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

GSBRNA2T00086890001

Common Name

GSBRNA2T00086890001

Organism

Brassica napus

Taxonomic ID

3708

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 780aa MW: 87153.5 Da PI: 7.4073

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSBRNA2T00086890001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	117.9	5.1e-37	120	196	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cqv+gCe+d+se+k yh+rh+vC ++++a++v+++g+ +r+CqqC++fh l +fDe+krsCrr+L++hn+rr++k GSBRNA2T00086890001 120 RCQVPGCEVDISELKGYHKRHRVCLACANASSVVLEGVDKRYCQQCGKFHVLPDFDEGKRSCRRKLERHNNRRKRKP 196 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	1.0E-28	114	182	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	29.436	118	195	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	2.88E-34	119	199	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.2E-27	121	194	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
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: 780 aa Download sequence Send to blast
MSQPPPPPEM DIQPPALLDD DPSSATWDWG DLLDFAADDD RLLFSPLPPP AMITTQSESY 60 PSPDESGSGS DRVRKRDPRL LCSNFVQGMV PCSCPELDQK LEEAELPKRK RVRGGSGVVR 120 CQVPGCEVDI SELKGYHKRH RVCLACANAS SVVLEGVDKR YCQQCGKFHV LPDFDEGKRS 180 CRRKLERHNN RRKRKPVDKG GVASKQQQVL SQNDNSVIDV DDGKADNTCS SDQRVEQEAS 240 LISEDRNIPT QGSVPFPHSI NADNFVPVTG SGEAQPDEGM NDTKFEPSPS SGDNKSAYST 300 VCPTGRISFK LYDWNPAEFP RRLRHQIFQW LATMPVELEG YIRPGCTILT VFIAMPEIMW 360 AKLSKDPVAY LDEFILKPGK MLFGRGSMTV YLNNMIFRGT TLKRVDVKLE SPKLQFVYPT 420 CFEAGKPMEL IVCGLNLVQP KCRFLVSFSG KYLPHNYSVV PAPDQDGKRS CSNKLYRITI 480 VNSDPNLFGP AFVEVENESG LSNFIPLIIG DKAICSEMKL IEQKFNATLF PEEQDVTACY 540 CSLTCRCRDF KERQSTFTGL LLDIAWSVKV PSAECTELTV NRCQIKRYNR VLNYLKQSSN 600 SPSILGNILH NLETLVKKMD PGSLIHSKCD CDVRLLHENM NLARKQQSDE DSKVNPVTSA 660 CCCESSFHKD KPSRTLNFNQ DPEAGLDCKE RIQAASPDTG VNETDPLLKK EVVMNVSDKG 720 DWPRKSCIPI HSAQTIRSRQ TAFLITTFVV CFAVCAVIYH PNKVTQFAVA IRARLAHKL*

Sequence ? help Back to Top

Protein Sequence Length: 780 aa Download sequence Send to blast

MSQPPPPPEM DIQPPALLDD DPSSATWDWG DLLDFAADDD RLLFSPLPPP AMITTQSESY  60
PSPDESGSGS DRVRKRDPRL LCSNFVQGMV PCSCPELDQK LEEAELPKRK RVRGGSGVVR  120
CQVPGCEVDI SELKGYHKRH RVCLACANAS SVVLEGVDKR YCQQCGKFHV LPDFDEGKRS  180
CRRKLERHNN RRKRKPVDKG GVASKQQQVL SQNDNSVIDV DDGKADNTCS SDQRVEQEAS  240
LISEDRNIPT QGSVPFPHSI NADNFVPVTG SGEAQPDEGM NDTKFEPSPS SGDNKSAYST  300
VCPTGRISFK LYDWNPAEFP RRLRHQIFQW LATMPVELEG YIRPGCTILT VFIAMPEIMW  360
AKLSKDPVAY LDEFILKPGK MLFGRGSMTV YLNNMIFRGT TLKRVDVKLE SPKLQFVYPT  420
CFEAGKPMEL IVCGLNLVQP KCRFLVSFSG KYLPHNYSVV PAPDQDGKRS CSNKLYRITI  480
VNSDPNLFGP AFVEVENESG LSNFIPLIIG DKAICSEMKL IEQKFNATLF PEEQDVTACY  540
CSLTCRCRDF KERQSTFTGL LLDIAWSVKV PSAECTELTV NRCQIKRYNR VLNYLKQSSN  600
SPSILGNILH NLETLVKKMD PGSLIHSKCD CDVRLLHENM NLARKQQSDE DSKVNPVTSA  660
CCCESSFHKD KPSRTLNFNQ DPEAGLDCKE RIQAASPDTG VNETDPLLKK EVVMNVSDKG  720
DWPRKSCIPI HSAQTIRSRQ TAFLITTFVV CFAVCAVIYH PNKVTQFAVA IRARLAHKL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul5_A	3e-46	118	203	3	88	squamosa promoter binding protein-like 7
Search in ModeBase

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	GSBRNA2T00086890001

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK353552	0.0	AK353552.1 Thellungiella halophila mRNA, complete cds, clone: RTFL01-52-E05.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009126287.1	0.0	PREDICTED: squamosa promoter-binding-like protein 7
Swissprot	Q8S9G8	0.0	SPL7_ARATH; Squamosa promoter-binding-like protein 7
TrEMBL	A0A078I8E4	0.0	A0A078I8E4_BRANA; BnaAnng08550D protein
STRING	Bra023695.1-P	0.0	(Brassica rapa)

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
Chalhoub B, et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014. 345(6199): p. 950-3 [PMID:25146293] 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]