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

XP_009104082.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 323aa MW: 36057.2 Da PI: 9.3833

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009104082.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	127.4	5.4e-40	58	135	1	78
--SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +CqvegC++dls+ak+y++rhkvC +hsk+++v+vsgl+qrfCqqCsrfh+lsefD ekrsCrrrLa hnerrrk+qa XP_009104082.1 58 RCQVEGCRMDLSNAKTYYSRHKVCCIHSKSSKVIVSGLHQRFCQQCSRFHQLSEFDLEKRSCRRRLACHNERRRKPQA 135 6**************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.5E-30	55	120	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	31	56	133	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	3.53E-37	57	137	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	4.5E-29	59	132	IPR004333	Transcription factor, SBP-box

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0008361	Biological Process	regulation of cell size
GO:0010228	Biological Process	vegetative to reproductive phase transition of meristem
GO:0042127	Biological Process	regulation of cell proliferation
GO:0048653	Biological Process	anther development
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 323 aa Download sequence Send to blast
MELLTGSGQN QPESAGSSST TLSGGLRFGQ KIYFEDGSGA GSSKNRVKST SRKLMTARCQ 60 VEGCRMDLSN AKTYYSRHKV CCIHSKSSKV IVSGLHQRFC QQCSRFHQLS EFDLEKRSCR 120 RRLACHNERR RKPQATTTLL TSHYSPSLYG NAIRSVLGDP TRWSTTRGSA PWQSHQLMNV 180 FSYGSSGFTN STDSSCALSL LSNYTNPNQQ EQQQLQTPTN TWRPSSIAAD RVTMAQTPPV 240 SVQNQYLNQT LEFMSGEKSN AQYTTPVLGL SQISEPVVDF QISNGATMGG FELSLHQQVL 300 RQYMEPDNTR AYDSSPQHFN WSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	6e-29	59	132	11	84	squamosa promoter binding protein-like 4
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Probable transcription factor required for the flowering response to vernalization in the shoot apical meristem (SAM) (PubMed:30679374). Defines the competence of shoot meristems to flower in response to vernalization in perennials (PubMed:30679374). {ECO:0000269\|PubMed:30679374}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00412	DAP	Transfer from AT3G57920	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_009104082.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced in the shoot apical meristem (SAM) during vernalization. {ECO:0000269\|PubMed:30679374}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC189445	0.0	AC189445.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB070L01, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009104082.1	0.0	PREDICTED: squamosa promoter-binding-like protein 15
Swissprot	S4WUL1	1e-160	SPL15_ARAAL; Squamosa promoter-binding protein-like 15
TrEMBL	A0A3P6B363	0.0	A0A3P6B363_BRACM; Uncharacterized protein
STRING	Bra003305.1-P	0.0	(Brassica rapa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2144	27	75

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G57920.1	1e-144	squamosa promoter binding protein-like 15

Publications ? help Back to Top
Willing EM, et al. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants, 2015. 1: p. 14023 [PMID:27246759] Hyun Y, et al. A regulatory circuit conferring varied flowering response to cold in annual and perennial plants. Science, 2019. 363(6425): p. 409-412 [PMID:30679374]