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

RrC5705_p2

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: 324aa MW: 35411.5 Da PI: 7.8734

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC5705_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	68	1.9e-21	158	204	1	47
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTS CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCs 47 +Cqv+gCe dls+ak+yhr+h+vCe hsk+p+++v gle+rfCqqC RrC5705_p2 158 RCQVDGCELDLSSAKDYHRKHRVCENHSKCPKITVGGLERRFCQQCC 204 6*********************************************6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.9E-22	151	203	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	17.307	156	233	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.83E-20	157	204	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	4.6E-16	159	203	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: 324 aa Download sequence Send to blast
MDCNMTSSLW DWEHLIMSNP SKTENDKRQP STEWEYEKGE GIESMFPSFT GLNRVSSGST 60 TGFSTNSSSP IFKLASEGSP GDSFSNIDFV QAKTSTAVSV ASAESDLCLK LGKQTYSEDY 120 WGRSNNEVSA VSTKLLAPCV VARKKSKAYG QSSMQVPRCQ VDGCELDLSS AKDYHRKHRV 180 CENHSKCPKI TVGGLERRFC QQCCMRSLNL MRRNEAAVNV FLITMLGVAS HKECFQRGIA 240 MESGFTLSFQ RGRGPEEQLY AGSSRSFSAF QTSGGFSAGR SSSQLPGKGV GEYSGGLHES 300 QDFYSALSLL STSSDSHGTK HNPM

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1wj0_A	3e-14	159	203	6	50	squamosa promoter-binding protein-like 12
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	AC189649	1e-123	AC189649.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrS010I09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018438765.1	0.0	PREDICTED: squamosa promoter-binding-like protein 10 isoform X2
Swissprot	Q8S9L0	1e-134	SPL10_ARATH; Squamosa promoter-binding-like protein 10
TrEMBL	A0A0D3CE03	1e-164	A0A0D3CE03_BRAOL; Uncharacterized protein
STRING	Bo5g051980.1	1e-165	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5004	16	53

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G27370.4	1e-115	squamosa promoter binding protein-like 10

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Yu N,Niu QW,Ng KH,Chua NH The role of miR156/SPLs modules in Arabidopsis lateral root development. Plant J., 2015. 83(4): p. 673-85 [PMID:26096676] 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] Gao R,Wang Y,Gruber MY,Hannoufa A miR156/SPL10 Modulates Lateral Root Development, Branching and Leaf Morphology in Arabidopsis by Silencing AGAMOUS-LIKE 79. Front Plant Sci, 2017. 8: p. 2226 [PMID:29354153] Dotto M,Gómez MS,Soto MS,Casati P UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana. Plant Cell Environ., 2018. 41(6): p. 1394-1406 [PMID:29447428]