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

PGSC0003DMP400011136

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

SBP

Protein Properties

Length: 214aa MW: 23565.3 Da PI: 5.1363

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400011136	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	64.8	1.9e-20	149	198	1	50
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEE CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfh 50 +Cqv++Cead+se+k yh+rh+vC +++a++v+++g+++r+CqqC+++ PGSC0003DMP400011136 149 RCQVPDCEADISELKGYHKRHRVCLRCANATAVVLDGHSKRYCQQCGKYV 198 6**********************************************985 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.1E-18	146	197	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	17.307	147	213	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	6.15E-19	149	201	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.1E-14	150	197	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0055070	Biological Process	copper ion homeostasis
GO:0005634	Cellular Component	nucleus
GO:0016021	Cellular Component	integral component of membrane
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 214 aa Download sequence Send to blast
MHNQPSSPSQ TGAPTELRNT QMISSLLSGT PDDPAASSIF DWSDLLEFDL HEQLSISFDD 60 PLHQEQQPET ELVAPVIPSS EDSPQSQDTD AGRIRKRDPR MACSNFLAGQ IPCACPELDE 120 KMEEEEMAGI GPGKKRARTV RASAGAGARC QVPDCEADIS ELKGYHKRHR VCLRCANATA 180 VVLDGHSKRY CQQCGKYVYF FSDEYKKLYA GRV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	2e-26	145	197	1	53	squamosa promoter binding protein-like 7
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcription factor that participates in reprogramming global gene expression during copper deficiency in order to improve the metal uptake and prioritize its distribution to copper proteins of major importance (Probable). Binds directly to 5'-GTAC-3' motifs in the microRNA (miRNA) promoter of the stress-responsive miRNAs miR398b and miR398c to activate their transcription. During copper deficiency, activates the copper transporters COPT1 and COPT2, and the copper chaperone CCH, directly or indirectly via miRNAs. Required for the expression of the miRNAs miR397, miR408 and miR857 (PubMed:19122104). Acts coordinately with HY5 to regulate miR408 and its target genes in response to changes in light and copper conditions (PubMed:25516599). Activates miR857 and its target genes in response to low copper conditions (PubMed:26511915). Involved in cadmium stress response by regulating miR397a, miR398b, miR398c and miR857 (PubMed:27352843). Required for iron homeostasis during copper deficiency (PubMed:22374396). {ECO:0000269\|PubMed:19122104, ECO:0000269\|PubMed:22374396, ECO:0000269\|PubMed:25516599, ECO:0000269\|PubMed:26511915, ECO:0000269\|PubMed:27352843}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00604	PBM	Transfer from AT5G18830	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	PGSC0003DMP400011136

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HG975440	0.0	HG975440.1 Solanum pennellii chromosome ch01, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006356993.1	1e-139	PREDICTED: squamosa promoter-binding-like protein 7 isoform X1
Refseq	XP_006356994.1	1e-139	PREDICTED: squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	2e-49	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	M1A716	1e-158	M1A716_SOLTU; Uncharacterized protein
STRING	PGSC0003DMT400016072	1e-139	(Solanum tuberosum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18830.2	5e-46	squamosa promoter binding protein-like 7

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400011136

Publications ? help Back to Top
Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] Zhang H, et al. MicroRNA408 is critical for the HY5-SPL7 gene network that mediates the coordinated response to light and copper. Plant Cell, 2014. 26(12): p. 4933-53 [PMID:25516599] Zhao Y, et al. MicroRNA857 Is Involved in the Regulation of Secondary Growth of Vascular Tissues in Arabidopsis. Plant Physiol., 2015. 169(4): p. 2539-52 [PMID:26511915] Perea-García A, et al. Modulation of copper deficiency responses by diurnal and circadian rhythms in Arabidopsis thaliana. J. Exp. Bot., 2016. 67(1): p. 391-403 [PMID:26516126] Gielen H,Remans T,Vangronsveld J,Cuypers A Toxicity responses of Cu and Cd: the involvement of miRNAs and the transcription factor SPL7. BMC Plant Biol., 2016. 16(1): p. 145 [PMID:27352843] Yan J, et al. Arabidopsis Pollen Fertility Requires the Transcription Factors CITF1 and SPL7 That Regulate Copper Delivery to Anthers and Jasmonic Acid Synthesis. Plant Cell, 2017. 29(12): p. 3012-3029 [PMID:29114014] Araki R, et al. SPL7 locally regulates copper-homeostasis-related genes in Arabidopsis. J. Plant Physiol., 2018. [PMID:29635212]