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_009142812.1

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: 369aa MW: 40060.1 Da PI: 8.733

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009142812.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	137.3	4.6e-43	73	149	2	78
-SSTT-----TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 CqvegC +dl++ak y+ rh+vC +hsk+p+v+v+g+eqrfCqqCsrfh+l efD ekrsCrrrLa+hnerrrk+q+ XP_009142812.1 73 CQVEGCGMDLTNAKGYYTRHRVCGMHSKTPKVIVAGIEQRFCQQCSRFHQLPEFDLEKRSCRRRLAGHNERRRKPQP 149 **************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	1.3E-34	65	134	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	31.804	70	147	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	1.7E-40	71	151	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	1.8E-32	73	146	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: 369 aa Download sequence Send to blast
MDRGSNSGLG LGPGQTESGG SSTESSSLSG GLMFGQRIYF EDAGGGTGSS SSGGSNRRVR 60 GSGSGPSGQI PKCQVEGCGM DLTNAKGYYT RHRVCGMHSK TPKVIVAGIE QRFCQQCSRF 120 HQLPEFDLEK RSCRRRLAGH NERRRKPQPA SLSVLSSRYG RITPSLYGNG ETTMNGSFLG 180 SQEMGWNSAR TLDTRVMRRP PSWQINPMNV FSHGSVSGGG GGGISFSSPE IMDTKPESYK 240 GIGSVTNCAL SLLSNPHQPH DNNNSNNTWR TSSGFGPMTV TMAQPPPAPS QQHQYLNPPW 300 VFKDDDNSCP NDMSPVLNLG RFTETEISGG TTLGEFELSD HHHQNRRQYM ESENTRAYGS 360 SSHHNNWSL

Sequence ? help Back to Top

Protein Sequence Length: 369 aa Download sequence Send to blast

MDRGSNSGLG LGPGQTESGG SSTESSSLSG GLMFGQRIYF EDAGGGTGSS SSGGSNRRVR  60
GSGSGPSGQI PKCQVEGCGM DLTNAKGYYT RHRVCGMHSK TPKVIVAGIE QRFCQQCSRF  120
HQLPEFDLEK RSCRRRLAGH NERRRKPQPA SLSVLSSRYG RITPSLYGNG ETTMNGSFLG  180
SQEMGWNSAR TLDTRVMRRP PSWQINPMNV FSHGSVSGGG GGGISFSSPE IMDTKPESYK  240
GIGSVTNCAL SLLSNPHQPH DNNNSNNTWR TSSGFGPMTV TMAQPPPAPS QQHQYLNPPW  300
VFKDDDNSCP NDMSPVLNLG RFTETEISGG TTLGEFELSD HHHQNRRQYM ESENTRAYGS  360
SSHHNNWSL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	9e-29	63	146	1	84	squamosa promoter binding protein-like 4
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed constitutively during plant development, with a strong increase during flower development. {ECO:0000269\|PubMed:10524240, 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_009142812.1

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	AC155337	0.0	AC155337.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH117N09, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009142812.1	0.0	PREDICTED: squamosa promoter-binding-like protein 9
Swissprot	Q700W2	0.0	SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBL	M4CKD9	0.0	M4CKD9_BRARP; Uncharacterized protein
STRING	Bra004674.1-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
AT2G42200.1	1e-167	squamosa promoter binding protein-like 9

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] Stief A, et al. Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors. Plant Cell, 2014. 26(4): p. 1792-1807 [PMID:24769482] Yu ZX, et al. Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors. Mol Plant, 2015. [PMID:25355059] 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] 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] Mahmood K,Xu Z,El-Kereamy A,Casaretto JA,Rothstein SJ The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin Biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses. Front Plant Sci, 2016. 7: p. 1548 [PMID:27790239] Mao YB, et al. Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance. Nat Commun, 2017. 8: p. 13925 [PMID:28067238] Nguyen ST,Greaves T,McCurdy DW Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module. Plant Physiol., 2017. 173(3): p. 1676-1691 [PMID:28082719] Duan HC, et al. ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition. Plant Cell, 2017. 29(12): p. 2995-3011 [PMID:29180595] 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] He J, et al. Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana. PLoS Genet., 2018. 14(4): p. e1007337 [PMID:29672610]