PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | RrC5510_p4 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
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Family | MIKC_MADS | ||||||||
Protein Properties | Length: 242aa MW: 28571.2 Da PI: 6.6779 | ||||||||
Description | MIKC_MADS family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | SRF-TF | 81.2 | 6.8e-26 | 9 | 59 | 1 | 51 |
S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS SRF-TF 1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51 krien + rqvtfskRr g++KK +ELSvLCda + +i+fs tgkl ey+s RrC5510_p4 9 KRIENRTSRQVTFSKRRSGLIKKTHELSVLCDAHIGLIVFSATGKLTEYCS 59 79***********************************************96 PP | |||||||
2 | K-box | 62.7 | 1.5e-21 | 85 | 168 | 13 | 96 |
K-box 13 kaeslqqelakLkkeienLqreqRhllGedLesLslkeLqqLeqqLekslkkiRskKnellleqieelqkkekelqeenkaLrk 96 +e+l+qe++ L++e+ +L+ +R + G dL s+ eL +LeqqLe+s+ k+R++Knell +q+e+l +k ++l+++n+++ + RrC5510_p4 85 GQEELCQEIEVLRRETCKLELRLRPYHGHDLASIPPHELDRLEQQLEHSVLKVRERKNELLQQQLENLSRKRRMLEDDNNNMYR 168 5789***************************************************************************99866 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
SMART | SM00432 | 1.8E-39 | 1 | 60 | IPR002100 | Transcription factor, MADS-box |
PROSITE profile | PS50066 | 30.81 | 1 | 61 | IPR002100 | Transcription factor, MADS-box |
SuperFamily | SSF55455 | 4.19E-31 | 2 | 87 | IPR002100 | Transcription factor, MADS-box |
CDD | cd00265 | 3.43E-43 | 2 | 79 | No hit | No description |
PRINTS | PR00404 | 3.0E-28 | 3 | 23 | IPR002100 | Transcription factor, MADS-box |
PROSITE pattern | PS00350 | 0 | 3 | 57 | IPR002100 | Transcription factor, MADS-box |
Pfam | PF00319 | 7.9E-24 | 10 | 57 | IPR002100 | Transcription factor, MADS-box |
PRINTS | PR00404 | 3.0E-28 | 23 | 38 | IPR002100 | Transcription factor, MADS-box |
PRINTS | PR00404 | 3.0E-28 | 38 | 59 | IPR002100 | Transcription factor, MADS-box |
Pfam | PF01486 | 4.2E-20 | 84 | 170 | IPR002487 | Transcription factor, K-box |
PROSITE profile | PS51297 | 14.088 | 86 | 176 | IPR002487 | Transcription factor, K-box |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0006355 | Biological Process | regulation of transcription, DNA-templated | ||||
GO:0008360 | Biological Process | regulation of cell shape | ||||
GO:0019252 | Biological Process | starch biosynthetic process | ||||
GO:0043068 | Biological Process | positive regulation of programmed cell death | ||||
GO:0048316 | Biological Process | seed development | ||||
GO:0048481 | Biological Process | plant ovule development | ||||
GO:0080155 | Biological Process | regulation of double fertilization forming a zygote and endosperm | ||||
GO:2000029 | Biological Process | regulation of proanthocyanidin biosynthetic process | ||||
GO:0005634 | Cellular Component | nucleus | ||||
GO:0003677 | Molecular Function | DNA binding | ||||
GO:0003700 | Molecular Function | transcription factor activity, sequence-specific DNA binding | ||||
GO:0046983 | Molecular Function | protein dimerization activity |
Sequence ? help Back to Top |
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Protein Sequence Length: 242 aa Download sequence Send to blast |
MGRGKIEIKR IENRTSRQVT FSKRRSGLIK KTHELSVLCD AHIGLIVFSA TGKLTEYCSE 60 PSKMPQLIDR YLQTNGLRLP DPNDGQEELC QEIEVLRRET CKLELRLRPY HGHDLASIPP 120 HELDRLEQQL EHSVLKVRER KNELLQQQLE NLSRKRRMLE DDNNNMYRWL HEHRTAMEFQ 180 QAGIETKPGE YQQFLEQVQY YNDHQQQQEQ QPNSVLQLAT LPSEIDPNYH LQLAQPNLQN 240 DN |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5f28_A | 4e-18 | 1 | 75 | 1 | 73 | MEF2C |
5f28_B | 4e-18 | 1 | 75 | 1 | 73 | MEF2C |
5f28_C | 4e-18 | 1 | 75 | 1 | 73 | MEF2C |
5f28_D | 4e-18 | 1 | 75 | 1 | 73 | MEF2C |
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Nucleic Localization Signal ? help Back to Top | |||
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No. | Start | End | Sequence |
1 | 152 | 157 | SRKRRM |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Transcription 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}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | - |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | EU192029 | 0.0 | EU192029.1 Brassica napus MADS-box DNA-binding domain transcription factor (TT16.2) mRNA, complete cds. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_018481949.1 | 1e-173 | PREDICTED: protein TRANSPARENT TESTA 16-like | ||||
Refseq | XP_018481991.1 | 1e-173 | PREDICTED: protein TRANSPARENT TESTA 16-like | ||||
Swissprot | Q8RYD9 | 1e-142 | TT16_ARATH; Protein TRANSPARENT TESTA 16 | ||||
TrEMBL | A0A0D3DDD0 | 1e-168 | A0A0D3DDD0_BRAOL; Uncharacterized protein | ||||
TrEMBL | A0A3P6E5I9 | 1e-168 | A0A3P6E5I9_BRAOL; Uncharacterized protein | ||||
TrEMBL | B6RFA3 | 1e-168 | B6RFA3_BRANA; BnaC02g42240D protein | ||||
TrEMBL | G8Z8Z9 | 1e-168 | G8Z8Z9_BRAOL; MADS DNA domain binding transcription factor BolC.TT16a | ||||
STRING | Bo7g097810.1 | 1e-168 | (Brassica oleracea) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Malvids | OGEM6506 | 25 | 43 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT5G23260.2 | 1e-124 | MIKC_MADS family protein |