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

Cagra.0263s0012.1.p

Organism

Capsella grandiflora

Taxonomic ID

264402

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 818aa MW: 90985.8 Da PI: 6.7421

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cagra.0263s0012.1.p	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	152	228	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+rr++k Cagra.0263s0012.1.p 152 RCQVPGCEVDISELKGYHRRHRVCLRCANASFVVLDGDNKRYCQQCGKFHVLSDFDEGKRSCRRKLERHNNRRKRKP 228 6************************************************************************9975 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101447	4.18E-5	65	75	No hit	No description
Gene3D	G3DSA:4.10.1100.10	1.7E-28	146	214	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.581	150	227	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	4.45E-34	151	231	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.4E-27	153	226	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: 818 aa Download sequence Send to blast
MSSLSQSPTP PEMEIQPPAL LNDDPSTYSS ALWDWGDLLD FAADDRLLVS FDSSDQQAPF 60 SPLLPPPPPP PPPPPLPQLI PTQPLADSEL AYPSPDESGS GSDRVRKRDP RLICSNFIEG 120 MLPCSCPELD QKLEEAELPK KKRVRGGSGV ARCQVPGCEV DISELKGYHR RHRVCLRCAN 180 ASFVVLDGDN KRYCQQCGKF HVLSDFDEGK RSCRRKLERH NNRRKRKPVD KGGVATKQQQ 240 VLSQNDNSVI DVEDGKDNTC SSDQRAEQDA SLIFEDPHIP AQGSVLFTHS INADNFVSVT 300 GSGEPQPDDG MNDTKFELSP SGGDNKSAYS TVCPTGRISF KLYDWNPAEF PRRLRHQIFQ 360 WLSTMPVELE GYIRPGCTIL TVFIAMPEIM WAKLSKDPVA YLDEFILKPG KMLFGRGSMT 420 VYLNNMIFRL IKGGTTLKRV DVKLESPKLQ FVYPTCFEAG KPIEFVVCGR NLLQPKCRFL 480 VSFSGKYLPH NYSVVPTPAQ DGKLSCNNKF YKINIVNSDP NLFGPAFVEV ENESGLSNFI 540 PLIIGDESIC SEMKEIEQKF NATLVPEGQG VTACCSSTCC CMDFGERQSS FSGLLLDIAW 600 SVKVPSTECT EKTINRCQIK RYNRVLNYLI QNNSSSILGN VLHNLETLVK KMEPDSLVHC 660 TCDCDVRLLH ENMNLASDAN RKHQSHEESK VNPGNVLPSS GCCCESSFQK DKSSRIINFN 720 QDPEAGLDCK ADCSPDIGGK ETDPLLNKEV VMNVNDIGDW RRKSCIPIHS TLKFRSRQTV 780 FLIATFAVCF AVCAVLYHPN KVTQLAVAIR TRLAQKL*

Sequence ? help Back to Top

Protein Sequence Length: 818 aa Download sequence Send to blast

MSSLSQSPTP PEMEIQPPAL LNDDPSTYSS ALWDWGDLLD FAADDRLLVS FDSSDQQAPF  60
SPLLPPPPPP PPPPPLPQLI PTQPLADSEL AYPSPDESGS GSDRVRKRDP RLICSNFIEG  120
MLPCSCPELD QKLEEAELPK KKRVRGGSGV ARCQVPGCEV DISELKGYHR RHRVCLRCAN  180
ASFVVLDGDN KRYCQQCGKF HVLSDFDEGK RSCRRKLERH NNRRKRKPVD KGGVATKQQQ  240
VLSQNDNSVI DVEDGKDNTC SSDQRAEQDA SLIFEDPHIP AQGSVLFTHS INADNFVSVT  300
GSGEPQPDDG MNDTKFELSP SGGDNKSAYS TVCPTGRISF KLYDWNPAEF PRRLRHQIFQ  360
WLSTMPVELE GYIRPGCTIL TVFIAMPEIM WAKLSKDPVA YLDEFILKPG KMLFGRGSMT  420
VYLNNMIFRL IKGGTTLKRV DVKLESPKLQ FVYPTCFEAG KPIEFVVCGR NLLQPKCRFL  480
VSFSGKYLPH NYSVVPTPAQ DGKLSCNNKF YKINIVNSDP NLFGPAFVEV ENESGLSNFI  540
PLIIGDESIC SEMKEIEQKF NATLVPEGQG VTACCSSTCC CMDFGERQSS FSGLLLDIAW  600
SVKVPSTECT EKTINRCQIK RYNRVLNYLI QNNSSSILGN VLHNLETLVK KMEPDSLVHC  660
TCDCDVRLLH ENMNLASDAN RKHQSHEESK VNPGNVLPSS GCCCESSFQK DKSSRIINFN  720
QDPEAGLDCK ADCSPDIGGK ETDPLLNKEV VMNVNDIGDW RRKSCIPIHS TLKFRSRQTV  780
FLIATFAVCF AVCAVLYHPN KVTQLAVAIR TRLAQKL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	8e-49	150	235	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	Cagra.0263s0012.1.p

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.
GenBank	AY078050	0.0	AY078050.1 Arabidopsis thaliana AT5g18830/F17K4_80 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006289414.1	0.0	squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	R0FIT6	0.0	R0FIT6_9BRAS; Uncharacterized protein
STRING	Cagra.0263s0012.1.p	0.0	(Capsella grandiflora)

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	Cagra.0263s0012.1.p

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]