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

MDP0000173151

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

ARF

Protein Properties

Length: 708aa MW: 76990.2 Da PI: 6.6598

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000173151	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	76.9	2.2e-24	145	246	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 f+k+lt sd++++g +++p++ ae++ + ++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + ++ MDP0000173151 145 FCKTLTASDTSTHGGFSVPRRAAEDCfppldytQ--QRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGDD 236 99**************************9743..345679********************************************..3489 PP E..EEEEE-S CS B3 90 felvvkvfrk 99 +el+++++r+ MDP0000173151 237 GELRLGIRRA 246 999**996 PP
2	Auxin_resp	113.4	2.2e-37	271	352	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+ k++F+v+YnPr+s+seF+++ +k++++l++ +++GmR+km+feted++err++G+++g+s+ldpvrWp+SkWr+L MDP0000173151 271 VVNAIFAKNAFNVYYNPRSSSSEFIIPSHKFLRSLDHCFCAGMRIKMRFETEDAAERRYTGLITGISELDPVRWPGSKWRCL 352 5789999**************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.9E-40	138	254	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.88E-42	140	252	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.34E-22	143	245	No hit	No description
SMART	SM01019	4.0E-23	145	247	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.366	145	247	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.0E-22	145	246	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.0E-33	272	352	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: 708 aa Download sequence Send to blast
MAGLIDLNSA TEDEETPSSG SPSSASSVSD ALGSSASVCM ELWHACAGPL ISLPKKGSVV 60 VYLPQGHLEQ VSDFPTSAYD LPPHLFCRVV DVKLHAETGT DDVFAXVSLV PESEEIEHRL 120 REGVTDADAE EDVEAMGTST TPHMFCKTLT ASDTSTHGGF SVPRRAAEDC FPPLDYTQQR 180 PSQELVAKDL HGLEWRFRHI YRGQPRRHLL TTGWSAFVNK KKLVSGDAVL FLRGDDGELR 240 LGIRRAAQFK SSATCPTLCS QQLNYSTITD VVNAIFAKNA FNVYYNPRSS SSEFIIPSHK 300 FLRSLDHCFC AGMRIKMRFE TEDAAERRYT GLITGISELD PVRWPGSKWR CLVVRWDDXD 360 TSKHGRVSPW EVERSGSVSS SHTLMTTGLK RSRIGLSATK PEXPXPSMSC NXGIGTSDFG 420 ESLRFQKVLQ GQEISGFDTP FSGLGGLNSH PSEARRVFHG SGGSGIAAGG NGLRQSLVDS 480 EIASKGIGFG ESFRFHKVLQ GQEIFPSSPY GRAPASNEAH EYGGPGLYDG FQVPGFRNGX 540 STMMQSNNTN VHSSAPSVQV SSPSSVLMFQ QAMNPVAEFN SVYNGHNQED HRVNRTPHVL 600 EHDGGRQTSS SFGERNFSRE DRGGTHSYNQ HGISPHPVIS QSTISGSQDS VSPIKGSCRL 660 FGFSLSEDKC VPDQEGNPNV GVQFHSKPPL MTSTVGITCT KVSNLFAA

Sequence ? help Back to Top

Protein Sequence Length: 708 aa Download sequence Send to blast

MAGLIDLNSA TEDEETPSSG SPSSASSVSD ALGSSASVCM ELWHACAGPL ISLPKKGSVV  60
VYLPQGHLEQ VSDFPTSAYD LPPHLFCRVV DVKLHAETGT DDVFAXVSLV PESEEIEHRL  120
REGVTDADAE EDVEAMGTST TPHMFCKTLT ASDTSTHGGF SVPRRAAEDC FPPLDYTQQR  180
PSQELVAKDL HGLEWRFRHI YRGQPRRHLL TTGWSAFVNK KKLVSGDAVL FLRGDDGELR  240
LGIRRAAQFK SSATCPTLCS QQLNYSTITD VVNAIFAKNA FNVYYNPRSS SSEFIIPSHK  300
FLRSLDHCFC AGMRIKMRFE TEDAAERRYT GLITGISELD PVRWPGSKWR CLVVRWDDXD  360
TSKHGRVSPW EVERSGSVSS SHTLMTTGLK RSRIGLSATK PEXPXPSMSC NXGIGTSDFG  420
ESLRFQKVLQ GQEISGFDTP FSGLGGLNSH PSEARRVFHG SGGSGIAAGG NGLRQSLVDS  480
EIASKGIGFG ESFRFHKVLQ GQEIFPSSPY GRAPASNEAH EYGGPGLYDG FQVPGFRNGX  540
STMMQSNNTN VHSSAPSVQV SSPSSVLMFQ QAMNPVAEFN SVYNGHNQED HRVNRTPHVL  600
EHDGGRQTSS SFGERNFSRE DRGGTHSYNQ HGISPHPVIS QSTISGSQDS VSPIKGSCRL  660
FGFSLSEDKC VPDQEGNPNV GVQFHSKPPL MTSTVGITCT KVSNLFAA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-110	18	381	7	361	Auxin response factor 1
4ldy_B	1e-110	18	381	7	361	Auxin response factor 1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.9257	0.0	leaf\| root\| stem

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

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	KP283470	0.0	KP283470.1 Prunus armeniaca auxin response factor 3 (ARF3) gene, complete cds.
GenBank	KP283471	0.0	KP283471.1 Prunus incisa isolate 462-2010A auxin response factor 3 (ARF3) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028959003.1	0.0	LOW QUALITY PROTEIN: auxin response factor 3-like
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A498K1C7	0.0	A0A498K1C7_MALDO; Auxin response factor
STRING	XP_008371422.1	0.0	(Malus domestica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4576	33	55

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

Link Out ? help Back to Top
Phytozome	MDP0000173151

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]