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

Carubv10018238m

Common Name

CARUB_v10018238mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 129aa MW: 14209.1 Da PI: 8.109

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10018238m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	142.3	1.5e-44	8	106	1	99
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeqpkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +CaaCk+lrrkC++dCv+apyfp e+p kfanvh++FGasnv+k+l+++ +++reda++sl+yeAear++dPvyG+vg i+ lq+q+ +l+ el Carubv10018238m 8 PCAACKFLRRKCTSDCVFAPYFPPEEPTKFANVHRIFGASNVSKILQEVAPHQREDAVNSLAYEAEARLKDPVYGCVGAISVLQRQVLRLQREL 101 7********************************************************************************************* PP DUF260 95 allke 99 +++++ Carubv10018238m 102 EETNA 106 99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	27.446	7	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	3.1E-44	8	105	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 129 aa Download sequence Send to blast
MSNYTNSPCA ACKFLRRKCT SDCVFAPYFP PEEPTKFANV HRIFGASNVS KILQEVAPHQ 60 REDAVNSLAY EAEARLKDPV YGCVGAISVL QRQVLRLQRE LEETNADLMR YASCLGGETT 120 SAYGGRRG*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	3e-60	6	121	9	125	LOB family transfactor Ramosa2.1
5ly0_B	3e-60	6	121	9	125	LOB family transfactor Ramosa2.1
Search in ModeBase

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10018238m

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	AC237336	1e-154	AC237336.1 Arabidopsis lyrata clone JGIFAFI-69G3, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006292048.2	5e-92	LOW QUALITY PROTEIN: LOB domain-containing protein 25, partial
Refseq	XP_010425543.1	5e-92	PREDICTED: LOB domain-containing protein 25
Refseq	XP_010502770.1	5e-92	PREDICTED: LOB domain-containing protein 25
Swissprot	Q8L8Q3	1e-91	LBD25_ARATH; LOB domain-containing protein 25
TrEMBL	R0FRU7	1e-90	R0FRU7_9BRAS; Uncharacterized protein
STRING	Cagra.5575s0004.1.p	2e-91	(Capsella grandiflora)
STRING	XP_006292048.1	2e-91	(Capsella rubella)
STRING	XP_010425543.1	2e-91	(Camelina sativa)
STRING	XP_010502770.1	2e-91	(Camelina sativa)

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-80	LOB domain-containing protein 25

Link Out ? help Back to Top
Phytozome	Carubv10018238m
Entrez Gene	17885542

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]