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

RrC5429_p1

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

ARF

Protein Properties

Length: 426aa MW: 47365.1 Da PI: 9.8061

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC5429_p1	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	56.9	3.9e-18	6	72	31	99
.--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 31 eesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 + s++l +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + ++++l+++v+r+ RrC5429_p1 6 RPSQELLARDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGDDGKLRLGVRRA 72 45679999*******************************************..3489999**997 PP
2	Auxin_resp	113.4	2.2e-37	98	179	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +aha+st+++F+++YnP+as+s+F++++ k++k+++ ++++GmRfk ++e+ed+serr G+++g+++ldp+rWp+SkWr+L RrC5429_p1 98 VAHAISTNTAFNIYYNPKASWSNFIIPAPKFLKTVDYPFCIGMRFKARVESEDASERRSPGIITGINELDPIRWPGSKWRCL 179 79*******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50863	12.774	1	73	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	2.35E-20	1	77	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.7E-22	2	80	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	0.0033	2	73	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-15	5	72	IPR003340	B3 DNA binding domain
CDD	cd10017	7.85E-13	5	71	No hit	No description
Pfam	PF06507	2.8E-31	98	179	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009725	Biological Process	response to hormone
GO:0010050	Biological Process	vegetative phase change
GO:0010158	Biological Process	abaxial cell fate specification
GO:0010582	Biological Process	floral meristem determinacy
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 426 aa Download sequence Send to blast
DYSQPRPSQE LLARDLHGLE WRFRHIYRGQ PRRHLLTTGW SAFVNKKKLV SGDAVLFLRG 60 DDGKLRLGVR RASQIEGASS AFSSQYNQNM NHNNFAEVAH AISTNTAFNI YYNPKASWSN 120 FIIPAPKFLK TVDYPFCIGM RFKARVESED ASERRSPGII TGINELDPIR WPGSKWRCLL 180 VRWDDIEANG HHQQRLSPWE IEPSGSISSS GSFITTGPKR SRIGSDIPVS QGIRSTDFEE 240 SLRFQMVLQG QEIFHGGFIN TSSDGGAGAR RGKFKGTEFG DSYGGFHKVL QGQETVPAYP 300 MMTDHHHRQH QGMMMMSQRN IWCGPFQNFS TRILPPSSVH VSSSSSSPSS GGPNARLEEQ 360 HHGGSGRCRL FGFPLRDETT AVVGPCVEGQ NGSSMRGGGG ASAVQSNHHG RRDIYGMRDM 420 LLDIAL

Sequence ? help Back to Top

Protein Sequence Length: 426 aa Download sequence Send to blast

DYSQPRPSQE LLARDLHGLE WRFRHIYRGQ PRRHLLTTGW SAFVNKKKLV SGDAVLFLRG  60
DDGKLRLGVR RASQIEGASS AFSSQYNQNM NHNNFAEVAH AISTNTAFNI YYNPKASWSN  120
FIIPAPKFLK TVDYPFCIGM RFKARVESED ASERRSPGII TGINELDPIR WPGSKWRCLL  180
VRWDDIEANG HHQQRLSPWE IEPSGSISSS GSFITTGPKR SRIGSDIPVS QGIRSTDFEE  240
SLRFQMVLQG QEIFHGGFIN TSSDGGAGAR RGKFKGTEFG DSYGGFHKVL QGQETVPAYP  300
MMTDHHHRQH QGMMMMSQRN IWCGPFQNFS TRILPPSSVH VSSSSSSPSS GGPNARLEEQ  360
HHGGSGRCRL FGFPLRDETT AVVGPCVEGQ NGSSMRGGGG ASAVQSNHHG RRDIYGMRDM  420
LLDIAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-58	1	210	154	361	Auxin response factor 1
4ldw_A	1e-58	1	210	154	361	Auxin response factor 1
4ldw_B	1e-58	1	210	154	361	Auxin response factor 1
4ldy_A	1e-58	1	210	154	361	Auxin response factor 1
4ldy_B	1e-58	1	210	154	361	Auxin response factor 1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00021	PBM	Transfer from AT2G33860	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

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	JN979462	0.0	JN979462.1 Brassica rapa subsp. pekinensis auxin response factor 3-1 (ARF3-1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018441820.1	0.0	PREDICTED: auxin response factor 3-like isoform X2
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A0D3BSB5	0.0	A0A0D3BSB5_BRAOL; Auxin response factor
TrEMBL	A0A3P6BKJ9	0.0	A0A3P6BKJ9_BRAOL; Auxin response factor
STRING	Bo4g041340.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4924	28	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	0.0	ARF family protein

Publications ? help Back to Top
Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] Wójcikowska B,Gaj MD Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep., 2017. 36(6): p. 843-858 [PMID:28255787] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]