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_009126287.1

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: 781aa MW: 87396.9 Da PI: 7.5174

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009126287.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	117.9	5.1e-37	119	195	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cqv+gCe+d+se+k yh+rh+vC ++++a++v+++g+ +r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k XP_009126287.1 119 RCQVPGCEVDISELKGYHKRHRVCLACANASSVVLEGVDKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 195 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	1.0E-28	113	181	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.436	117	194	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	2.88E-34	118	198	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.2E-27	120	193	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: 781 aa Download sequence Send to blast
MSQPPPPPEM DIQPPALLDD DPSSATWDWG DLLDFAADDD RLLFSPLPPA MITTQSESYP 60 SPDESGSGSD RVRKRDPRLL CSNFVQGMVP CSCPELDQKL EEAELPKRKR VRGGSGVVRC 120 QVPGCEVDIS ELKGYHKRHR VCLACANASS VVLEGVDKRY CQQCGKFHVL PDFDEGKRSC 180 RRKLERHNNR RKRKPVDKGG VASKQQQVLS QNDNSVIDVD DGKDNTCSSD QRVEQEASLI 240 SEDRNIPTQG SVPFPHSINA DNFVPVTGSG EAQPDEGMND TKFEPSPSSG DNKSAYSTVC 300 PTGRISFKLY DWNPAEFPRR LRHQIFQWLA TMPVELEGYI RPGCTILTVF IAMPEIMWAK 360 LSKDPVAYLD EFILKPGKML FGRGSMTVYL NNMIFRLLKG GTTLKRVDVK LESPKLQFVY 420 PTCFEAGKPM ELIVCGLNLV QPKCRFLVSF SGKYLPHNYS VVPAPDQDGK RSCSNKLYRI 480 TIVNSDPNLF GPAFVEVENE SGLSNFIPLI IGDKAICSEM KLIEQKFNAT LFPEEQDVTA 540 CYCSLTCRCR DFKERQSTFT GLLLDIAWSV KVPSAECTEL TVNRCQIKRY NRVLNYLKQS 600 SNSPSILGNI LHNLETLVKK MDPGSLIHSK CDCDVRLLHE NMNLARKQQS DEDSKVNPVT 660 SACCCESSFH KDKPSRTLNF NQDPEAGLDC KERIQAASPD TGVNETDPLL KKEVVMNVSD 720 KGDWPRKSCI PIHSAQTIRS RQTAFLITTF VVCFAVCAVI YHPNKVTQFA VAIRARLAHK 780 L

Sequence ? help Back to Top

Protein Sequence Length: 781 aa Download sequence Send to blast

MSQPPPPPEM DIQPPALLDD DPSSATWDWG DLLDFAADDD RLLFSPLPPA MITTQSESYP  60
SPDESGSGSD RVRKRDPRLL CSNFVQGMVP CSCPELDQKL EEAELPKRKR VRGGSGVVRC  120
QVPGCEVDIS ELKGYHKRHR VCLACANASS VVLEGVDKRY CQQCGKFHVL PDFDEGKRSC  180
RRKLERHNNR RKRKPVDKGG VASKQQQVLS QNDNSVIDVD DGKDNTCSSD QRVEQEASLI  240
SEDRNIPTQG SVPFPHSINA DNFVPVTGSG EAQPDEGMND TKFEPSPSSG DNKSAYSTVC  300
PTGRISFKLY DWNPAEFPRR LRHQIFQWLA TMPVELEGYI RPGCTILTVF IAMPEIMWAK  360
LSKDPVAYLD EFILKPGKML FGRGSMTVYL NNMIFRLLKG GTTLKRVDVK LESPKLQFVY  420
PTCFEAGKPM ELIVCGLNLV QPKCRFLVSF SGKYLPHNYS VVPAPDQDGK RSCSNKLYRI  480
TIVNSDPNLF GPAFVEVENE SGLSNFIPLI IGDKAICSEM KLIEQKFNAT LFPEEQDVTA  540
CYCSLTCRCR DFKERQSTFT GLLLDIAWSV KVPSAECTEL TVNRCQIKRY NRVLNYLKQS  600
SNSPSILGNI LHNLETLVKK MDPGSLIHSK CDCDVRLLHE NMNLARKQQS DEDSKVNPVT  660
SACCCESSFH KDKPSRTLNF NQDPEAGLDC KERIQAASPD TGVNETDPLL KKEVVMNVSD  720
KGDWPRKSCI PIHSAQTIRS RQTAFLITTF VVCFAVCAVI YHPNKVTQFA VAIRARLAHK  780
L

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	3e-46	117	202	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009126287.1

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	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_009126287.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	A0A0D2ZQ95	0.0	A0A0D2ZQ95_BRAOL; Uncharacterized protein
STRING	Bo00629s160.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6358	26	44

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]