PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

Plant Transcription Factor Database

v4.0

Previous version: v3.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT5G18830.3

Common Name

ATSPL7, SPL7

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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: 818aa MW: 91550.4 Da PI: 6.4985

Description

squamosa promoter binding protein-like 7

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G18830.3	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	114	8.6e-36	137	213	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 AT5G18830.3 137 RCQVPDCEADISELKGYHKRHRVCLRCATASFVVLDGENKRYCQQCGKFHLLPDFDEGKRSCRRKLERHNNRRKRKP 213 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	6.0E-28	131	199	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.137	135	212	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	6.93E-34	136	216	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.7E-26	138	211	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
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025195	anatomy	pollen tube cell
PO:0025281	anatomy	pollen
PO:0001016	developmental stage	L mature pollen stage
PO:0001017	developmental stage	M germinated pollen stage
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 818 aa Download sequence Send to blast
MSSLSQSPPP PEMDIQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLVD QIHFPPVLSP 60 PLPPLIPTQT PAESELDPSP EESGSGSDRV RKRDPRLICS NFIEGMLPCS CPELDQKLED 120 AELPKKKRVR GGSGVARCQV PDCEADISEL KGYHKRHRVC LRCATASFVV LDGENKRYCQ 180 QCGKFHLLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA AEQQQVLSQN DNSVIDVEDG 240 KDITCSSDQR AEEEPSLIFE DRHITTQGSV PFTRSINADN FVSVTGSGEA QPDEGMNDTK 300 FERSPSNGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLANM PVELEGYIRP 360 GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN MIFRLIKGGT 420 TLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG KYLPHNYSVV 480 PAPDQDGKRS CNNKFYKINI VNSDPSLFGP AFVEVENESG LSNFIPLIIG DAAVCSEMKL 540 IEQKFNATLF PEGQEVTACS SLTCCCRDFG ERQSTFSGLL LDIAWSVKVP SAERTEQPVN 600 RCQIKRYNRV LNYLIQNNSA SILGNVLHNL ETLVKKMEPD SLVHCTCDCD VRLLHENMDL 660 ASDIHRKHQS PIESKVNPPS SGCCCVSSQK DIPSRILNFN KDPEAGLDCK ERIQADCSPD 720 SGGKETDPLL NKEVVMNVND IGDWPRKSCI KTHSALAFRS RQTMFLIATF AVCFAVCAVL 780 YHPNKVTQLA VAIRMRLCST ELSHNSFSES FPSERDRI

Sequence ? help Back to Top

Protein Sequence Length: 818 aa Download sequence Send to blast

MSSLSQSPPP PEMDIQPPAL VNDDPSTYSS ALWDWGDLLD FAADERLLVD QIHFPPVLSP  60
PLPPLIPTQT PAESELDPSP EESGSGSDRV RKRDPRLICS NFIEGMLPCS CPELDQKLED  120
AELPKKKRVR GGSGVARCQV PDCEADISEL KGYHKRHRVC LRCATASFVV LDGENKRYCQ  180
QCGKFHLLPD FDEGKRSCRR KLERHNNRRK RKPVDKGGVA AEQQQVLSQN DNSVIDVEDG  240
KDITCSSDQR AEEEPSLIFE DRHITTQGSV PFTRSINADN FVSVTGSGEA QPDEGMNDTK  300
FERSPSNGDN KSAYSTVCPT GRISFKLYDW NPAEFPRRLR HQIFQWLANM PVELEGYIRP  360
GCTILTVFIA MPEIMWAKLS KDPVAYLDEF ILKPGKMLFG RGSMTVYLNN MIFRLIKGGT  420
TLKRVDVKLE SPKLQFVYPT CFEAGKPIEL VVCGQNLLQP KCRFLVSFSG KYLPHNYSVV  480
PAPDQDGKRS CNNKFYKINI VNSDPSLFGP AFVEVENESG LSNFIPLIIG DAAVCSEMKL  540
IEQKFNATLF PEGQEVTACS SLTCCCRDFG ERQSTFSGLL LDIAWSVKVP SAERTEQPVN  600
RCQIKRYNRV LNYLIQNNSA SILGNVLHNL ETLVKKMEPD SLVHCTCDCD VRLLHENMDL  660
ASDIHRKHQS PIESKVNPPS SGCCCVSSQK DIPSRILNFN KDPEAGLDCK ERIQADCSPD  720
SGGKETDPLL NKEVVMNVND IGDWPRKSCI KTHSALAFRS RQTMFLIATF AVCFAVCAVL  780
YHPNKVTQLA VAIRMRLCST ELSHNSFSES FPSERDRI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	5e-54	135	220	3	88	squamosa promoter binding protein-like 7
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.495	0.0	flower\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	30687027	0.0
Genevisible	249960_at	0.0
Expression Atlas	AT5G18830	-
AtGenExpress	AT5G18830	-
ATTED-II	AT5G18830	-

Functional Description ? help Back to Top
Source	Description
TAIR	Encodes a member of the Squamosa Binding Protein family of transcriptional regulators. SPL7 is expressed highly in roots and appears to play a role in copper homeostasis. Mutants are hypersensitive to copper deficient conditions and display a retarded growth phenotype. SPL7 binds to the promoter of the copper responsive miRNAs miR398b and miR389c.

Function -- GeneRIF ? help Back to Top
SPL7 activates the transcription of multiple genes involved in copper homeostasis. [PMID: 19122104] Cu uptake into roots of Cu-deficient plants is dependent on FRO4/FRO5 and SPL7. [PMID: 22374396] COPT6 expression is regulated by copper availability that, in part, is controlled by a master regulator of copper homeostasis, SPL7 [PMID: 22865877] SPL7 directly regulates miR408 expression. [PMID: 23289771] Data suggest that iron superoxide dismutase gene FSD1 and SPL7 transcriptional regulator SPL7 may associate withi copper homeostasis. [PMID: 23455955] Data indicate that cadmium (Cd) elicits SPL7-dependent copper (Cu) deficiency responses by altering expression of COPT1, COPT2, COPT6, CSD1, CSD2, miRNA398 b/c precursors and FSD1. [PMID: 23835944] The data presented here provide evidence for SPL7 and KIN17 protein interaction as a point of convergence in response to both Copper deficiency and oxidative stress. [PMID: 24335506] Cytological and biochemical approaches confirmed an operative transmembrane domain (TMD) and uncovered a dual localisation of SPL7 between the nucleus and an endomembrane system, most likely the endoplasmic reticulum (ER). [PMID: 25207797]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00604	PBM	24477691	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G18830.3

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G23020(A), AT3G46900(A), AT3G56240(A), AT5G24380(A), AT5G59030(A), AT5G59520(A)

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G18830

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G18830

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	NP_001190333.1	0.0	squamosa promoter-binding-like protein 7
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	F4JZI4	0.0	F4JZI4_ARATH; Squamosa promoter-binding-like protein 7
STRING	AT5G18830.3	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM6358	26	44
Representative plant	OGRP4828	13	20

Link Out ? help Back to Top
Phytozome	AT5G18830.3
Entrez Gene	832001
iHOP	AT5G18830
wikigenes	AT5G18830

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Kamada T, et al. Functional differentiation of peroxisomes revealed by expression profiles of peroxisomal genes in Arabidopsis thaliana. Plant Cell Physiol., 2003. 44(12): p. 1275-89 [PMID:14701923] Yamasaki K, et al. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J. Mol. Biol., 2004. 337(1): p. 49-63 [PMID:15001351] Kropat J, et al. A regulator of nutritional copper signaling in Chlamydomonas is an SBP domain protein that recognizes the GTAC core of copper response element. Proc. Natl. Acad. Sci. U.S.A., 2005. 102(51): p. 18730-5 [PMID:16352720] Wang Y, et al. Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. Plant Physiol., 2008. 148(3): p. 1201-11 [PMID:18775970] Yamasaki H,Hayashi M,Fukazawa M,Kobayashi Y,Shikanai T SQUAMOSA Promoter Binding Protein-Like7 Is a Central Regulator for Copper Homeostasis in Arabidopsis. Plant Cell, 2009. 21(1): p. 347-61 [PMID:19122104] Pilon M,Cohu CM,Ravet K,Abdel-Ghany SE,Gaymard F Essential transition metal homeostasis in plants. Curr. Opin. Plant Biol., 2009. 12(3): p. 347-57 [PMID:19481497] Pe Regulation of copper transport in Arabidopsis thaliana: a biochemical oscillator? J. Biol. Inorg. Chem., 2010. 15(1): p. 29-36 [PMID:19798519] Cohu CM, et al. Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Mol Plant, 2009. 2(6): p. 1336-50 [PMID:19969519] Bernal M, et al. Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell, 2012. 24(2): p. 738-61 [PMID:22374396] Ren L,Tang G Identification of sucrose-responsive microRNAs reveals sucrose-regulated copper accumulations in an SPL7-dependent and independent manner in Arabidopsis thaliana. Plant Sci., 2012. 187: p. 59-68 [PMID:22404833] Jung HI, et al. COPT6 is a plasma membrane transporter that functions in copper homeostasis in Arabidopsis and is a novel target of SQUAMOSA promoter-binding protein-like 7. J. Biol. Chem., 2012. 287(40): p. 33252-67 [PMID:22865877] Zhang H,Li L SQUAMOSA promoter binding protein-like7 regulated microRNA408 is required for vegetative development in Arabidopsis. Plant J., 2013. 74(1): p. 98-109 [PMID:23289771] Andr Comparison of global responses to mild deficiency and excess copper levels in Arabidopsis seedlings. Metallomics, 2013. 5(9): p. 1234-46 [PMID:23455955] Gayomba SR, et al. The CTR/COPT-dependent copper uptake and SPL7-dependent copper deficiency responses are required for basal cadmium tolerance in A. thaliana. Metallomics, 2013. 5(9): p. 1262-75 [PMID:23835944] Garcia-Molina A,Xing S,Huijser P A conserved KIN17 curved DNA-binding domain protein assembles with SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE7 to adapt Arabidopsis growth and development to limiting copper availability. Plant Physiol., 2014. 164(2): p. 828-40 [PMID:24335506] Garcia-Molina A,Xing S,Huijser P Functional characterisation of Arabidopsis SPL7 conserved protein domains suggests novel regulatory mechanisms in the Cu deficiency response. BMC Plant Biol., 2014. 14: p. 231 [PMID:25207797] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178]