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

XP_009111580.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

LBD

Protein Properties

Length: 131aa MW: 14582.5 Da PI: 7.7887

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009111580.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	138.1	3e-43	12	109	1	98
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeqpkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaela 95 +CaaCk+lrrkC++dCv+apyfp e+p kfanvh++FGasnv+k+l+++ +++reda++sl+yeAear++dPvyG+vg i+ lq+++ +l+ el+ XP_009111580.1 12 PCAACKFLRRKCTSDCVFAPYFPPEEPLKFANVHRIFGASNVSKILHEVAPHQREDAVNSLAYEAEARLKDPVYGCVGAISVLQREVLRLQRELE 106 7********************************************************************************************99 PP DUF260 96 llk 98 +++ XP_009111580.1 107 ETN 109 876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	26.88	11	112	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	6.7E-43	12	108	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 131 aa Download sequence Send to blast
MSSSYSNYTN SPCAACKFLR RKCTSDCVFA PYFPPEEPLK FANVHRIFGA SNVSKILHEV 60 APHQREDAVN SLAYEAEARL KDPVYGCVGA ISVLQREVLR LQRELEETNV DLMRYASCLG 120 GETSAYGGRR G

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	2e-59	10	125	9	125	LOB family transfactor Ramosa2.1
5ly0_B	2e-59	10	125	9	125	LOB family transfactor Ramosa2.1
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Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in young shoots, roots, stems, leaves and flowers. {ECO:0000269\|PubMed:12068116}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009111580.1

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	AB018114	1e-123	AB018114.1 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone: MGF10.
GenBank	AB164304	1e-123	AB164304.1 Arabidopsis thaliana ASL3 mRNA for ASYMMETRIC LEAVES2-like gene 3 protein, partial cds.
GenBank	AB473836	1e-123	AB473836.1 Arabidopsis thaliana ASL3 mRNA for ASYMMETRIC LEAVES2-like 3 protein, complete cds.
GenBank	AF447892	1e-123	AF447892.1 Arabidopsis thaliana LOB DOMAIN 25 (LBD25) mRNA, complete cds.
GenBank	CP002686	1e-123	CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009111580.1	5e-94	PREDICTED: LOB domain-containing protein 25
Refseq	XP_013725057.1	5e-94	LOB domain-containing protein 25
Refseq	XP_013725058.1	5e-94	LOB domain-containing protein 25
Swissprot	Q8L8Q3	6e-87	LBD25_ARATH; LOB domain-containing protein 25
TrEMBL	A0A291LR18	1e-92	A0A291LR18_BRARR; Transcription factor LBD25
TrEMBL	A0A397Y063	1e-92	A0A397Y063_BRACM; Uncharacterized protein
TrEMBL	M4FDA2	1e-92	M4FDA2_BRARP; Uncharacterized protein
STRING	Bra039072.1-P	2e-93	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM131	28	340

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G27650.1	2e-76	LOB domain-containing protein 25

Publications ? help Back to Top
Kim M,Kim MJ,Pandey S,Kim J Expression and Protein Interaction Analyses Reveal Combinatorial Interactions of LBD Transcription Factors During Arabidopsis Pollen Development. Plant Cell Physiol., 2016. 57(11): p. 2291-2299 [PMID:27519310]