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

Medtr4g088210.1

Common Name

MTR_4g088210

Organism

Medicago truncatula

Taxonomic ID

3880

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago

Family

ARF

Protein Properties

Length: 713aa MW: 79088.6 Da PI: 6.9633

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Medtr4g088210.1	genome	Mt	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79.9	2.6e-25	148	249	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g++W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + + Medtr4g088210.1 148 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGQEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGE 238 99**************************963.3445679********************************************..449 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 ++el+++++r+ Medtr4g088210.1 239 DGELRLGIRRA 249 999***996 PP
2	Auxin_resp	110.9	1.3e-36	275	355	2	82
Auxin_resp 2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 ++a+st+++F++ YnPr ++seF+++++k++k+l+ ++svGmRf+m+fe+ed++err++G+++ ++d+dpvrWp+SkW++L Medtr4g088210.1 275 VNALSTRCAFSIHYNPRIGSSEFIIPIHKFLKSLDYSYSVGMRFRMRFESEDAAERRFTGLIIRITDVDPVRWPGSKWKCL 355 6899****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	5.89E-43	140	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.5E-41	142	251	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.47E-23	146	248	No hit	No description
PROSITE profile	PS50863	13.747	148	250	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.8E-23	148	249	IPR003340	B3 DNA binding domain
SMART	SM01019	7.8E-24	148	250	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.9E-31	275	355	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:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 713 aa Download sequence Send to blast
MMGLIDLNTT EEDETPSSGS SSSTSIGSVG AGSSVCLELW HACAGPMISL PKKGSVVVYF 60 PQGHLEHLHD FPLSFSDNIP SHVFCRVVDV KLHAEEGNDE VYCQVLLVPE SEQVQQKLRE 120 GVIDGDGDGD GEGEDTDAVM KSTTPHMFCK TLTASDTSTH GGFSVPRRAA EDCFPPLDYS 180 QQRPSQELVA KDLHGQEWKF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD AVLFLRGEDG 240 ELRLGIRRAA QLKSCSNFSS ISGQQLNLGS LRDIVNALST RCAFSIHYNP RIGSSEFIIP 300 IHKFLKSLDY SYSVGMRFRM RFESEDAAER RFTGLIIRIT DVDPVRWPGS KWKCLVVRWD 360 DMEASRLNRV SPWEIEPSGS SSTTNSLMAT SLKRTKTGLP SSKLEFPVPS RIGTSDFGES 420 LRFQKVLQGQ EILGVDTTFN SINAHSHHQL SELRRCYPGS TYPGIASTGN NIRIPQMNSD 480 VSCNGFGESF RFQKVLQGQE ILPSQPYGQA FSVDEACRNG RFGLFDGHHQ VPRSTNGWSS 540 QTSNNSHFHP SVLMYQQASN MDYNSKINPV MEDNVLQRGS YYASEMKDGT FASTPTNKPI 600 FRGLAHEDTN SFGTHSRDLV TLQRSGQELV STCKNSCRVF GFSLTEGAPI ANKDAEPSAV 660 TCQINPGPPS FTRHIEDDFN PRHSLRSKAV ESYCTKVSNI HPVRDMIIDR VF*

Sequence ? help Back to Top

Protein Sequence Length: 713 aa Download sequence Send to blast

MMGLIDLNTT EEDETPSSGS SSSTSIGSVG AGSSVCLELW HACAGPMISL PKKGSVVVYF  60
PQGHLEHLHD FPLSFSDNIP SHVFCRVVDV KLHAEEGNDE VYCQVLLVPE SEQVQQKLRE  120
GVIDGDGDGD GEGEDTDAVM KSTTPHMFCK TLTASDTSTH GGFSVPRRAA EDCFPPLDYS  180
QQRPSQELVA KDLHGQEWKF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD AVLFLRGEDG  240
ELRLGIRRAA QLKSCSNFSS ISGQQLNLGS LRDIVNALST RCAFSIHYNP RIGSSEFIIP  300
IHKFLKSLDY SYSVGMRFRM RFESEDAAER RFTGLIIRIT DVDPVRWPGS KWKCLVVRWD  360
DMEASRLNRV SPWEIEPSGS SSTTNSLMAT SLKRTKTGLP SSKLEFPVPS RIGTSDFGES  420
LRFQKVLQGQ EILGVDTTFN SINAHSHHQL SELRRCYPGS TYPGIASTGN NIRIPQMNSD  480
VSCNGFGESF RFQKVLQGQE ILPSQPYGQA FSVDEACRNG RFGLFDGHHQ VPRSTNGWSS  540
QTSNNSHFHP SVLMYQQASN MDYNSKINPV MEDNVLQRGS YYASEMKDGT FASTPTNKPI  600
FRGLAHEDTN SFGTHSRDLV TLQRSGQELV STCKNSCRVF GFSLTEGAPI ANKDAEPSAV  660
TCQINPGPPS FTRHIEDDFN PRHSLRSKAV ESYCTKVSNI HPVRDMIIDR VF*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-113	34	384	18	361	Auxin response factor 1
4ldw_A	1e-113	34	384	18	361	Auxin response factor 1
4ldw_B	1e-113	34	384	18	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Medtr4g088210.1

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_013456935.1	0.0	auxin response factor 3 isoform X1
Refseq	XP_024638577.1	0.0	auxin response factor 3 isoform X1
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A072UNL3	0.0	A0A072UNL3_MEDTR; Auxin response factor
STRING	XP_004505103.1	0.0	(Cicer arietinum)

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	Medtr4g088210.1
Entrez Gene	25493074

Publications ? help Back to Top
Young ND, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 2011. 480(7378): p. 520-4 [PMID:22089132] 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]