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_013631127.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 608aa MW: 66607.5 Da PI: 6.998

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013631127.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	76	4.3e-24	160	261	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+lt sd++++g +++p++ ae++ +++ s++l +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + +++ XP_013631127.1 160 FCKTLTASDTSTHGGFSVPRRAAEDCfppldYTQPRPSQELLARDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGDDG 252 99**************************9444566789********************************************..34899 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 +l+++v+r+ XP_013631127.1 253 KLRLGVRRA 261 99**997 PP
2	Auxin_resp	114.1	1.3e-37	286	367	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +aha+st+s+F+++YnP+as+s+F++++ k++k+++ ++++GmRfk ++e+ed+serr G+++g++dldp+rWp+SkWr+L XP_013631127.1 286 VAHAISTNSAFNIYYNPKASWSNFIIPAPKFLKTVDYPFCIGMRFKARVESEDASERRSPGIITGINDLDPIRWPGSKWRCL 367 79*******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.97E-42	151	277	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.0E-38	155	269	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.00E-21	158	260	No hit	No description
SMART	SM01019	2.2E-22	160	262	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.8E-22	160	261	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.296	160	262	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.3E-31	286	367	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: 608 aa Download sequence Send to blast
MGGLIDLNVT DEQEEETTPS SGSGSLSPCD SSSSASAFGV SGSSSRSSSS GVCLELWHAC 60 AGPLISLPKR GSLVLYFPQG HLEQAPDFSA AIYGLPPHVF CRILDVKLHA ETATDEVYAQ 120 VSLLPESEDI ERKVREGVID VDGGEEDYEV LKRTNTPHMF CKTLTASDTS THGGFSVPRR 180 AAEDCFPPLD YTQPRPSQEL LARDLHGLEW RFRHIYRGQP RRHLLTTGWS AFVNKKKLVS 240 GDAVLFLRGD DGKLRLGVRR ASQIEGASAF SSHYNQNMNH NNFAEVAHAI STNSAFNIYY 300 NPKASWSNFI IPAPKFLKTV DYPFCIGMRF KARVESEDAS ERRSPGIITG INDLDPIRWP 360 GSKWRCLLVR WDDIEANGHH QQRISPWEIE PSGSISSSGS FVTTGPKRSR IGFSSGKPDI 420 PVSGSGATDF EESLRFQRVL QGQEIFHGFI NTSSDGGAGA RRGRFKGTEF GDSYGFHKVL 480 QGQETVPAYP MMTDQRHQGM SQRNIWCGPF QNFSTRILPP SSVHVSSPLP SSGTNVRLED 540 HHGGSGRCRL FGFPLRDETT AVGSGMVVGP CVEGQNGSSI RGGVSAVQGN HHGRDIYGMR 600 DMLLDIAL

Sequence ? help Back to Top

Protein Sequence Length: 608 aa Download sequence Send to blast

MGGLIDLNVT DEQEEETTPS SGSGSLSPCD SSSSASAFGV SGSSSRSSSS GVCLELWHAC  60
AGPLISLPKR GSLVLYFPQG HLEQAPDFSA AIYGLPPHVF CRILDVKLHA ETATDEVYAQ  120
VSLLPESEDI ERKVREGVID VDGGEEDYEV LKRTNTPHMF CKTLTASDTS THGGFSVPRR  180
AAEDCFPPLD YTQPRPSQEL LARDLHGLEW RFRHIYRGQP RRHLLTTGWS AFVNKKKLVS  240
GDAVLFLRGD DGKLRLGVRR ASQIEGASAF SSHYNQNMNH NNFAEVAHAI STNSAFNIYY  300
NPKASWSNFI IPAPKFLKTV DYPFCIGMRF KARVESEDAS ERRSPGIITG INDLDPIRWP  360
GSKWRCLLVR WDDIEANGHH QQRISPWEIE PSGSISSSGS FVTTGPKRSR IGFSSGKPDI  420
PVSGSGATDF EESLRFQRVL QGQEIFHGFI NTSSDGGAGA RRGRFKGTEF GDSYGFHKVL  480
QGQETVPAYP MMTDQRHQGM SQRNIWCGPF QNFSTRILPP SSVHVSSPLP SSGTNVRLED  540
HHGGSGRCRL FGFPLRDETT AVGSGMVVGP CVEGQNGSSI RGGVSAVQGN HHGRDIYGMR  600
DMLLDIAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-107	49	398	16	361	Auxin response factor 1
4ldw_A	1e-107	49	398	16	361	Auxin response factor 1
4ldw_B	1e-107	49	398	16	361	Auxin response factor 1
4ldy_A	1e-107	49	398	16	361	Auxin response factor 1
4ldy_B	1e-107	49	398	16	361	Auxin response factor 1
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected during gynoecium development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078, ECO:0000269\|PubMed:9409666}.

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

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013631127.1

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	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_013631127.1	0.0	PREDICTED: auxin response factor 3-like
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]