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_009139002.1

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: 309aa MW: 34533.6 Da PI: 9.4316

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009139002.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	126.2	1.3e-39	59	136	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+l efD ekrsCrrrLa hnerrrk+qa XP_009139002.1 59 RCQVEGCKMDLSNAKTYYSRHKVCGIHSKSSKVTVSGLHQRFCQQCSRFHQLCEFDLEKRSCRRRLACHNERRRKPQA 136 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	2.7E-30	54	121	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	30.573	57	134	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	2.75E-36	58	137	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	7.7E-29	60	133	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: 309 aa Download sequence Send to blast
MELLMGSGQN RTETVGSSSR ESSSLSGGLR IGQKIYFEDG SGSGKDRANK YRKTTTGARC 60 QVEGCKMDLS NAKTYYSRHK VCGIHSKSSK VTVSGLHQRF CQQCSRFHQL CEFDLEKRSC 120 RRRLACHNER RRKPQATRAT LFTSGLSRIS PSLYGSVLGD PSWDRSVFSQ GSSRFSITYP 180 EMVKNSSTDS SCVLSLLSNS NTTQQQQQQL QTSTNAYLMD AERVTIMAKS PPVSVHNQYS 240 NQTWEFMSGE KSNSPCVSSP ALRLSQISEP DDDLQFLMSN GATMGGFELN LQQQVLRQYS 300 STQHFTWPL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	1e-28	60	133	11	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Weak increase of expression during floral induction. {ECO:0000269\|PubMed:14573523}.

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	XP_009139002.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by microRNAs 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	AC189469	0.0	AC189469.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB078G17, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009139002.1	0.0	PREDICTED: squamosa promoter-binding-like protein 15 isoform X1
Swissprot	Q9M2Q6	1e-117	SPL15_ARATH; Squamosa promoter-binding-like protein 15
TrEMBL	A0A3P6BWF2	0.0	A0A3P6BWF2_BRACM; Uncharacterized protein
STRING	Bra014599.1-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-105	squamosa promoter binding protein-like 15

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] Morea EG, et al. Functional and evolutionary analyses of the miR156 and miR529 families in land plants. BMC Plant Biol., 2016. 16: p. 40 [PMID:26841873] Hyun Y, et al. Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem. Dev. Cell, 2016. 37(3): p. 254-66 [PMID:27134142] 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]