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_010540471.1

Organism

Tarenaya hassleriana

Taxonomic ID

28532

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Cleomaceae; Tarenaya

Family

ARF

Protein Properties

Length: 625aa MW: 67896.5 Da PI: 6.963

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_010540471.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.5	1.5e-24	165	266	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_010540471.1 165 FCKTLTASDTSTHGGFSVPRRAAEDCfppldYSQPRPSQELVARDLHGLEWRFRHIYRGQPRRHLLTTGWSGFVNKKKLVSGDAVLFL--RGDDG 257 99**************************955566788*********************************************..34899 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 +l+++++r+ XP_010540471.1 258 KLRLGIRRA 266 99**996 PP
2	Auxin_resp	118.6	5e-39	292	372	2	82
Auxin_resp 2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 aha+s +svF+++YnP++s+s+F++++++++k+++ ++++GmRfkm++e+eds err++G+++g+ d+dp+rWp+SkWr+L XP_010540471.1 292 AHAISAQSVFNIYYNPKSSWSDFIIPAHRFLKSVDYPFCIGMRFKMRVESEDSTERRCTGIITGIGDMDPLRWPGSKWRCL 372 89******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.01E-42	157	269	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.2E-39	159	268	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.45E-22	163	265	No hit	No description
Pfam	PF02362	7.1E-23	165	266	IPR003340	B3 DNA binding domain
SMART	SM01019	1.7E-23	165	267	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.38	165	267	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.0E-33	292	372	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:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 625 aa Download sequence Send to blast
MGGLIDLNVT DTEEDETPSS ASGSLSPSSS SASASASVSA FGGSYPSSSS SGVCLELWHA 60 CAGPLISLPK RGSLVLYLPQ GHLEQSPDFS AAVYGLASHV FCRVLDVKLH AEAATDDVYA 120 QVSLLPESED IEQRLREGSI EIDGGGGGGE DDYEVLRRSS TPHMFCKTLT ASDTSTHGGF 180 SVPRRAAEDC FPPLDYSQPR PSQELVARDL HGLEWRFRHI YRGQPRRHLL TTGWSGFVNK 240 KKLVSGDAVL FLRGDDGKLR LGIRRAAQMK GASLLSTQFA QNLNQSNFAI IAHAISAQSV 300 FNIYYNPKSS WSDFIIPAHR FLKSVDYPFC IGMRFKMRVE SEDSTERRCT GIITGIGDMD 360 PLRWPGSKWR CLLVKWDDTE ANGHQRRVSP WEIEPSGSIS SSGSFLTIGP KRSRIGLPPL 420 KPDIPFPEGI QATNFGESIR FQRVLQGQEI FPGFDCMALT GQTRRGFPRK GPDFRESFMF 480 HKVLPGQETV TSSYPSGRGG GGCGQVVPMW SEPYIHAMSP TSSMAMSQLP NHETAVSVSD 540 VSHKNCTDGR SGTGGTCESS CRLFGFSLTE ETRGGVEKGS NVIMECGEGQ IGTAMKGGGV 600 VLPSSHSKGR RDIYAVRDML LDIAL

Sequence ? help Back to Top

Protein Sequence Length: 625 aa Download sequence Send to blast

MGGLIDLNVT DTEEDETPSS ASGSLSPSSS SASASASVSA FGGSYPSSSS SGVCLELWHA  60
CAGPLISLPK RGSLVLYLPQ GHLEQSPDFS AAVYGLASHV FCRVLDVKLH AEAATDDVYA  120
QVSLLPESED IEQRLREGSI EIDGGGGGGE DDYEVLRRSS TPHMFCKTLT ASDTSTHGGF  180
SVPRRAAEDC FPPLDYSQPR PSQELVARDL HGLEWRFRHI YRGQPRRHLL TTGWSGFVNK  240
KKLVSGDAVL FLRGDDGKLR LGIRRAAQMK GASLLSTQFA QNLNQSNFAI IAHAISAQSV  300
FNIYYNPKSS WSDFIIPAHR FLKSVDYPFC IGMRFKMRVE SEDSTERRCT GIITGIGDMD  360
PLRWPGSKWR CLLVKWDDTE ANGHQRRVSP WEIEPSGSIS SSGSFLTIGP KRSRIGLPPL  420
KPDIPFPEGI QATNFGESIR FQRVLQGQEI FPGFDCMALT GQTRRGFPRK GPDFRESFMF  480
HKVLPGQETV TSSYPSGRGG GGCGQVVPMW SEPYIHAMSP TSSMAMSQLP NHETAVSVSD  540
VSHKNCTDGR SGTGGTCESS CRLFGFSLTE ETRGGVEKGS NVIMECGEGQ IGTAMKGGGV  600
VLPSSHSKGR RDIYAVRDML LDIAL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-110	50	402	16	361	Auxin response factor 1
4ldy_B	1e-110	50	402	16	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_010540471.1

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	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010540471.1	0.0	PREDICTED: auxin response factor 3-like
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	R0G0L1	0.0	R0G0L1_9BRAS; Auxin response factor
STRING	XP_010540471.1	0.0	(Tarenaya hassleriana)

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]