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

Csa08g011360.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 817aa MW: 90876.4 Da PI: 6.7178

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa08g011360.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	114.7	5.1e-36	147	223	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 Csa08g011360.1 147 RCQVPGCEVDISELKGYHRRHRVCLRCANATFVVLDGDNNRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 223 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	2.2E-28	141	209	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.333	145	222	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	5.76E-34	146	226	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	3.2E-27	148	221	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: 817 aa Download sequence Send to blast
MSSLSQSQSP TPPEMEIQPP ALVNDDPSTY SSALWDWGDL LDFAADERLL VSFDSSDQLT 60 PFPPVPSPPP PPPQLIPTQP LAESESYPSP DESGSGSDRV RKRDPRLICS NFVEGLLPCS 120 CPELDQKLEE AELPKKKRVR GGSGVARCQV PGCEVDISEL KGYHRRHRVC LRCANATFVV 180 LDGDNNRYCQ QCGKFHVLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA TKQQQVPSHN 240 DNSVIDVEDG KDNTCSSDQR AEQEASLIFE DGHIPPQGSV PFTHSINADN FVSVTGSGEP 300 QPDEGMNDKK FELSPSGGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLSTM 360 PVELEGYIRP GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN 420 MIFRLIKGGT SLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG 480 KYLPHNYSVV PTPAQDGKRS CNNKFYKINI VNSDPNLFGP AFVEVENESG LSNFIPLIIG 540 DESICSEMKQ IEQKFNATLV PEGQEVTACC SSACCCSDFG ERQSTFSGLL LDIAWSVKVP 600 SAECTEKRIN RCQIKRYNRV LNYLIQNNSS SILGNVLHNL EALVKKMEPD SLVHCTCDCD 660 VRLLHENMNL ATDANRKHQS HEDSKVNPGN VLPSSGCCCE SSFQKDKPSK IVNFNQDPEA 720 GLDCKERIQA DCSPDIGGKE TDPLLNKEVV MNVNDVGDWP RKSCIPLHST LTFRSRQTVF 780 LIATFAVCFA VCAVLYHPNK VTQLAVAIRT RLAHKL*

Sequence ? help Back to Top

Protein Sequence Length: 817 aa Download sequence Send to blast

MSSLSQSQSP TPPEMEIQPP ALVNDDPSTY SSALWDWGDL LDFAADERLL VSFDSSDQLT  60
PFPPVPSPPP PPPQLIPTQP LAESESYPSP DESGSGSDRV RKRDPRLICS NFVEGLLPCS  120
CPELDQKLEE AELPKKKRVR GGSGVARCQV PGCEVDISEL KGYHRRHRVC LRCANATFVV  180
LDGDNNRYCQ QCGKFHVLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA TKQQQVPSHN  240
DNSVIDVEDG KDNTCSSDQR AEQEASLIFE DGHIPPQGSV PFTHSINADN FVSVTGSGEP  300
QPDEGMNDKK FELSPSGGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLSTM  360
PVELEGYIRP GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN  420
MIFRLIKGGT SLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG  480
KYLPHNYSVV PTPAQDGKRS CNNKFYKINI VNSDPNLFGP AFVEVENESG LSNFIPLIIG  540
DESICSEMKQ IEQKFNATLV PEGQEVTACC SSACCCSDFG ERQSTFSGLL LDIAWSVKVP  600
SAECTEKRIN RCQIKRYNRV LNYLIQNNSS SILGNVLHNL EALVKKMEPD SLVHCTCDCD  660
VRLLHENMNL ATDANRKHQS HEDSKVNPGN VLPSSGCCCE SSFQKDKPSK IVNFNQDPEA  720
GLDCKERIQA DCSPDIGGKE TDPLLNKEVV MNVNDVGDWP RKSCIPLHST LTFRSRQTVF  780
LIATFAVCFA VCAVLYHPNK VTQLAVAIRT RLAHKL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	4e-49	145	230	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	Csa08g011360.1

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	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_010420661.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	R0FIT6	0.0	R0FIT6_9BRAS; Uncharacterized protein
STRING	XP_010420659.1	0.0	(Camelina sativa)

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]