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

PSME_00049570-RA

Organism

Pseudotsuga menziesii

Taxonomic ID

3357

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga

Family

LBD

Protein Properties

Length: 117aa MW: 12867 Da PI: 8.2864

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PSME_00049570-RA	genome	PRS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	109.2	3.2e-34	7	96	1	88
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq..pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqle 88 +C aCk+lrrkC+k+Cv+apyf++++ + +f +hk+FGasn +kll +lp eer d+++++ yeA+ar+ dPvyG+v+++++lq+q+ PSME_00049570-RA 7 SCGACKFLRRKCVKGCVFAPYFCSDEmgAPHFGEIHKVFGASNFSKLLMHLPVEERYDTVATVSYEAQARLLDPVYGCVSHLFALQHQVP 96 6*********************995569*******************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	20.222	6	109	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	6.6E-33	7	97	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 117 aa Download sequence Send to blast
MGGGGASCGA CKFLRRKCVK GCVFAPYFCS DEMGAPHFGE IHKVFGASNF SKLLMHLPVE 60 ERYDTVATVS YEAQARLLDP VYGCVSHLFA LQHQVPLSIQ SLLSSKPNCF YFITPKL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-33	3	95	7	97	LOB family transfactor Ramosa2.1
5ly0_B	1e-33	3	95	7	97	LOB family transfactor Ramosa2.1
Search in ModeBase

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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006443870.1	8e-47	LOB domain-containing protein 29
Refseq	XP_006480093.1	8e-47	LOB domain-containing protein 29-like
Refseq	XP_009398033.1	6e-47	PREDICTED: LOB domain-containing protein 29
Swissprot	Q5UG13	2e-44	LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBL	A0A067FYE5	2e-45	A0A067FYE5_CITSI; Uncharacterized protein
TrEMBL	A0A2H5QGT7	1e-45	A0A2H5QGT7_CITUN; Uncharacterized protein
TrEMBL	M0SRY0	1e-45	M0SRY0_MUSAM; Uncharacterized protein
STRING	XP_006480093.1	3e-46	(Citrus sinensis)
STRING	GSMUA_Achr4P25190_001	2e-46	(Musa acuminata)
STRING	XP_006443870.1	3e-46	(Citrus clementina)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42440.1	2e-46	LBD family protein

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]