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

Ciclev10004348m

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: 799aa MW: 88545.5 Da PI: 7.08

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10004348m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	118	4.8e-37	130	207	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +Cqv+gCead+se+k yh+rh+vC +++a++vl++g+++r+CqqC++fh ls+fDe+krsCrr+L++hn+rrr+k+ Ciclev10004348m 130 RCQVPGCEADISELKGYHKRHRVCLRCANASTVLLDGESKRYCQQCGKFHLLSDFDEGKRSCRRKLERHNNRRRRKSV 207 6*************************************************************************9875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	8.5E-29	124	192	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.846	128	205	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	6.8E-34	129	208	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.4E-27	131	205	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: 799 aa Download sequence Send to blast
MERDGVERPR IPEMEVHPAM VTEADPSASA LWDWSDLLDF TTDDHFNLPL DPAQLELNPL 60 LEPQPEPPVV NNLERVRKRD PRLTCSNFLA GRIPCACPEL DEMLEEQEAG LPGKKRARTV 120 RAGHGQGKAR CQVPGCEADI SELKGYHKRH RVCLRCANAS TVLLDGESKR YCQQCGKFHL 180 LSDFDEGKRS CRRKLERHNN RRRRKSVDSK GAVDSEPPGA SRCEDIICDD DSGKDSLCLS 240 SQITDQEAFL ESEDGLVSAL NSAPNTQNVN SDSGISAVAS GEIRAERGKD DSKASLSPSN 300 CDNKSSYSSL CPTGRISFKL YDWNPAEFPR RLRHQIFHWL ASMPVELEGY IRPGCTILTV 360 FIAMPKIMWA KLYEDPIRYV HNFVVEPGTA SMLSGRGSMF VHLNNMIFHV KGGTSVVKVD 420 VKVQAPKLHY VQPSCFEAGK PLEFVACGSN LIQPKLRFLI SFAGKYLPHD YCIVSPLGGS 480 EGESLALEHQ FYKINVPHIE ANLFGPAFIE VENESGLSNF IPVLIGDKGT CSEIKIIQQR 540 FEASFFSKRS QFMASGLLSD LCEVSALRQK ALTELLVDIA WLLKAPASES FRQTISSSEV 600 QRFNQLLSFL IYNESTTILE KMLQNMKILM NNIESNIAVN GISDSDMGLL LKYMDYARGI 660 LCQKVKKDEG PMQHSGNIVP KMISSSQSCL QANSLVPSTK QDLRSNDKIG AVMDSATVDR 720 CEVVPLLNRE VVMNVNLIKE LPRKSCSPIF SGRVLSSLPT VTVIAMAAVC FGVCLVVLHP 780 QKVGHFATSI RRSLFGNL*

Sequence ? help Back to Top

Protein Sequence Length: 799 aa Download sequence Send to blast

MERDGVERPR IPEMEVHPAM VTEADPSASA LWDWSDLLDF TTDDHFNLPL DPAQLELNPL  60
LEPQPEPPVV NNLERVRKRD PRLTCSNFLA GRIPCACPEL DEMLEEQEAG LPGKKRARTV  120
RAGHGQGKAR CQVPGCEADI SELKGYHKRH RVCLRCANAS TVLLDGESKR YCQQCGKFHL  180
LSDFDEGKRS CRRKLERHNN RRRRKSVDSK GAVDSEPPGA SRCEDIICDD DSGKDSLCLS  240
SQITDQEAFL ESEDGLVSAL NSAPNTQNVN SDSGISAVAS GEIRAERGKD DSKASLSPSN  300
CDNKSSYSSL CPTGRISFKL YDWNPAEFPR RLRHQIFHWL ASMPVELEGY IRPGCTILTV  360
FIAMPKIMWA KLYEDPIRYV HNFVVEPGTA SMLSGRGSMF VHLNNMIFHV KGGTSVVKVD  420
VKVQAPKLHY VQPSCFEAGK PLEFVACGSN LIQPKLRFLI SFAGKYLPHD YCIVSPLGGS  480
EGESLALEHQ FYKINVPHIE ANLFGPAFIE VENESGLSNF IPVLIGDKGT CSEIKIIQQR  540
FEASFFSKRS QFMASGLLSD LCEVSALRQK ALTELLVDIA WLLKAPASES FRQTISSSEV  600
QRFNQLLSFL IYNESTTILE KMLQNMKILM NNIESNIAVN GISDSDMGLL LKYMDYARGI  660
LCQKVKKDEG PMQHSGNIVP KMISSSQSCL QANSLVPSTK QDLRSNDKIG AVMDSATVDR  720
CEVVPLLNRE VVMNVNLIKE LPRKSCSPIF SGRVLSSLPT VTVIAMAAVC FGVCLVVLHP  780
QKVGHFATSI RRSLFGNL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	8e-44	129	211	4	86	squamosa promoter binding protein-like 7
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	191	203	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_006419724.1	0.0	squamosa promoter-binding-like protein 7 isoform X1
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	V4U134	0.0	V4U134_9ROSI; Uncharacterized protein
STRING	XP_006419724.1	0.0	(Citrus clementina)

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	Ciclev10004348m
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]