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

Rsa1.0_00012.1_g00032.1

Organism

Raphanus sativus

Taxonomic ID

3726

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: 325aa MW: 37267.5 Da PI: 8.9961

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00012.1_g00032.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	135.5	1.7e-42	104	179	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+++v+v+g+eqrfCqqCsrfh lsefD++krsCrrrLa+hnerrrk++ Rsa1.0_00012.1_g00032.1 104 CQVYGCNMDLSSSKDYHKRHRVCETHSKSSMVIVNGIEQRFCQQCSRFHFLSEFDDGKRSCRRRLAGHNERRRKPS 179 **************************************************************************86 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	5.7E-34	98	165	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	32.949	101	178	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	3.66E-40	102	181	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	6.0E-33	104	177	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: 325 aa Download sequence Send to blast
MDSWSYGTSV FLPNEISLPP SDSFPENPRS MSLGLSNEFD KDDVNGFSAL SSSLLDDDEN 60 LSSSSSNLSR LDFKLRSFMD YGNYDGRDFT LAAKKPRASS SPLCQVYGCN MDLSSSKDYH 120 KRHRVCETHS KSSMVIVNGI EQRFCQQCSR FHFLSEFDDG KRSCRRRLAG HNERRRKPSF 180 YFLPGKQQKN RHKLVPQGNK FPGSFLYRVM DEQDHHRASR LVSFKDEPTC GAHSHLSAHS 240 QQHVSETPNK IFSITQPNKT FSHSTISYHH MQPPLRTDLG KTKTSTSSST VDLMQLSLHL 300 RRIEQQQRSF TGDVKQEYNN ELYFP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	6e-31	98	177	5	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00012.1_g00032.1

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	AC189298	1e-121	AC189298.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB028I01, complete sequence.
GenBank	AC189458	1e-121	AC189458.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB073F16, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018454871.1	0.0	PREDICTED: squamosa promoter-binding-like protein 6
Refseq	XP_018454872.1	0.0	PREDICTED: squamosa promoter-binding-like protein 6
Swissprot	Q94JW8	1e-125	SPL6_ARATH; Squamosa promoter-binding-like protein 6
TrEMBL	A0A078JQD3	1e-130	A0A078JQD3_BRANA; BnaCnng61400D protein
STRING	Bo6g108620.1	1e-129	(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-106	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]