PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Sobic.001G503000.1.p

Common Name

Sb01g046990, SORBIDRAFT_01g046990

Organism

Sorghum bicolor

Taxonomic ID

4558

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

Family

LBD

Protein Properties

Length: 246aa MW: 25678.4 Da PI: 5.9595

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sobic.001G503000.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	127.7	5.5e-40	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqle 88 +C aCk+lrrkC+++Cv+apyf++eq +++fa++hk+FGasnv+kll++lp +r++a+ ++ yeA+ar+rdP+yG+v++i++lqqq++ Sobic.001G503000.1.p 7 PCGACKFLRRKCVRGCVFAPYFCHEQgAAHFAAIHKVFGASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVM 95 7***********************89********************************************************* PP DUF260 89 qlkaelallkee 100 +l+a+la+lk++ Sobic.001G503000.1.p 96 TLQAQLASLKAQ 107 *****99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.574	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	6.3E-38	7	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 246 aa Download sequence Send to blast
MTGFGSPCGA CKFLRRKCVR GCVFAPYFCH EQGAAHFAAI HKVFGASNVS KLLAHLPLAD 60 RPEAAVTISY EAQARLRDPI YGCVAHIFAL QQQVMTLQAQ LASLKAQAAQ GQQGVHEDAK 120 GYVGSAAAEQ LGYGYPWCNG NGGVAAAGTV GAPAAQLAGA YGNGGHESLT ALLGSSDYMQ 180 QSLYHAFEHA GADDDDGRQG NDAFEAAAES SSFGAEESGG WRSSSGYQDC EDLQSVAYAY 240 LNHRS*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	7e-35	3	101	7	104	LOB family transfactor Ramosa2.1
5ly0_B	7e-35	3	101	7	104	LOB family transfactor Ramosa2.1
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in unelongating basal internodes, at the base of shoot in parenchyma cells adjacent to the peripheral vascular cylinder of the stem, and root pericycle cells (PubMed:15829602). Expressed in lateral and adventitious root primordia, tiller primordia, vascular tissues, scutellum, and young pedicels (PubMed:15960615). {ECO:0000269\|PubMed:15829602, ECO:0000269\|PubMed:15960615}.

Functional Description ? help Back to Top
Source	Description
UniProt	Acts as positive regulator of adventitious (crown) root formation by promoting its initiation (PubMed:15829602, PubMed:15960615). Acts as positive regulator of lateral root formation. Regulated by the auxin response factor and transcriptional activator ARF23/ARF1 (PubMed:15829602). Involved in auxin-mediated cell dedifferentiation, and may promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder at the base of the stem (PubMed:15960615). May act upstream of the gene regulatory network controlling adventitious root (crown) development (PubMed:21806801). {ECO:0000269\|PubMed:15829602, ECO:0000269\|PubMed:15960615, ECO:0000269\|PubMed:21806801}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Sobic.001G503000.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by auxin (PubMed:15829602, PubMed:15960615). Induced by ethylene (PubMed:15960615). {ECO:0000269\|PubMed:15829602, ECO:0000269\|PubMed:15960615}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	EF051732	0.0	EF051732.1 Zea mays rootless concerning crown and seminal lateral roots (rtcs) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002465851.1	1e-179	LOB domain-containing protein 6
Swissprot	Q5UG13	1e-110	LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBL	C5WXW9	1e-178	C5WXW9_SORBI; Uncharacterized protein
STRING	Sb01g046990.1	1e-179	(Sorghum bicolor)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP2501	38	93
Representative plant	OGRP405	15	100

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42440.1	1e-56	LBD family protein

Link Out ? help Back to Top
Phytozome	Sobic.001G503000.1.p
Entrez Gene	8085476

Publications ? help Back to Top
Coudert Y,Périn C,Courtois B,Khong NG,Gantet P Genetic control of root development in rice, the model cereal. Trends Plant Sci., 2010. 15(4): p. 219-26 [PMID:20153971] Kitomi Y, et al. The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling. Plant J., 2011. 67(3): p. 472-84 [PMID:21481033] Coudert Y, et al. Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice. BMC Genomics, 2011. 12: p. 387 [PMID:21806801]