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

Carubv10002913m

Common Name

CARUB_v10002913mg

Organism

Capsella rubella

Taxonomic ID

81985

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: 817aa MW: 90994.8 Da PI: 6.6817

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10002913m	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	151	227	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 Carubv10002913m 151 RCQVPGCEVDISELKGYHRRHRVCLRCANASFVVLDGDNKRYCQQCGKFHVLSDFDEGKRSCRRKLERHNNRRKRKP 227 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	1.7E-28	145	213	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.581	149	226	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	4.45E-34	150	230	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.4E-27	152	225	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: 817 aa Download sequence Send to blast
MSSLSQSPTP PEMEMEIQPP ALLNDDPSTY SSALWDWGDL LDFAADDRLL VSFDSSDQQA 60 PFSPVLLPPP PPPPLPQLIP TQPLAESELA YPSPDESGSG SDRVRKRDPR LICSNFIEGM 120 LPCSCPELDQ KLEEAELPKK KRVRGGSGVA RCQVPGCEVD ISELKGYHRR HRVCLRCANA 180 SFVVLDGDNK RYCQQCGKFH VLSDFDEGKR SCRRKLERHN NRRKRKPVDK GGVAAKQQQV 240 LSQNDNSVID VEDGKDNTCF SDQRAEQDAS LIFEDPHIPA QGSVLFTHSI NADNFVSVTG 300 SGEPQPDEGM NDTKFELSPS GGDNKSAYST VCPTGRISFK LYDWNPAEFP RRLRHQIFQW 360 LSTMPVELEG YIRPGCTILT VFIAMPEIMW AKLSKDPVAY LDEFILKPGK MLFGRGSMTV 420 YLNNMIFRLI KGGTTLKRVD VKLESPKLQF VYPTCFEAGK PIEFVVCGRN LLQPKCRFLV 480 SFSGKYLPHN YSVVPTPAQD GKLSCNNKFY KINIVNSDPN LFGPAFVEVE NESGLSNFIP 540 LIIGDESICS EMKEIEQKFN ATLVPEGQGV TACCSSTCCC MDFGERQSSF SGLLLDIAWS 600 VKVPSAECTE KTINRCQIKR YNRVLNYLIQ NNSSSILGNV LHNLETLVKK MEPDSLVHCT 660 CDCDVRLLHE NMNLASDANR KHQSHEESKV NPGNVLPSSG CCCESSFQKH KSSRIINFNQ 720 DQEAGLDCKA DCSPDIGGKE TDPLLNKEVV MNVNDIGDWP RKSCIPIHST LKFRSRQTVF 780 LIATFAVCFS VCAVLYHPNK VTQLAVAIRT RLAQKL*

Sequence ? help Back to Top

Protein Sequence Length: 817 aa Download sequence Send to blast

MSSLSQSPTP PEMEMEIQPP ALLNDDPSTY SSALWDWGDL LDFAADDRLL VSFDSSDQQA  60
PFSPVLLPPP PPPPLPQLIP TQPLAESELA YPSPDESGSG SDRVRKRDPR LICSNFIEGM  120
LPCSCPELDQ KLEEAELPKK KRVRGGSGVA RCQVPGCEVD ISELKGYHRR HRVCLRCANA  180
SFVVLDGDNK RYCQQCGKFH VLSDFDEGKR SCRRKLERHN NRRKRKPVDK GGVAAKQQQV  240
LSQNDNSVID VEDGKDNTCF SDQRAEQDAS LIFEDPHIPA QGSVLFTHSI NADNFVSVTG  300
SGEPQPDEGM NDTKFELSPS GGDNKSAYST VCPTGRISFK LYDWNPAEFP RRLRHQIFQW  360
LSTMPVELEG YIRPGCTILT VFIAMPEIMW AKLSKDPVAY LDEFILKPGK MLFGRGSMTV  420
YLNNMIFRLI KGGTTLKRVD VKLESPKLQF VYPTCFEAGK PIEFVVCGRN LLQPKCRFLV  480
SFSGKYLPHN YSVVPTPAQD GKLSCNNKFY KINIVNSDPN LFGPAFVEVE NESGLSNFIP  540
LIIGDESICS EMKEIEQKFN ATLVPEGQGV TACCSSTCCC MDFGERQSSF SGLLLDIAWS  600
VKVPSAECTE KTINRCQIKR YNRVLNYLIQ NNSSSILGNV LHNLETLVKK MEPDSLVHCT  660
CDCDVRLLHE NMNLASDANR KHQSHEESKV NPGNVLPSSG CCCESSFQKH KSSRIINFNQ  720
DQEAGLDCKA DCSPDIGGKE TDPLLNKEVV MNVNDIGDWP RKSCIPIHST LKFRSRQTVF  780
LIATFAVCFS VCAVLYHPNK VTQLAVAIRT RLAQKL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	8e-49	149	234	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	Carubv10002913m

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	XP_006289414.1	0.0	(Capsella rubella)

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	Carubv10002913m
Entrez Gene	17882403

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]