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

XP_009120940.1

Organism

Brassica rapa

Taxonomic ID

3711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica

Family

SBP

Protein Properties

Length: 795aa MW: 89010.4 Da PI: 6.9515

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009120940.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	116.1	1.8e-36	136	212	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 l +fDe+krsCrr+L++hn+rr++k XP_009120940.1 136 RCQVPGCEVDISELKGYHRRHRVCLRCANASFVVIEGEDKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 212 6************************************************************************9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.5E-28	130	198	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.581	134	211	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	2.88E-34	135	215	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.7E-27	137	210	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: 795 aa Download sequence Send to blast
MSSLSQSQSP SPPEMEIQPP ALLDDDPSAY SSSALWDWGD LLDFAADEPL LVSLDSDQPP 60 FVPPPPLIAT QSDTYHSPDE SGGSGSDRVR KRDPRLLCSN FVEGLLPCSC PELDQKLEEA 120 ELPKKKRVRG GSGVARCQVP GCEVDISELK GYHRRHRVCL RCANASFVVI EGEDKRYCQQ 180 CGKFHVLPDF DEGKRSCRRK LERHNNRRKR KPVDKGGVAS KQQQVLSQND NSVIDVDDGK 240 DNTCSSDQRM EQEASLNFED RHIPTQGSVP FTHSINADNF VSGTGSDEAQ PDEGINDAKF 300 ERSPSGGDNK SAYSTMCPTG RISFKLYDWN PAEFPRRLRH QIFQWLATMP VELEGYIRPG 360 CTILTVFIAM PEIMWAKLSK DPVAYLDEFI LKPGKMLFGR GSMTVYLNNM IFRLIKGGTT 420 LRRVDVKLES PKLQFVYPTC FEAGKPIELV VCGLNLVQPK CRFLVSFSGK YLPHNYSVVP 480 GPGQDGKRSC NNKLYRINIV NSDPNLFGPA FVEVENESGL SNFIPLIVGD KAICSEMKLI 540 EQKFNARLFP EEQDITACCC LTCCCKDFKE RQSTFTGLLL DIAWSVKVPS SECTEQTVNR 600 CQIKRYNRVL NYLIQSNSPS ILGNVLQNLE TLVKKMEPDS FVHCTCDCDV RLLHENMNTA 660 RKQQSHEDSK VNPITSACCC DSSFQDMPSR VLNVNQESEA GLDCTKRIHT ASPDTGRKET 720 DPLLNKEVVM NVNDIGDWPR KSCIPIQSAQ TFRSRQTVLF IATIAVCFAV CAVLYHPNKV 780 TQLAVSIRTR LAHKL

Sequence ? help Back to Top

Protein Sequence Length: 795 aa Download sequence Send to blast

MSSLSQSQSP SPPEMEIQPP ALLDDDPSAY SSSALWDWGD LLDFAADEPL LVSLDSDQPP  60
FVPPPPLIAT QSDTYHSPDE SGGSGSDRVR KRDPRLLCSN FVEGLLPCSC PELDQKLEEA  120
ELPKKKRVRG GSGVARCQVP GCEVDISELK GYHRRHRVCL RCANASFVVI EGEDKRYCQQ  180
CGKFHVLPDF DEGKRSCRRK LERHNNRRKR KPVDKGGVAS KQQQVLSQND NSVIDVDDGK  240
DNTCSSDQRM EQEASLNFED RHIPTQGSVP FTHSINADNF VSGTGSDEAQ PDEGINDAKF  300
ERSPSGGDNK SAYSTMCPTG RISFKLYDWN PAEFPRRLRH QIFQWLATMP VELEGYIRPG  360
CTILTVFIAM PEIMWAKLSK DPVAYLDEFI LKPGKMLFGR GSMTVYLNNM IFRLIKGGTT  420
LRRVDVKLES PKLQFVYPTC FEAGKPIELV VCGLNLVQPK CRFLVSFSGK YLPHNYSVVP  480
GPGQDGKRSC NNKLYRINIV NSDPNLFGPA FVEVENESGL SNFIPLIVGD KAICSEMKLI  540
EQKFNARLFP EEQDITACCC LTCCCKDFKE RQSTFTGLLL DIAWSVKVPS SECTEQTVNR  600
CQIKRYNRVL NYLIQSNSPS ILGNVLQNLE TLVKKMEPDS FVHCTCDCDV RLLHENMNTA  660
RKQQSHEDSK VNPITSACCC DSSFQDMPSR VLNVNQESEA GLDCTKRIHT ASPDTGRKET  720
DPLLNKEVVM NVNDIGDWPR KSCIPIQSAQ TFRSRQTVLF IATIAVCFAV CAVLYHPNKV  780
TQLAVSIRTR LAHKL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	6e-49	134	219	3	88	squamosa promoter binding protein-like 7
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed constitutively during plant development. {ECO:0000269\|PubMed:10524240}.
Uniprot	TISSUE SPECIFICITY: Expressed in roots rosette leaves, cauline leaves, stems, flowers and siliques. {ECO:0000269\|PubMed:24335506}.

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	XP_009120940.1

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	AK353552	0.0	AK353552.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-52-E05.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009120940.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	A0A397XL67	0.0	A0A397XL67_BRACM; Uncharacterized protein
STRING	Bo9g154530.1	0.0	(Brassica oleracea)

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]