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

RrC3853_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

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

Family

SBP

Protein Properties

Length: 583aa MW: 65450.7 Da PI: 6.5576

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3853_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	98.9	4.4e-31	100	168	2	77
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 Cqv gC++dls k+yh+rh+vCe+hsk++vv+vsg+eqr fh lsefD++krsCrrrLa+hnerrrk++ RrC3853_p1 100 CQVYGCNMDLSFSKDYHKRHRVCEAHSKTSVVIVSGTEQR-------FHFLSEFDDGKRSCRRRLAGHNERRRKPS 168 ************************************97.......7************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	4.8E-23	94	154	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	25.136	97	167	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.44E-30	98	170	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	2.6E-21	100	166	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 583 aa Download sequence Send to blast
MDSWSYGRSV FLANGSDSFT ENQRFMPGFE QGLSPELETS NGFITKVASS SSCVVEENQS 60 SNLSRIDFKL RSFMDYGNQS SLPAKKTRAA SNSCSQSPLC QVYGCNMDLS FSKDYHKRHR 120 VCEAHSKTSV VIVSGTEQRF HFLSEFDDGK RSCRRRLAGH NERRRKPSFY FLPGKRHKLL 180 PQESFPGSFL YRVVDEHDHH RPSRLVSFKD EPKQESGVSY IWDLQEAVPP PPRSTCALSL 240 LSAQSQPETN PNKSFSITQP NQSFNHSTVD YYHQMQPLRI DPGKKTKSVT SSSSCNGNGS 300 STVDLVQLSS HLQRIQQQQR TFTDECYFAQ GAKAAWFGLI SLWYWFGDYW IVPFSVMPSL 360 VKLSSLLELR LLHRISLSSS SSSTIEIYLT IGRCGYKCRR GDGGCRDSGC YGSECGYRDG 420 RCEKEVVVVD TLVVDIVAVD VNMEMEAVRK TKCFSSLLDL RLLRRISLSS SSSSTIGESH 480 HESRNSNPFS IFQDLMLKMN DVGSCGGEAV DTLMDAVVED VRVKTVVEMV MDDVVDAVMV 540 DTMMVDVDTN VEDEEVVVDA LVVDDVAVDV NMKMEAVRKS KWS

Sequence ? help Back to Top

Protein Sequence Length: 583 aa Download sequence Send to blast

MDSWSYGRSV FLANGSDSFT ENQRFMPGFE QGLSPELETS NGFITKVASS SSCVVEENQS  60
SNLSRIDFKL RSFMDYGNQS SLPAKKTRAA SNSCSQSPLC QVYGCNMDLS FSKDYHKRHR  120
VCEAHSKTSV VIVSGTEQRF HFLSEFDDGK RSCRRRLAGH NERRRKPSFY FLPGKRHKLL  180
PQESFPGSFL YRVVDEHDHH RPSRLVSFKD EPKQESGVSY IWDLQEAVPP PPRSTCALSL  240
LSAQSQPETN PNKSFSITQP NQSFNHSTVD YYHQMQPLRI DPGKKTKSVT SSSSCNGNGS  300
STVDLVQLSS HLQRIQQQQR TFTDECYFAQ GAKAAWFGLI SLWYWFGDYW IVPFSVMPSL  360
VKLSSLLELR LLHRISLSSS SSSTIEIYLT IGRCGYKCRR GDGGCRDSGC YGSECGYRDG  420
RCEKEVVVVD TLVVDIVAVD VNMEMEAVRK TKCFSSLLDL RLLRRISLSS SSSSTIGESH  480
HESRNSNPFS IFQDLMLKMN DVGSCGGEAV DTLMDAVVED VRVKTVVEMV MDDVVDAVMV  540
DTMMVDVDTN VEDEEVVVDA LVVDDVAVDV NMKMEAVRKS KWS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	5e-21	99	166	10	84	squamosa promoter binding protein-like 4
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Trans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs miR156 and miR157. {ECO:0000305\|PubMed:12202040}.

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	KC815953	1e-46	KC815953.1 Arabis alpina SQUAMOSA promoter binding protein-like protein 6 (SPL6) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018453505.1	0.0	PREDICTED: squamosa promoter-binding-like protein 6 isoform X1
Refseq	XP_018453510.1	0.0	PREDICTED: squamosa promoter-binding-like protein 6 isoform X2
Swissprot	Q94JW8	1e-120	SPL6_ARATH; Squamosa promoter-binding-like protein 6
TrEMBL	A0A0D3AP84	1e-162	A0A0D3AP84_BRAOL; Uncharacterized protein
STRING	Bo2g062840.1	1e-163	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9275	24	35

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G69170.1	1e-111	SBP family protein

Publications ? help Back to Top
Jorgensen SA,Preston JC Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis. Mol. Phylogenet. Evol., 2014. 73: p. 129-39 [PMID:24508602] Xu M, et al. Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana. PLoS Genet., 2016. 12(8): p. e1006263 [PMID:27541584]