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

evm_27.model.AmTr_v1.0_scaffold00211.4

Common Name

AMTR_s00211p00025860

Organism

Amborella trichopoda

Taxonomic ID

13333

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella

Family

ARF

Protein Properties

Length: 725aa MW: 80176.3 Da PI: 4.9835

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00211.4	genome	TAGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	62.6	6.1e-20	45	145	1	98
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TT CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkG 64 f+k+lt sd++++g +++p++ ae+ ++++++ +++ +d++ + W++++iyr++++r++lt+G evm_27.model.AmTr_v1.0_scaffold00211.4 45 FCKTLTASDTSTHGGFSVPRRAAEKLfppldftMQPPAQ--EIVARDLHDNLWTFRHIYRGQPKRHLLTTG 113 99*******************999*96555544..8************************* PP HHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS B3 65 WkeFvkangLkegDfvvFkldgrsefelvvkvfr 98 W+ Fv a++Lk+ +v+F ++++ +l+++v+r evm_27.model.AmTr_v1.0_scaffold00211.4 114 WSLFVGAKRLKADVSVLFI--RDEKSHLCLGVRR 145 *****************..4577778999988 PP
2	Auxin_resp	105.3	6.9e-35	171	254	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdld 70 a++aa+ +s+F+v+YnPras+seFvv+++kv+ka++ ++ s+GmRf m+fete+s +rr++Gt++g+ d+d evm_27.model.AmTr_v1.0_scaffold00211.4 171 ASQAATYHSPFTVFYNPRASPSEFVVPLAKVHKAVYgRHTSIGMRFGMMFETEESGKRRYMGTITGICDID 241 6789999***************************8999*************************** PP Auxin_resp 71 pvrWpnSkWrsLk 83 ++WpnSkW +L+ evm_27.model.AmTr_v1.0_scaffold00211.4 242 AIQWPNSKWHNLQ 254 ********997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.66E-41	32	173	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.7E-36	37	158	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.25E-19	44	145	No hit	No description
SMART	SM01019	1.4E-19	45	147	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.8E-18	45	145	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.362	45	147	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-31	171	254	IPR010525	Auxin response factor
Pfam	PF02309	2.6E-9	607	698	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	22.654	610	694	IPR000270	PB1 domain
SuperFamily	SSF54277	5.17E-8	626	689	No hit	No description

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:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 725 aa Download sequence Send to blast
MDPQADKDTD EVYAQMTLQP VKSEMDLFSV PDFGQKQSKH PSEFFCKTLT ASDTSTHGGF 60 SVPRRAAEKL FPPLDFTMQP PAQEIVARDL HDNLWTFRHI YRGQPKRHLL TTGWSLFVGA 120 KRLKADVSVL FIRDEKSHLC LGVRREMRQQ TILSSSVLSV DSMHIGVLAA ASQAATYHSP 180 FTVFYNPRAS PSEFVVPLAK VHKAVYGRHT SIGMRFGMMF ETEESGKRRY MGTITGICDI 240 DAIQWPNSKW HNLQVEWDEP EAGDRQNRVS VWEIEIADCP FLLCPLTMSG LKRPYQADLI 300 SSAEETEGSS MVKRSSSWFR ETDISGLQNP VNLNMNIEHL MKMLRKPRSA PMAQLGSQEL 360 GNIEDLILHT PCFQSITGFL KSSGPQFGLN KPDASILSSL ISSDTSIHVP EIGNTVDKLQ 420 FPCNSSADFV DATQYIESLS QELFGLADLP NVKNACQTEQ NALESQQNEL ESQLSRRGLI 480 SLLVGTTIPS TVNSCGLGDF SEESNEQSET YSNIQFEGSN GSILIDSSIS SSGLEGFGTL 540 RAPSEGLLGG ISSSLDLQSQ VTSTSGVDNQ SLSILGMPVN SGATSSSNVE INENSFFPRN 600 SWRQVTPQMR TYTKVQKLGS VGRSIDVTQF KNYEELTFAI ACMFGLKGKL EDPRTSSWKL 660 VYVDYENDVL LVGDDPWEEF VACVKCIRIL SPSEVQQMSQ EGLQLLNNSA KLATGSGDHV 720 WDRP*

Sequence ? help Back to Top

Protein Sequence Length: 725 aa Download sequence Send to blast

MDPQADKDTD EVYAQMTLQP VKSEMDLFSV PDFGQKQSKH PSEFFCKTLT ASDTSTHGGF  60
SVPRRAAEKL FPPLDFTMQP PAQEIVARDL HDNLWTFRHI YRGQPKRHLL TTGWSLFVGA  120
KRLKADVSVL FIRDEKSHLC LGVRREMRQQ TILSSSVLSV DSMHIGVLAA ASQAATYHSP  180
FTVFYNPRAS PSEFVVPLAK VHKAVYGRHT SIGMRFGMMF ETEESGKRRY MGTITGICDI  240
DAIQWPNSKW HNLQVEWDEP EAGDRQNRVS VWEIEIADCP FLLCPLTMSG LKRPYQADLI  300
SSAEETEGSS MVKRSSSWFR ETDISGLQNP VNLNMNIEHL MKMLRKPRSA PMAQLGSQEL  360
GNIEDLILHT PCFQSITGFL KSSGPQFGLN KPDASILSSL ISSDTSIHVP EIGNTVDKLQ  420
FPCNSSADFV DATQYIESLS QELFGLADLP NVKNACQTEQ NALESQQNEL ESQLSRRGLI  480
SLLVGTTIPS TVNSCGLGDF SEESNEQSET YSNIQFEGSN GSILIDSSIS SSGLEGFGTL  540
RAPSEGLLGG ISSSLDLQSQ VTSTSGVDNQ SLSILGMPVN SGATSSSNVE INENSFFPRN  600
SWRQVTPQMR TYTKVQKLGS VGRSIDVTQF KNYEELTFAI ACMFGLKGKL EDPRTSSWKL  660
VYVDYENDVL LVGDDPWEEF VACVKCIRIL SPSEVQQMSQ EGLQLLNNSA KLATGSGDHV  720
WDRP*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-145	4	278	116	391	Auxin response factor 5
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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

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_006840655.2	0.0	auxin response factor 5 isoform X3
Swissprot	P93024	1e-147	ARFE_ARATH; Auxin response factor 5
TrEMBL	W1P5U2	0.0	W1P5U2_AMBTC; Auxin response factor
STRING	ERN02330	0.0	(Amborella trichopoda)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP8260	12	16

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	1e-149	ARF family protein

Link Out ? help Back to Top
Phytozome	evm_27.model.AmTr_v1.0_scaffold00211.4

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Amborella Genome Project The Amborella genome and the evolution of flowering plants. Science, 2013. 342(6165): p. 1241089 [PMID:24357323] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]