PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Carubv10002792m
Common NameCARUB_v10002792mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family MIKC_MADS
Protein Properties Length: 245aa    MW: 28795.4 Da    PI: 7.0009
Description MIKC_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10002792mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF77.59.8e-25959151
                     S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
           SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                     k+ien++ rqvtfskRr+g++KK  ELS+LCda + +i+fs tgkl e++s
  Carubv10002792m  9 KKIENQTARQVTFSKRRTGLIKKTRELSILCDAHIGLIVFSATGKLSEFCS 59
                     68***********************************************96 PP
2K-box44.66.1e-16821631096
            K-box  10 eeakaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 
                      ++ ++ +l++e++ L++e+ nL++ +R + G dL s+   eL  LeqqLe+s+ k+R++K++     +++l +k k+l+e+n+++ +
  Carubv10002792m  82 HQDDQDQLCHEIEVLRRETCNLEHRLRPYHGHDLASIPPHELDLLEQQLEHSVLKVRERKQQ-----LDNLSRKRKMLEEDNNNMYR 163
                      45567889****************************************************75.....68999999999999988765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006629.899161IPR002100Transcription factor, MADS-box
SMARTSM004329.8E-38160IPR002100Transcription factor, MADS-box
CDDcd002657.87E-43279No hitNo description
SuperFamilySSF554552.35E-30290IPR002100Transcription factor, MADS-box
PRINTSPR004042.5E-26323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003192.5E-231057IPR002100Transcription factor, MADS-box
PRINTSPR004042.5E-262338IPR002100Transcription factor, MADS-box
PRINTSPR004042.5E-263859IPR002100Transcription factor, MADS-box
PfamPF014869.1E-1682165IPR002487Transcription factor, K-box
PROSITE profilePS5129711.8186171IPR002487Transcription factor, K-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008360Biological Processregulation of cell shape
GO:0019252Biological Processstarch biosynthetic process
GO:0043068Biological Processpositive regulation of programmed cell death
GO:0048316Biological Processseed development
GO:0048481Biological Processplant ovule development
GO:0080155Biological Processregulation of double fertilization forming a zygote and endosperm
GO:2000029Biological Processregulation of proanthocyanidin biosynthetic process
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: 245 aa     Download sequence    Send to blast
MGRGKIEIKK IENQTARQVT FSKRRTGLIK KTRELSILCD AHIGLIVFSA TGKLSEFCSE  60
ANRMPQLIDR YLQTNGLRLP DHQDDQDQLC HEIEVLRRET CNLEHRLRPY HGHDLASIPP  120
HELDLLEQQL EHSVLKVRER KQQLDNLSRK RKMLEEDNNN MYRWLHEHRA AMELQQAGIE  180
TKPTEYQQFL EQLQYYNNDH QQQQQQRQPD SLLQLATLTS QIDPNYHLQL AQPNLQNDHA  240
PKSD*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A1e-15175173MEF2C
5f28_B1e-15175173MEF2C
5f28_C1e-15175173MEF2C
5f28_D1e-15175173MEF2C
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1147152SRKRKM
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the developmental regulation of the endothelium and in the accumulation of proanthocyanidins (PAs) or condensed tannins which give the seed its brown pigmentation after oxidation (PubMed:12368498, PubMed:16080001). Necessary for the normal activation of the BANYULS promoter in the endothelium body (PubMed:12368498). Is required, together with AGL11/STK for the maternal control of endothelium formation, which is essential for female gametophyte development and fertilization, and seed formation (PubMed:22176531). Interacts genetically with AGL1/SHP1 and AGL5/SHP2 in a partially antagonistic manner and represses AGL1/SHP1, AGL5/SHP2, and AGL8/FUL during flower development. Is essential for the coordination of cell divisions in ovule, seed coat development and endosperm formation (PubMed:27776173). Mediates the crosstalk between endothelium and nucellus to ensure proper seed formation. Functions redundantly with AGL63/GOA to repress nucellus growth and promote its degeneration. Represses the negative regulator of autophagy and programmed cell death HVA22D in the proximal nucellus (PubMed:27233529). Binds specifically to the CArG box DNA sequence 5'-CC (A/T)6 GG-3' (PubMed:16080001). {ECO:0000269|PubMed:12368498, ECO:0000269|PubMed:16080001, ECO:0000269|PubMed:22176531, ECO:0000269|PubMed:27233529, ECO:0000269|PubMed:27776173}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10002792m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY1412120.0AY141212.1 Arabidopsis thaliana MADS-box protein AGL32 mRNA, complete cds.
GenBankBT0300480.0BT030048.1 Arabidopsis thaliana At5g23260 mRNA, complete cds.
GenBankBT0313600.0BT031360.1 Arabidopsis thaliana unknown protein (At5g23260) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006289310.20.0protein TRANSPARENT TESTA 16 isoform X2
SwissprotQ8RYD91e-141TT16_ARATH; Protein TRANSPARENT TESTA 16
TrEMBLR0HEJ61e-180R0HEJ6_9BRAS; Uncharacterized protein
STRINGXP_006289310.11e-180(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM65062543
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G23260.11e-124MIKC_MADS family protein
Publications ? help Back to Top
  1. Kim K,Jiang K,Teng SL,Feldman LJ,Huang H
    Using biologically interrelated experiments to identify pathway genes in Arabidopsis.
    Bioinformatics, 2012. 28(6): p. 815-22
    [PMID:22271267]
  2. Rhodes DH, et al.
    Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm.
    J. Agric. Food Chem., 2014. 62(45): p. 10916-27
    [PMID:25272193]
  3. Xu W, et al.
    Endosperm and Nucellus Develop Antagonistically in Arabidopsis Seeds.
    Plant Cell, 2016. 28(6): p. 1343-60
    [PMID:27233529]
  4. Ehlers K, et al.
    The MADS Box Genes ABS, SHP1, and SHP2 Are Essential for the Coordination of Cell Divisions in Ovule and Seed Coat Development and for Endosperm Formation in Arabidopsis thaliana.
    PLoS ONE, 2016. 11(10): p. e0165075
    [PMID:27776173]
  5. Coen O, et al.
    Developmental patterning of the sub-epidermal integument cell layer in Arabidopsis seeds.
    Development, 2017. 144(8): p. 1490-1497
    [PMID:28348169]
  6. Xu W, et al.
    TRANSPARENT TESTA 16 and 15 act through different mechanisms to control proanthocyanidin accumulation in Arabidopsis testa.
    J. Exp. Bot., 2017. 68(11): p. 2859-2870
    [PMID:28830101]
  7. Fiume E,Coen O,Xu W,Lepiniec L,Magnani E
    Developmental patterning of sub-epidermal cells in the outer integument of Arabidopsis seeds.
    PLoS ONE, 2017. 12(11): p. e0188148
    [PMID:29141031]