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 | Pavir.1KG435200.1.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; Panicodae; Paniceae; Panicinae; Panicum
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Family | LBD | ||||||||
Protein Properties | Length: 206aa MW: 21506.5 Da PI: 7.934 | ||||||||
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 | 121.9 | 3.5e-38 | 22 | 123 | 1 | 101 |
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 +C aCk+lrr+C+++Cv+apyf +q +++fa++hk+FGasn +kll++lp +r +a+ +++yeA+ar+rdPvyG+v+ i++lqqq++ Pavir.1KG435200.1.p 22 PCGACKFLRRRCVPECVFAPYFSTDQgAARFAAIHKVFGASNASKLLSHLPVADRCEAVVTITYEAQARLRDPVYGCVAQIFALQQQVAI 111 7***********************9989************************************************************** PP DUF260 90 lkaelallkeel 101 l+a+l ++k++l Pavir.1KG435200.1.p 112 LQAQLMQAKAQL 123 *****9999875 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
PROSITE profile | PS50891 | 22.81 | 21 | 123 | IPR004883 | Lateral organ boundaries, LOB |
Pfam | PF03195 | 2.3E-37 | 22 | 120 | IPR004883 | Lateral organ boundaries, LOB |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0010311 | Biological Process | lateral root formation | ||||
GO:0005634 | Cellular Component | nucleus |
Sequence ? help Back to Top |
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Protein Sequence Length: 206 aa Download sequence Send to blast |
MAGATAASTG GAAAAATGAG SPCGACKFLR RRCVPECVFA PYFSTDQGAA RFAAIHKVFG 60 ASNASKLLSH LPVADRCEAV VTITYEAQAR LRDPVYGCVA QIFALQQQVA ILQAQLMQAK 120 AQLACGAAAH SPPLSHHHHH QWPADHASSI RKPGGPLDDC FMPDPSGGCF RDDVVAAQHC 180 AAKADAGDLQ YLAQTMMMRS PNYSL* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5ly0_A | 1e-37 | 12 | 132 | 1 | 123 | LOB family transfactor Ramosa2.1 |
5ly0_B | 1e-37 | 12 | 132 | 1 | 123 | 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 and faintly in shoots. {ECO:0000269|PubMed:12068116}. |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Transcriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269|PubMed:17259263, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:22974309, ECO:0000269|PubMed:23749813, ECO:0000269|PubMed:26059335}. |
Binding Motif ? help Back to Top | |||
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Motif ID | Method | Source | Motif file |
MP00309 | DAP | Transfer from AT2G42430 | Download |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | Pavir.1KG435200.1.p |
Regulation -- Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | INDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:17259263, 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 | AC243227 | 1e-141 | AC243227.1 Panicum virgatum clone PV_ABa011-D05, complete sequence. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_002454795.1 | 4e-99 | LOB domain-containing protein 16 isoform X2 | ||||
Swissprot | Q9SLB7 | 2e-58 | LBD16_ARATH; LOB domain-containing protein 16 | ||||
TrEMBL | A0A3L6RUC4 | 1e-104 | A0A3L6RUC4_PANMI; Uncharacterized protein | ||||
STRING | Pavir.J39638.1.p | 1e-148 | (Panicum virgatum) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Monocots | OGMP10599 | 34 | 43 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT3G58190.1 | 2e-43 | lateral organ boundaries-domain 29 |
Link Out ? help Back to Top | |
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Phytozome | Pavir.1KG435200.1.p |