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_19765.1_g00001.1

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: 94aa MW: 10832.5 Da PI: 11.2082

Description

SBP family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_19765.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	SBP	126.1	1.4e-39	1	70	9	78
---TT--HHHHHTT--HHHHT-S-EEETTEEEEE-TTTSSEEETTT--SS--S-STTTT-------S--- CS SBP 9 adlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 +dl++ak y++rh+vC +hsk+p+v+v+g+eqrfCqqCsrfh+l+efD ekrsCrrrLa+hnerrrk+q+ Rsa1.0_19765.1_g00001.1 1 MDLTNAKGYYSRHRVCGMHSKTPKVIVAGIEQRFCQQCSRFHQLQEFDLEKRSCRRRLAGHNERRRKPQP 70 59*****************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.1100.10	8.1E-28	1	55	IPR004333	Transcription factor, SBP-box
PROSITE profile	PS51141	28.103	1	68	IPR004333	Transcription factor, SBP-box
SuperFamily	SSF103612	7.59E-36	1	72	IPR004333	Transcription factor, SBP-box
Pfam	PF03110	5.2E-29	2	67	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: 94 aa Download sequence Send to blast
MDLTNAKGYY SRHRVCGMHS KTPKVIVAGI EQRFCQQCSR FHQLQEFDLE KRSCRRRLAG 60 HNERRRKPQP ASLSVLSSRF GRIAPSLYGS ILLA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1ul4_A	6e-28	2	67	19	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_19765.1_g00001.1

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	AJ011638	1e-106	AJ011638.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 9.
GenBank	AJ011639	1e-106	AJ011639.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 9.
GenBank	AJ628864	1e-106	AJ628864.1 Arabidopsis thaliana mRNA for putative squamosa-promoter binding protein (At2g42200 gene).
GenBank	AY046007	1e-106	AY046007.1 Arabidopsis thaliana putative squamosa-promoter binding protein (At2g42200) mRNA, complete cds.
GenBank	AY150378	1e-106	AY150378.1 Arabidopsis thaliana putative squamosa-promoter binding protein (At2g42200) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018478746.1	3e-59	PREDICTED: squamosa promoter-binding-like protein 9
Swissprot	Q700W2	2e-55	SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBL	R9THU2	7e-56	R9THU2_CARFL; SPL9 (Fragment)
STRING	scaffold_403069.1	4e-56	(Arabidopsis lyrata)
STRING	Bostr.25993s0559.1.p	5e-56	(Boechera stricta)

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	8e-58	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]