009. 149(1): p. 354-69
    [PMID:18997115]
  3. Mejía N, et al.
    Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine.
    BMC Plant Biol., 2011. 11: p. 57
    [PMID:21447172]
  4. Grimplet J,Martínez-Zapater JM,Carmona MJ
    Structural and functional annotation of the MADS-box transcription factor family in grapevine.
    BMC Genomics, 2016. 17: p. 80
    [PMID:26818751]
  5. Malabarba J, et al.
    The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine.
    J. Exp. Bot., 2017. 68(7): p. 1493-1506
    [PMID:28369525]
  6. Royo C, et al.
    The Major Origin of Seedless Grapes Is Associated with a Missense Mutation in the MADS-Box Gene VviAGL11.
    Plant Physiol., 2018. 177(3): p. 1234-1253
    [PMID:29853599]