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

Lj0g3v0135239.1

Common Name

nsp2, TINod

Organism

Lotus japonicus

Taxonomic ID

34305

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Loteae; Lotus

Family

GRAS

Protein Properties

Length: 174aa MW: 19087.5 Da PI: 10.7326

Description

GRAS family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lj0g3v0135239.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	GRAS	153.1	2.6e-47	1	171	120	292
GRAS 120 sqGlQWpaLlqaLasRpegppslRiTgvgspesg..skeeleetgerLakfAeelgvpfefnvlvakrledleleeLrvkpgEalaVnlvlqlh 211 ++G+QW++L+qaLas p+g p+lRiT+++++ g s +++etg+rL+ fA++lg pf+f+ ++ e++++ L++ +gEal+ n++l+l Lj0g3v0135239.1 1 MEGVQWASLMQALASNPNG-PHLRITALSRSGVGrrSMATVQETGRRLTAFATSLGQPFSFHHCRLESDETFRPAGLKLVRGEALVFNCMLNLP 93 58************999.9*****7666999**********************99999************************ PP GRAS 212 rlldesvsleserdevLklvkslsPkvvvvveqeadhnsesFlerflealeyysalfdsleaklpreseerikvErellgr 292 +l +s ++ ++L + k l+P++v+vve+e+ + F+erf+++l+++sa+fdslea++p + ++r+ vEr++lg+ Lj0g3v0135239.1 94 HLTYRSPNSVA---SILTAAKALRPRLVTVVEEEVGSALGGFVERFMDSLHHFSAVFDSLEAGFPMQGRARALVERVFLGP 171 9966666666...9*************************************************************9997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF03514	8.8E-45	1	171	IPR005202	Transcription factor GRAS
PROSITE profile	PS50985	28.843	1	174	IPR005202	Transcription factor GRAS

Sequence ? help Back to Top
Protein Sequence Length: 174 aa Download sequence Send to blast
MEGVQWASLM QALASNPNGP HLRITALSRS GVGRRSMATV QETGRRLTAF ATSLGQPFSF 60 HHCRLESDET FRPAGLKLVR GEALVFNCML NLPHLTYRSP NSVASILTAA KALRPRLVTV 120 VEEEVGSALG GFVERFMDSL HHFSAVFDSL EAGFPMQGRA RALVERVFLG PRXX

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5b3g_A	3e-23	1	169	138	296	Protein SCARECROW
5b3h_A	3e-23	1	169	137	295	Protein SCARECROW
5b3h_D	3e-23	1	169	137	295	Protein SCARECROW
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in roots, shoots and leaves. {ECO:0000269\|PubMed:15961668}.

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional regulator essential for Nod-factor-induced gene expression. Acts downstream of calcium spiking and DMI3, a calcium/calmodulin-dependent protein kinase (CCaMK). {ECO:0000269\|PubMed:15961668}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lj0g3v0135239.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced 24 hours after treatment with Nod factor or Sinorhizobium meliloti. {ECO:0000269\|PubMed:15961668}.

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	AP009782	0.0	AP009782.1 Lotus japonicus genomic DNA, clone: LjT26J05, TM1976, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004499407.1	1e-105	nodulation-signaling pathway 2 protein
Swissprot	Q5NE24	1e-103	NSP2_MEDTR; Nodulation-signaling pathway 2 protein
TrEMBL	Q2PEG7	1e-116	Q2PEG7_LOTJA; Nodulation signaling pathway 2
STRING	XP_004499407.1	1e-105	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF6264	31	52

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G08250.1	2e-69	GRAS family protein

Publications ? help Back to Top
Heckmann AB, et al. Lotus japonicus nodulation requires two GRAS domain regulators, one of which is functionally conserved in a non-legume. Plant Physiol., 2006. 142(4): p. 1739-50 [PMID:17071642] Murakami Y, et al. Positional cloning identifies Lotus japonicus NSP2, a putative transcription factor of the GRAS family, required for NIN and ENOD40 gene expression in nodule initiation. DNA Res., 2006. 13(6): p. 255-65 [PMID:17244637] Tang H, et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics, 2014. 15: p. 312 [PMID:24767513]