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

NNU_001645-RA

Organism

Nelumbo nucifera

Taxonomic ID

4432

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo

Family

SBP

Protein Properties

Length: 880aa MW: 98260.2 Da PI: 7.632

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_001645-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	116.6	1.3e-36	211	287	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cqv+gCe+d+se+k yhrrh+vC +++a++v+++g+++r+CqqC++fh ls+fDe+krsCrr+L++hn+rrr+k+ NNU_001645-RA 211 RCQVPGCEVDISELKGYHRRHRVCLRCANATSVVLDGQSKRYCQQCGKFHILSDFDEGKRSCRRKLERHNKRRRRKA 287 6*************************************************************************987 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.0E-28	208	273	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	30.026	209	286	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	9.29E-34	210	289	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	8.8E-28	212	286	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:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 880 aa Download sequence Send to blast
EQGLKCFCLK LLNSNFQRCG QGNFISADWL RRYDDIEYSP PTPPPVNRRS CLPLASPPPA 60 NLSPAASCLR ISRVRVSLGM EIPHPPPSDQ AVSLTRVRAP EMEFPQILDE ASAPWEWGNL 120 LDFTVDDQLV VSWDSDNNPT IAQAPELVPQ PFSNRGTDAS DRVRKRDPRL TCSNFLAGRI 180 PCACPEIDEK DEGEAAVGKK RARTAPVGTA RCQVPGCEVD ISELKGYHRR HRVCLRCANA 240 TSVVLDGQSK RYCQQCGKFH ILSDFDEGKR SCRRKLERHN KRRRRKAVDS RGAVEKEGQG 300 SLSPEDTSGD AEAGKDTLCL NDRVPQREVT LEPEDGHVSP PCSAPSSQNV QSDSVVSFAA 360 SGETPMDGRK ENSKNAISSP FCDNKSAYSS VCPTGRVSFK LYDWNPAEFP RRLRHQIFQW 420 LASMPVELEG YIRPGCTILT VFIAMPQVMW DKLSQDAASY IHGFVTSPEN ILWRKGVMRV 480 YLCNMIFQVL KDGMSLVNIK MEVRAPRLHY IHPTCFEAGK PMEFVACGSN LQQPKFRRFL 540 VSFCGKYLSY DYCLAISPTQ NVSDDTHSCD HQMYKIYIPH TDPKLFGPAF VEVENESGIS 600 NYIPILIANR EICSEMQVLQ HKLDGSFCAE RPQLAIAGSL SDECEVLVLR QTAVSELLLD 660 IAWLLKESEL GSIQSLSTST QIQRFNSLLD FLIKNNLTMV LMKILEAMKV VDKELNNTVN 720 ATDDAGVRLF HKYMDHASEI VCKKIQNIQD LPKYSGRDSY SKSFDKNDMI SGMPNNQDIS 780 RTGGVEIFGA VATSNSGDSS VNVPLINRDV VMNVNYEPRK SCGYILSNTT RNSRPLVFIV 840 VATAMCFGIC AVLLHPHKVG DLAISIRRCL FGNPKPYKLT

Sequence ? help Back to Top

Protein Sequence Length: 880 aa Download sequence Send to blast

EQGLKCFCLK LLNSNFQRCG QGNFISADWL RRYDDIEYSP PTPPPVNRRS CLPLASPPPA  60
NLSPAASCLR ISRVRVSLGM EIPHPPPSDQ AVSLTRVRAP EMEFPQILDE ASAPWEWGNL  120
LDFTVDDQLV VSWDSDNNPT IAQAPELVPQ PFSNRGTDAS DRVRKRDPRL TCSNFLAGRI  180
PCACPEIDEK DEGEAAVGKK RARTAPVGTA RCQVPGCEVD ISELKGYHRR HRVCLRCANA  240
TSVVLDGQSK RYCQQCGKFH ILSDFDEGKR SCRRKLERHN KRRRRKAVDS RGAVEKEGQG  300
SLSPEDTSGD AEAGKDTLCL NDRVPQREVT LEPEDGHVSP PCSAPSSQNV QSDSVVSFAA  360
SGETPMDGRK ENSKNAISSP FCDNKSAYSS VCPTGRVSFK LYDWNPAEFP RRLRHQIFQW  420
LASMPVELEG YIRPGCTILT VFIAMPQVMW DKLSQDAASY IHGFVTSPEN ILWRKGVMRV  480
YLCNMIFQVL KDGMSLVNIK MEVRAPRLHY IHPTCFEAGK PMEFVACGSN LQQPKFRRFL  540
VSFCGKYLSY DYCLAISPTQ NVSDDTHSCD HQMYKIYIPH TDPKLFGPAF VEVENESGIS  600
NYIPILIANR EICSEMQVLQ HKLDGSFCAE RPQLAIAGSL SDECEVLVLR QTAVSELLLD  660
IAWLLKESEL GSIQSLSTST QIQRFNSLLD FLIKNNLTMV LMKILEAMKV VDKELNNTVN  720
ATDDAGVRLF HKYMDHASEI VCKKIQNIQD LPKYSGRDSY SKSFDKNDMI SGMPNNQDIS  780
RTGGVEIFGA VATSNSGDSS VNVPLINRDV VMNVNYEPRK SCGYILSNTT RNSRPLVFIV  840
VATAMCFGIC AVLLHPHKVG DLAISIRRCL FGNPKPYKLT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	1e-40	209	294	3	88	squamosa promoter binding protein-like 7
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	272	284	RRKLERHNKRRRR
2	280	285	KRRRRK

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010279431.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	A0A1U8BQ89	0.0	A0A1U8BQ89_NELNU; squamosa promoter-binding-like protein 7
STRING	XP_010279426.1	0.0	(Nelumbo nucifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18830.1	0.0	squamosa promoter binding protein-like 7

Publications ? help Back to Top
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]