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 492389
Common NameARALYDRAFT_492389
Organism
Arabidopsis lyrata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family MIKC_MADS
Protein Properties Length: 221aa    MW: 25022.6 Da    PI: 7.3535
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
492389genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF88.24.5e-28959151
            S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
  SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
            k+i+n + rqvtfskRr gi+KKA ELSvLCda+va+iifs tgkl+e+ss
  492389  9 KKIDNITARQVTFSKRRRGIFKKADELSVLCDADVALIIFSATGKLFEFSS 59
            68***********************************************96 PP
2K-box609.8e-21851721299
   K-box  12 akaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrkkle 99 
             ++ +  + +l++L ke+e   +++R+l GedL+ L+l+eLq+Le+ Le++l+++ +kK e +++qi+ l k+  el +enk+Lr kle
  492389  85 THLQLENCNLSRLSKEVEDKTKQLRKLRGEDLDGLNLEELQRLEKLLESGLSRVSEKKGECVMSQISSLEKRGSELVDENKRLRDKLE 172
             55666677899**************************************************************************997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.59161IPR002100Transcription factor, MADS-box
SMARTSM004322.4E-37160IPR002100Transcription factor, MADS-box
CDDcd002652.96E-36269No hitNo description
SuperFamilySSF554557.19E-30372IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004046.0E-26323IPR002100Transcription factor, MADS-box
PfamPF003197.9E-251057IPR002100Transcription factor, MADS-box
PRINTSPR004046.0E-262338IPR002100Transcription factor, MADS-box
PRINTSPR004046.0E-263859IPR002100Transcription factor, MADS-box
PROSITE profilePS5129713.71787177IPR002487Transcription factor, K-box
PfamPF014861.5E-1890171IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000060Biological Processprotein import into nucleus, translocation
GO:0009739Biological Processresponse to gibberellin
GO:0010076Biological Processmaintenance of floral meristem identity
GO:0010077Biological Processmaintenance of inflorescence meristem identity
GO:0010220Biological Processpositive regulation of vernalization response
GO:0010582Biological Processfloral meristem determinacy
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048438Biological Processfloral whorl development
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0042803Molecular Functionprotein homodimerization activity
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046982Molecular Functionprotein heterodimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 221 aa     Download sequence    Send to blast
MAREKIRIKK IDNITARQVT FSKRRRGIFK KADELSVLCD ADVALIIFSA TGKLFEFSSS  60
RMRDILGRYS LHASNINRLM DPPSTHLQLE NCNLSRLSKE VEDKTKQLRK LRGEDLDGLN  120
LEELQRLEKL LESGLSRVSE KKGECVMSQI SSLEKRGSEL VDENKRLRDK LETLERAKLI  180
TFMEALETES VTTNVSSYDS GAPLEDDSDT SLKLGLPSWE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-18170170MEF2C
5f28_B1e-18170170MEF2C
5f28_C1e-18170170MEF2C
5f28_D1e-18170170MEF2C
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that mediates floral transition in response to vernalization. Promotes inflorescence fate in apical meristems. Acts in a dosage-dependent manner. Probably involved in the transduction of RLK-mediated signaling (e.g. IMK3 pathway). Together with AP1 and SVP, controls the identity of the floral meristem and regulates expression of class B, C and E genes. When associated with SOC1, mediates effect of gibberellins on flowering under short-day conditions, and regulates the expression of LEAFY (LFY), which links floral induction and floral development. Confers inflorescence characteristics to floral primordia and early flowering. {ECO:0000269|PubMed:12451184, ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:12881501, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:16679456, ECO:0000269|PubMed:18339670, ECO:0000269|PubMed:18466303, ECO:0000269|PubMed:18694458, ECO:0000269|PubMed:19656343}.
Cis-element ? help Back to Top
SourceLink
PlantRegMap492389
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by vernalization in a FLC-independent manner. Repressed by the floral homeotic genes AP1, LFY and SEP3 in emerging floral meristems to establish a floral identity and prevent inflorescence fate. Up-regulated at the shoot apex by SOC1. {ECO:0000269|PubMed:12609028, ECO:0000269|PubMed:14716314, ECO:0000269|PubMed:17428825, ECO:0000269|PubMed:18339670, ECO:0000269|PubMed:18694458}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0051580.0AF005158.1 Arabidopsis thaliana MADS-box Protein (AGL24) mRNA, complete cds.
GenBankBT0251710.0BT025171.1 Arabidopsis thaliana At4g24540 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020873726.11e-157MADS-box protein AGL24 isoform X2
SwissprotO827941e-152AGL24_ARATH; MADS-box protein AGL24
TrEMBLD7M8T21e-155D7M8T2_ARALL; Uncharacterized protein
STRINGfgenesh2_kg.7__1822__AT4G24540.11e-156(Arabidopsis lyrata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM145111521
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G24540.11e-134AGAMOUS-like 24
Publications ? help Back to Top
  1. Ramamoorthy R,Phua EE,Lim SH,Tan HT,Kumar PP
    Identification and characterization of RcMADS1, an AGL24 ortholog from the holoparasitic plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae).
    PLoS ONE, 2013. 8(6): p. e67243
    [PMID:23840638]
  2. Lei HJ, et al.
    Identification and characterization of FaSOC1, a homolog of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 from strawberry.
    Gene, 2013. 531(2): p. 158-67
    [PMID:24055423]
  3. Wells CE,Vendramin E,Jimenez Tarodo S,Verde I,Bielenberg DG
    A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch].
    BMC Plant Biol., 2015. 15: p. 41
    [PMID:25848674]
  4. Sacharowski SP, et al.
    SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development.
    Plant Cell, 2015. 27(7): p. 1889-906
    [PMID:26106148]
  5. Sun LM,Zhang JZ,Hu CG
    Characterization and Expression Analysis of PtAGL24, a SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 (SVP/AGL24)-Type MADS-Box Gene from Trifoliate Orange (Poncirus trifoliata L. Raf.).
    Front Plant Sci, 2016. 7: p. 823
    [PMID:27375669]