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

Ciclev10004528m

Common Name

CICLE_v10004348mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

SBP

Protein Properties

Length: 643aa MW: 71552.3 Da PI: 8.1747

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10004528m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	41.8	2.9e-13	22	51	49	78
EEETTT--SS--S-STTTT-------S--- CS SBP 49 fhelsefDeekrsCrrrLakhnerrrkkqa 78 fh ls+fDe+krsCrr+L++hn+rrr+k+ Ciclev10004528m 22 FHLLSDFDEGKRSCRRKLERHNNRRRRKSV 51 9*************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS51141	12.255	1	49	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	9.4E-7	22	49	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	4.71E-10	22	52	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: 643 aa Download sequence Send to blast
MRKRFYRFAR WREQEILSTV WFHLLSDFDE GKRSCRRKLE RHNNRRRRKS VDSKGAVDSE 60 PPGASRCEDI ICDDDSGKDS LCLSSQITDQ EAFLESEDGL VSALNSAPNT QNVNSDSGIS 120 AVASGEIRAE RGKDDSKASL SPSNCDNKSS YSSLCPTGRI SFKLYDWNPA EFPRRLRHQI 180 FHWLASMPVE LEGYIRPGCT ILTVFIAMPK IMWAKLYEDP IRYVHNFVVE PGTASMLSGR 240 GSMFVHLNNM IFHVKGGTSV VKVDVKVQAP KLHYVQPSCF EAGKPLEFVA CGSNLIQPKL 300 RFLISFAGKY LPHDYCIVSP LGGSEGESLA LEHQFYKINV PHIEANLFGP AFIEVENESG 360 LSNFIPVLIG DKGTCSEIKI IQQRFEASFF SKRSQFMASG LLSDLCEVSA LRQKALTELL 420 VDIAWLLKAP ASESFRQTIS SSEVQRFNQL LSFLIYNEST TILEKMLQNM KILMNNIESN 480 IAVNGISDSD MGLLLKYMDY ARGILCQKVK KDEGPMQHSG NIVPKMISSS QSCLQANSLV 540 PSTKQDLRSN DKIGAVMDSA TVDRCEVVPL LNREVVMNVN LIKELPRKSC SPIFSGRVLS 600 SLPTVTVIAM AAVCFGVCLV VLHPQKVGHF ATSIRRSLFG NL*

Sequence ? help Back to Top

Protein Sequence Length: 643 aa Download sequence Send to blast

MRKRFYRFAR WREQEILSTV WFHLLSDFDE GKRSCRRKLE RHNNRRRRKS VDSKGAVDSE  60
PPGASRCEDI ICDDDSGKDS LCLSSQITDQ EAFLESEDGL VSALNSAPNT QNVNSDSGIS  120
AVASGEIRAE RGKDDSKASL SPSNCDNKSS YSSLCPTGRI SFKLYDWNPA EFPRRLRHQI  180
FHWLASMPVE LEGYIRPGCT ILTVFIAMPK IMWAKLYEDP IRYVHNFVVE PGTASMLSGR  240
GSMFVHLNNM IFHVKGGTSV VKVDVKVQAP KLHYVQPSCF EAGKPLEFVA CGSNLIQPKL  300
RFLISFAGKY LPHDYCIVSP LGGSEGESLA LEHQFYKINV PHIEANLFGP AFIEVENESG  360
LSNFIPVLIG DKGTCSEIKI IQQRFEASFF SKRSQFMASG LLSDLCEVSA LRQKALTELL  420
VDIAWLLKAP ASESFRQTIS SSEVQRFNQL LSFLIYNEST TILEKMLQNM KILMNNIESN  480
IAVNGISDSD MGLLLKYMDY ARGILCQKVK KDEGPMQHSG NIVPKMISSS QSCLQANSLV  540
PSTKQDLRSN DKIGAVMDSA TVDRCEVVPL LNREVVMNVN LIKELPRKSC SPIFSGRVLS  600
SLPTVTVIAM AAVCFGVCLV VLHPQKVGHF ATSIRRSLFG NL*

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	35	47	RRKLERHNNRRRR

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00604	PBM	Transfer from AT5G18830	Download

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006419725.1	0.0	squamosa promoter-binding-like protein 7 isoform X2
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	V4S2K0	0.0	V4S2K0_9ROSI; Uncharacterized protein
STRING	XP_006419724.1	0.0	(Citrus clementina)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G18830.3	0.0	squamosa promoter binding protein-like 7

Link Out ? help Back to Top
Phytozome	Ciclev10004528m
Entrez Gene	18032345

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]