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

Pavir.6NG315100.1.p

Organism

Panicum virgatum

Taxonomic ID

38727

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum

Family

SBP

Protein Properties

Length: 286aa MW: 30517.9 Da PI: 8.5105

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pavir.6NG315100.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	88	1.1e-27	1	51	26	76
HHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S- CS SBP 26 vhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkk 76 +hskap v+v+g+eqrfCqqCsrfh+l+efD++krsCrrrL +hnerrr++ Pavir.6NG315100.1.p 1 MHSKAPLVVVNGIEQRFCQQCSRFHQLHEFDQQKRSCRRRLMGHNERRRRP 51 6************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF103612	6.54E-25	1	54	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.9E-20	1	50	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	22.572	1	51	IPR004333	Transcription factor, SBP-box
Gene3D	G3DSA:4.10.1100.10	2.8E-17	1	38	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 286 aa Download sequence Send to blast
MHSKAPLVVV NGIEQRFCQQ CSRFHQLHEF DQQKRSCRRR LMGHNERRRR PPAGPLASRY 60 GRLAASLGEP GRFRSFLLDF SYPRVPSSMR DGWQAAQPGE RVPGSMQWQS SLDPHHHSAI 120 AGYGAHSYGS QGSPSSGPPV FPGPELPPGG CLAGVPADSS CALSLLSTQP WDTTQSAGHS 180 RAASMPATAG FDGNPVAPSV MASSYIMPSP WMGSQGHAGG RNMTPQLPPE VPLDEVHSGS 240 SSRHGQFSGE LELALQGSRP APAPRIDQGS TSTFDQASNT SDWSL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	2e-18	1	50	35	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Pvr.11396	0.0	root\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in young panicles. {ECO:0000269\|PubMed:16861571}.

Functional Description ? help Back to Top
Source	Description
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' (By similarity). May be involved in panicle development. {ECO:0000250}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Pavir.6NG315100.1.p

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156b and miR156h. {ECO:0000305\|PubMed:16861571}.

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_025821402.1	0.0	squamosa promoter-binding-like protein 14
Swissprot	Q7EXZ2	1e-128	SPL14_ORYSJ; Squamosa promoter-binding-like protein 14
TrEMBL	A0A290G8S3	0.0	A0A290G8S3_PANVG; Squamosa promoter binding-like protein 4a
STRING	Pavir.Fb01946.1.p	0.0	(Panicum virgatum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP2527	37	87

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G42200.1	1e-27	squamosa promoter binding protein-like 9

Link Out ? help Back to Top
Phytozome	Pavir.6NG315100.1.p

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Miura K, et al. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat. Genet., 2010. 42(6): p. 545-9 [PMID:20495564] Jiao Y, et al. Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat. Genet., 2010. 42(6): p. 541-4 [PMID:20495565] Springer N Shaping a better rice plant. Nat. Genet., 2010. 42(6): p. 475-6 [PMID:20502488] Wang Y,Li J Branching in rice. Curr. Opin. Plant Biol., 2011. 14(1): p. 94-9 [PMID:21144796] Wang J,Kong L,Gao G,Luo J A brief introduction to web-based genome browsers. Brief. Bioinformatics, 2013. 14(2): p. 131-43 [PMID:22764121] Luo L,Li W,Miura K,Ashikari M,Kyozuka J Control of tiller growth of rice by OsSPL14 and Strigolactones, which work in two independent pathways. Plant Cell Physiol., 2012. 53(10): p. 1793-801 [PMID:22960246] Liu Q, et al. The alteration in the architecture of a T-DNA insertion rice mutant osmtd1 is caused by up-regulation of MicroRNA156f. J Integr Plant Biol, 2015. 57(10): p. 819-29 [PMID:25677853] Cruz-Garcia GS,Struik PC Spatial and Seasonal Diversity of Wild Food Plants in Home Gardens of Northeast Thailand1. Econ. Bot., 2015. 69(2): p. 99-113 [PMID:26160981] Srikanth B, et al. Enhanced expression of OsSPL14 gene and its association with yield components in rice (Oryza sativa) under low nitrogen conditions. Gene, 2016. 576(1 Pt 3): p. 441-50 [PMID:26519999] Perignon M, et al. Impact of Multi-Micronutrient Fortified Rice on Hemoglobin, Iron and Vitamin A Status of Cambodian Schoolchildren: a Double-Blind Cluster-Randomized Controlled Trial. Nutrients, 2016. [PMID:26751473] Kim SR, et al. Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L. Rice (N Y), 2016. 9(1): p. 12 [PMID:26987543]