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

909902

Common Name

ARALYDRAFT_909902

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 811aa MW: 90529.2 Da PI: 6.7814

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
909902	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	115.5	2.9e-36	140	216	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cqv++Cead+se+k yh+rh+vC +++a++v+++g+++r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k 909902 140 RCQVPDCEADISELKGYHKRHRVCLRCANASSVVLDGENKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 216 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	2.3E-28	134	202	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.188	138	215	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.2E-33	139	219	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	8.9E-27	141	214	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: 811 aa Download sequence Send to blast
MSSLSQSPTP PEMDVQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLSL DSDQTPFPPV 60 PSPPLPPLIP TQTPAESELY PSPEESGSGS DRVRKRDPRL ICSNFIEGML PCSCPELDQK 120 LEDAELPKKK RVRGGSGVAR CQVPDCEADI SELKGYHKRH RVCLRCANAS SVVLDGENKR 180 YCQQCGKFHV LPDFDEGKRS CRRKLERHNN RRKRKPVDKG GVAAKQQQVL SQNDNSVIDV 240 EDGKDNACSS DQRAEQEPSL IFEDRHIPTQ GSVPFTQSIN ADNFVSVTGS GEAQPDEGMN 300 DTKFERSPSN GDNKSAYSTV CPTGRISFKL YDWNPAEFPR RLRHQIFQWL ANMPVELEGY 360 IRPGCTILTV FIAMPEIMWA KLSKDPVAYL DEFILKPGKM LFGRGSMTVY LNNMIFRLIK 420 GGTTLKRVDV KLESPKLQFV YPTCFEAGKP IELVVCGQNL LQPKCRFLVS FSGKYLPHNY 480 SVIPAPDQDG KRSCNNKFYK INVVNSDPNL FGPAFVEVEN ESGLSNFIPL IIGDEAICSE 540 MKLIEQKFNA TLFPEEQGVT VCSSLTCCCR DFGERQSTFS GLLLDIAWSV KVPSAERTEQ 600 PVNRCQIKRY NRVLNYLIQN NSASILGSVL HNLETLVKKM EPDSLIHCTC DCDVRLLHEN 660 MDLASDVHRK HQSHKESKMN PGNVLPSSGC CCVSSFQKDI PSRILNFNQD PEAGLDCKER 720 IQADCSPDSG GKETDPLLNN EVVMNVNDIG DWSRKKSCIT AHSALTFRSR QTVFLIATFA 780 VCFAVCAVLY HPNKVTQLAV AIRMRLVHKI *

Sequence ? help Back to Top

Protein Sequence Length: 811 aa Download sequence Send to blast

MSSLSQSPTP PEMDVQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLSL DSDQTPFPPV  60
PSPPLPPLIP TQTPAESELY PSPEESGSGS DRVRKRDPRL ICSNFIEGML PCSCPELDQK  120
LEDAELPKKK RVRGGSGVAR CQVPDCEADI SELKGYHKRH RVCLRCANAS SVVLDGENKR  180
YCQQCGKFHV LPDFDEGKRS CRRKLERHNN RRKRKPVDKG GVAAKQQQVL SQNDNSVIDV  240
EDGKDNACSS DQRAEQEPSL IFEDRHIPTQ GSVPFTQSIN ADNFVSVTGS GEAQPDEGMN  300
DTKFERSPSN GDNKSAYSTV CPTGRISFKL YDWNPAEFPR RLRHQIFQWL ANMPVELEGY  360
IRPGCTILTV FIAMPEIMWA KLSKDPVAYL DEFILKPGKM LFGRGSMTVY LNNMIFRLIK  420
GGTTLKRVDV KLESPKLQFV YPTCFEAGKP IELVVCGQNL LQPKCRFLVS FSGKYLPHNY  480
SVIPAPDQDG KRSCNNKFYK INVVNSDPNL FGPAFVEVEN ESGLSNFIPL IIGDEAICSE  540
MKLIEQKFNA TLFPEEQGVT VCSSLTCCCR DFGERQSTFS GLLLDIAWSV KVPSAERTEQ  600
PVNRCQIKRY NRVLNYLIQN NSASILGSVL HNLETLVKKM EPDSLIHCTC DCDVRLLHEN  660
MDLASDVHRK HQSHKESKMN PGNVLPSSGC CCVSSFQKDI PSRILNFNQD PEAGLDCKER  720
IQADCSPDSG GKETDPLLNN EVVMNVNDIG DWSRKKSCIT AHSALTFRSR QTVFLIATFA  780
VCFAVCAVLY HPNKVTQLAV AIRMRLVHKI *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	2e-51	138	223	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	909902

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	AF367355	0.0	AF367355.1 Arabidopsis thaliana AT5g18830/F17K4_80 mRNA, complete cds.
GenBank	AJ011612	0.0	AJ011612.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 7.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_002871844.1	0.0	squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	D7LYI0	0.0	D7LYI0_ARALL; Uncharacterized protein
STRING	scaffold_601959.1	0.0	(Arabidopsis lyrata)

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

Link Out ? help Back to Top
Phytozome	909902
Entrez Gene	9307913

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]