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 | Sobic.001G261700.1.p | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
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Family | LBD | ||||||||
Protein Properties | Length: 261aa MW: 27046.6 Da PI: 7.1756 | ||||||||
Description | LBD 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 | DUF260 | 128.3 | 3.4e-40 | 34 | 134 | 1 | 100 |
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqle 88 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p+++r da+ +++yeA+ar+rdPvyG+v+++++lqqq+ Sobic.001G261700.1.p 34 PCGACKFLRRKCVTGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLQIPPHKRLDAVVTVCYEAQARIRDPVYGCVSHVFALQQQVV 122 7***********************9989************************************************************* PP DUF260 89 qlkaelallkee 100 +l++el +l+ + Sobic.001G261700.1.p 123 NLQTELTYLQGH 134 ******998865 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
PROSITE profile | PS50891 | 23.15 | 33 | 135 | IPR004883 | Lateral organ boundaries, LOB |
Pfam | PF03195 | 2.0E-39 | 34 | 132 | IPR004883 | Lateral organ boundaries, LOB |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0010089 | Biological Process | xylem development | ||||
GO:0010311 | Biological Process | lateral root formation | ||||
GO:0005634 | Cellular Component | nucleus |
Sequence ? help Back to Top |
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Protein Sequence Length: 261 aa Download sequence Send to blast |
MSSSVLGASA GAGGGGSSSS VPSGGVGCGG GGPPCGACKF LRRKCVTGCI FAPYFDSEQG 60 AAHFAAVHKV FGASNVSKLL LQIPPHKRLD AVVTVCYEAQ ARIRDPVYGC VSHVFALQQQ 120 VVNLQTELTY LQGHLSTIEL PTPPPFGAQN QMPMTATFCV SNLPSASSNI IPGTVDVSTV 180 FEPQTQESHW VSLSQQQQQV QQHQFNQQQS VMVGEGPGTG MSGSGAIGGG DLQLLARELL 240 DRHGITAVGS QSQPKPPPFT * |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5ly0_A | 4e-39 | 30 | 128 | 7 | 104 | LOB family transfactor Ramosa2.1 |
5ly0_B | 4e-39 | 30 | 128 | 7 | 104 | LOB family transfactor Ramosa2.1 |
Search in ModeBase |
Expression -- Description ? help Back to Top | ||||||
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Source | Description | |||||
Uniprot | DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269|PubMed:19717544}. | |||||
Uniprot | TISSUE SPECIFICITY: Expressed in roots, stems, leaves and flowers (PubMed:12068116, PubMed:24484953). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269|PubMed:12068116, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:24484953}. |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:22974309, ECO:0000269|PubMed:23749813, ECO:0000269|PubMed:23872272, ECO:0000269|PubMed:26059335}. |
Binding Motif ? help Back to Top | |||
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Motif ID | Method | Source | Motif file |
MP00314 | DAP | Transfer from AT2G45420 | Download |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | Sobic.001G261700.1.p |
Regulation -- Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | INDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:23749813}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | Retrieve |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | AC226706 | 3e-92 | AC226706.2 Oryza minuta clone OM__Ba0084M12, complete sequence. | |||
GenBank | BT061431 | 3e-92 | BT061431.1 Zea mays full-length cDNA clone ZM_BFb0145J09 mRNA, complete cds. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_021307456.1 | 0.0 | LOB domain-containing protein 30 | ||||
Swissprot | O22131 | 5e-68 | LBD18_ARATH; LOB domain-containing protein 18 | ||||
TrEMBL | A0A1B6QL50 | 0.0 | A0A1B6QL50_SORBI; Uncharacterized protein | ||||
STRING | Sb01g024400.1 | 1e-146 | (Sorghum bicolor) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Monocots | OGMP3346 | 37 | 82 | Representative plant | OGRP405 | 15 | 100 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT2G45420.1 | 2e-63 | LOB domain-containing protein 18 |
Link Out ? help Back to Top | |
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Phytozome | Sobic.001G261700.1.p |
Publications ? help Back to Top | |||
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