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

Rsa1.0_00075.1_g00017.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 784aa MW: 87702.2 Da PI: 7.4797

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00075.1_g00017.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	115.4	3.1e-36	127	203	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cqv+gCe+d+ e+k yhrrhkvC ++++a++v+++g+ +r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k Rsa1.0_00075.1_g00017.1 127 RCQVPGCEVDIRELKGYHRRHKVCLQCANATSVVLEGEDKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 203 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	1.2E-28	121	189	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.12	125	202	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.83E-33	126	206	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	4.1E-27	128	201	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: 784 aa Download sequence Send to blast
MEIQPPALLD DDPSSAAMWD WGDLLLDFAA DERLLVSLDS DQPPFSPAPP PMIATSQPPA 60 QSESYPSPDE SGSGSDRVRK RDPRLLCSNF VEGLLPCSCP ELDQKLEEAE LPKKKRIRGG 120 GVSGVARCQV PGCEVDIREL KGYHRRHKVC LQCANATSVV LEGEDKRYCQ QCGKFHVLPD 180 FDEGKRSCRR KLERHNNRRK RKPVDKGGVA SKQQQVLSQN DNSVIDVDDG KDNTCSSDQR 240 VEQEASFSFE DRRIPTQGSV PFTHSINADS FVSGTGSGEA LPDEGINDTK FERSPSGGDN 300 KSAYSTMCPT GRISFKLYDW NPAEFPRRLR HQIFQWLATM PVELEGYIRP GCTILTVFIA 360 MPEIMWAKQL SKDPVAYLDE FILKPGKMLF GRGSMTVYLN NMIFRGTTLR RVDVKLESPK 420 LQFVYPTCFE AGKPIELVVC GLNLVQPKCR FLVSFSGKYL PHNYSVVPSL GQDGKRSCNN 480 KLYRINIVNS DPNLFGPAFV EVENESGLSN FIPLIIGDKA ICSEMKVIEQ KFNATLFPEE 540 QGITACCSLT CCCRDFKERQ STFTGLLLDI AWSVKVPSTE CTEQTVNRCQ IKRYNRVLNY 600 LIQSNSPSIL GNVLHNLETL VKKMKPDSLV HCTCDCDVRL LHENMNTARK QQSHEDSKVN 660 PVTSVCCCDS SFQKDIPSRV LNFNQEPEAG LGCNERIRAA SPDTGRKETD PLLNNEVIMN 720 VNDIGDWPRK SCIPIQSAQT CRSRQTVLFI ATIAVCFAVC VVLYHPNKVT QLAVSIRTRL 780 AHKL

Sequence ? help Back to Top

Protein Sequence Length: 784 aa Download sequence Send to blast

MEIQPPALLD DDPSSAAMWD WGDLLLDFAA DERLLVSLDS DQPPFSPAPP PMIATSQPPA  60
QSESYPSPDE SGSGSDRVRK RDPRLLCSNF VEGLLPCSCP ELDQKLEEAE LPKKKRIRGG  120
GVSGVARCQV PGCEVDIREL KGYHRRHKVC LQCANATSVV LEGEDKRYCQ QCGKFHVLPD  180
FDEGKRSCRR KLERHNNRRK RKPVDKGGVA SKQQQVLSQN DNSVIDVDDG KDNTCSSDQR  240
VEQEASFSFE DRRIPTQGSV PFTHSINADS FVSGTGSGEA LPDEGINDTK FERSPSGGDN  300
KSAYSTMCPT GRISFKLYDW NPAEFPRRLR HQIFQWLATM PVELEGYIRP GCTILTVFIA  360
MPEIMWAKQL SKDPVAYLDE FILKPGKMLF GRGSMTVYLN NMIFRGTTLR RVDVKLESPK  420
LQFVYPTCFE AGKPIELVVC GLNLVQPKCR FLVSFSGKYL PHNYSVVPSL GQDGKRSCNN  480
KLYRINIVNS DPNLFGPAFV EVENESGLSN FIPLIIGDKA ICSEMKVIEQ KFNATLFPEE  540
QGITACCSLT CCCRDFKERQ STFTGLLLDI AWSVKVPSTE CTEQTVNRCQ IKRYNRVLNY  600
LIQSNSPSIL GNVLHNLETL VKKMKPDSLV HCTCDCDVRL LHENMNTARK QQSHEDSKVN  660
PVTSVCCCDS SFQKDIPSRV LNFNQEPEAG LGCNERIRAA SPDTGRKETD PLLNNEVIMN  720
VNDIGDWPRK SCIPIQSAQT CRSRQTVLFI ATIAVCFAVC VVLYHPNKVT QLAVSIRTRL  780
AHKL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	7e-46	125	210	3	88	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	Rsa1.0_00075.1_g00017.1

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_018446607.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7 isoform X1
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	A0A3N6PYF5	0.0	A0A3N6PYF5_BRACR; Uncharacterized protein
STRING	Bo9g154530.1	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]