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 XP_009104908.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family MIKC_MADS
Protein Properties Length: 212aa    MW: 24002.7 Da    PI: 7.4355
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009104908.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF81.84.6e-26957149
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEE CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyey 49
                    krien   rqvtf+kRr+g+lKKA+ELSvLCdaev v+ifs++gkl+e 
  XP_009104908.1  9 KRIENPVHRQVTFCKRRTGLLKKAKELSVLCDAEVGVMIFSPQGKLFEL 57
                    79********************************************996 PP
2K-box57.94.5e-2010118219100
           K-box  19 qelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkklee 100
                      +++ Lk+ei++Lq+ +R + G + ++++l+eL  Le++Le  +++iRs K++++l++i+ l++ e  l+++nk+L +k+ee
  XP_009104908.1 101 DQVNELKQEIDMLQKGIRYMFGGGDGTMNLQELLLLEKHLEYWISHIRSAKMDIMLQEIQSLRNTEGVLKNANKYLLEKIEE 182
                     6899***************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM004325.0E-37160IPR002100Transcription factor, MADS-box
PROSITE profilePS5006629.885161IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.23E-28175IPR002100Transcription factor, MADS-box
CDDcd002652.93E-40274No hitNo description
PRINTSPR004042.9E-27323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003199.7E-241056IPR002100Transcription factor, MADS-box
PRINTSPR004042.9E-272338IPR002100Transcription factor, MADS-box
PRINTSPR004042.9E-273859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129712.09396186IPR002487Transcription factor, K-box
PfamPF014861.3E-19100180IPR002487Transcription 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: 212 aa     Download sequence    Send to blast
MARGKIQLKR IENPVHRQVT FCKRRTGLLK KAKELSVLCD AEVGVMIFSP QGKLFELATK  60
GTMEGMIDKY MKCTGGGGRG SSSATFTAQE QLQPPTLDPK DQVNELKQEI DMLQKGIRYM  120
FGGGDGTMNL QELLLLEKHL EYWISHIRSA KMDIMLQEIQ SLRNTEGVLK NANKYLLEKI  180
EENNNSVLDA NFATVETNYS YPLTMPSEIF EF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A9e-16170169MEF2C
5f28_B9e-16170169MEF2C
5f28_C9e-16170169MEF2C
5f28_D9e-16170169MEF2C
6byy_A9e-16170169MEF2 CHIMERA
6byy_B9e-16170169MEF2 CHIMERA
6byy_C9e-16170169MEF2 CHIMERA
6byy_D9e-16170169MEF2 CHIMERA
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.315540.0bud
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During embryo development, expressed in a punctate pattern from the globular stage to the torpedo stage. {ECO:0000269|PubMed:11855641}.
UniprotTISSUE SPECIFICITY: Preferentially expressed in roots (PubMed:7549482). In root meristem, expressed in external cells of columella, lateral root cap and atrichoblasts. In mature root, expressed in the central cylinder (PubMed:11855641). Expressed in leaf vasculature, young floral meristems and nectaries (PubMed:18203871). {ECO:0000269|PubMed:11855641, ECO:0000269|PubMed:18203871, ECO:0000269|PubMed:7549482}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator that regulates root development by controlling cell proliferation in root meristem. May mediate responses to auxin in the root. May act as promoter of the flowering transition through up-regulation of SOC, FT and LFY. {ECO:0000269|PubMed:18203871}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009104908.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin in root phloem. {ECO:0000269|PubMed:18203871}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2281900.0AK228190.1 Arabidopsis thaliana mRNA for MADS-box protein AGL12, complete cds, clone: RAFL14-63-K22.
GenBankBT0061570.0BT006157.1 Arabidopsis thaliana clone RAFL17-04-C08 (R50439) putative MADS-box protein (At1g71692) mRNA, complete cds.
GenBankBT0083320.0BT008332.1 Arabidopsis thaliana At1g71692 gene, complete cds.
GenBankBT0085240.0BT008524.1 Arabidopsis thaliana clone U50439 putative MADS-box protein (At1g71692) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009104908.11e-158PREDICTED: agamous-like MADS-box protein AGL12
RefseqXP_013652182.11e-158agamous-like MADS-box protein AGL12
SwissprotQ388411e-135AGL12_ARATH; Agamous-like MADS-box protein AGL12
TrEMBLA0A397YNZ11e-156A0A397YNZ1_BRACM; Uncharacterized protein
TrEMBLM4CI861e-156M4CI86_BRARP; Uncharacterized protein
STRINGBra003919.1-P1e-157(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM70522641
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G71692.11e-129AGAMOUS-like 12
Publications ? help Back to Top
  1. Zimmermann P,Hirsch-Hoffmann M,Hennig L,Gruissem W
    GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
    Plant Physiol., 2004. 136(1): p. 2621-32
    [PMID:15375207]
  2. Pacheco-Escobedo MA, et al.
    Longitudinal zonation pattern in Arabidopsis root tip defined by a multiple structural change algorithm.
    Ann. Bot., 2018.
    [PMID:27358290]
  3. García-Cruz KV, et al.
    The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components.
    Ann. Bot., 2018.
    [PMID:27474508]