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

RrC7158_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: 112aa MW: 13160.1 Da PI: 10.3068

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC7158_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	128.5	2.6e-40	5	81	1	77
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S-- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 +Cq++gC+ dls+ak+yhr+h+vCe hsk+p v+v g+e+rfCqqCsr h++sefDe+krsCr+rL++hn+rrrk+q RrC7158_p1 5 RCQIDGCQLDLSSAKDYHRKHRVCENHSKCPLVTVGGMERRFCQQCSRLHAVSEFDEKKRSCRKRLSHHNARRRKPQ 81 6**************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	2.1E-32	2	67	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	31.53	3	80	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.23E-37	4	81	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	3.1E-31	6	79	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: 112 aa Download sequence Send to blast
MQVPRCQIDG CQLDLSSAKD YHRKHRVCEN HSKCPLVTVG GMERRFCQQC SRLHAVSEFD 60 EKKRSCRKRL SHHNARRRKP QGVFPLHAQR VYIYLRQIQD SIQDLKKSTD GV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	4e-26	6	79	11	84	squamosa promoter binding protein-like 4
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	61	78	KKRSCRKRLSHHNARRRK

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	KM096582	6e-76	KM096582.1 Cardamine hirsuta squamosa promoter-binding-like protein 11 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018492236.1	1e-61	PREDICTED: squamosa promoter-binding-like protein 10
Refseq	XP_018492237.1	1e-61	PREDICTED: squamosa promoter-binding-like protein 10
Refseq	XP_018492238.1	1e-61	PREDICTED: squamosa promoter-binding-like protein 10
Refseq	XP_018492239.1	1e-61	PREDICTED: squamosa promoter-binding-like protein 10
Refseq	XP_018492240.1	1e-61	PREDICTED: squamosa promoter-binding-like protein 10
Swissprot	Q8S9L0	2e-55	SPL10_ARATH; Squamosa promoter-binding-like protein 10
TrEMBL	A0A3N6R0F9	9e-57	A0A3N6R0F9_BRACR; Uncharacterized protein
TrEMBL	A0A3P6EAD5	1e-56	A0A3P6EAD5_BRAOL; Uncharacterized protein
STRING	Bra030041.1-P	3e-57	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4111	27	59

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G27370.4	7e-58	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]