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

Cucsa.053450.1

Common Name

Csa_3G396920, LOC101214764

Organism

Cucumis sativus

Taxonomic ID

3659

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Cucumis

Family

LBD

Protein Properties

Length: 244aa MW: 27011.9 Da PI: 6.4981

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cucsa.053450.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	123.6	1e-38	7	107	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkael 94 +C aCk+lrrkC+++Cv+apyf++eq + +fa++hk+FGasnv+kll++lp +er +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+a+l Cucsa.053450.1 7 PCGACKFLRRKCVRGCVFAPYFCHEQgATHFAAIHKVFGASNVSKLLARLPITERCEAAVTISYEAQARLQDPIYGCVSHIFALQQQVVSLQAQL 101 7***********************89***************************************************************** PP DUF260 95 allkee 100 a+lke+ Cucsa.053450.1 102 ASLKEQ 107 *99987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.092	6	108	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	7.5E-37	7	105	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 244 aa Download sequence Send to blast
MTGSGSPCGA CKFLRRKCVR GCVFAPYFCH EQGATHFAAI HKVFGASNVS KLLARLPITE 60 RCEAAVTISY EAQARLQDPI YGCVSHIFAL QQQVVSLQAQ LASLKEQAAE SIMNASSNVG 120 GVNEKVNSRK VPSHPQDLHS WFQSEQPNVT LEFNPNPTPN NNCASNANYY DENYRIMVNS 180 QSNGNYENHH IAKMEESGSY GSFEETSGYS MYTLDQLHSN VQQWSFSDTV DDLQSVAFGN 240 RHW*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	2e-35	3	122	7	122	LOB family transfactor Ramosa2.1
5ly0_B	2e-35	3	122	7	122	LOB family transfactor Ramosa2.1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19. {ECO:0000269\|PubMed:17259263}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263}.

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	LN681827	0.0	LN681827.1 Cucumis melo genomic scaffold, anchoredscaffold00018.
GenBank	LN713258	0.0	LN713258.1 Cucumis melo genomic chromosome, chr_4.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004152038.1	0.0	PREDICTED: LOB domain-containing protein 29
Swissprot	Q9M2J7	2e-66	LBD29_ARATH; LOB domain-containing protein 29
TrEMBL	A0A0A0L817	0.0	A0A0A0L817_CUCSA; Uncharacterized protein
STRING	XP_004152038.1	0.0	(Cucumis sativus)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF3571	33	66

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G58190.1	4e-58	lateral organ boundaries-domain 29

Link Out ? help Back to Top
Phytozome	Cucsa.053450.1
Entrez Gene	101214764

Publications ? help Back to Top
Ren Y, et al. An integrated genetic and cytogenetic map of the cucumber genome. PLoS ONE, 2009. 4(6): p. e5795 [PMID:19495411] Guo S, et al. Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics, 2010. 11: p. 384 [PMID:20565788] Li Z, et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics, 2011. 12: p. 540 [PMID:22047402] Gupta A,Singh M,Laxmi A Interaction between glucose and brassinosteroid during the regulation of lateral root development in Arabidopsis. Plant Physiol., 2015. 168(1): p. 307-20 [PMID:25810094] Porco S, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development, 2016. 143(18): p. 3340-9 [PMID:27578783] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Xu C,Cao H,Xu E,Zhang S,Hu Y Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation. Plant Cell Physiol., 2018. 59(4): p. 744-755 [PMID:29121271] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751]