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

maker-scaffold06891-augustus-gene-0.11-mRNA-1

Organism

Castanea mollissima

Taxonomic ID

60419

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Castanea

Family

ARF

Protein Properties

Length: 915aa MW: 100914 Da PI: 4.8303

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
maker-scaffold06891-augustus-gene-0.11-mRNA-1	genome	THGP	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	30.7	5.6e-10	152	220	1	60
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE......E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliy....r 53 f+k+lt sd++++g +++p++ ae+ ++++ + ++l+++d++ ++W++++iy r maker-scaffold06891-augustus-gene-0.11-mRNA-1 152 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytMQPP-T-QELVVRDLHDNTWTFRHIYrgvrR 213 99*******************999*954444.4.38***************66655 PP EETTEEE CS B3 54 kksgryv 60 ++++++ maker-scaffold06891-augustus-gene-0.11-mRNA-1 214 ANRQQTT 220 5555555 PP
2	Auxin_resp	112.9	3e-37	239	322	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtv 63 aahaa+++s+F+++YnPra++seFv+++++++k++ +++svGmRf m+fete+s +rr++Gt+ maker-scaffold06891-augustus-gene-0.11-mRNA-1 239 AAHAAANRSPFTIFYNPRACPSEFVIPLSRFRKSVFgTQLSVGMRFGMMFETEESGKRRYMGTI 302 79******************************988*********************** PP Auxin_resp 64 vgvsdldpvrWpnSkWrsLk 83 vg+sdldp+rWp+SkWr+L+ maker-scaffold06891-augustus-gene-0.11-mRNA-1 303 VGISDLDPLRWPGSKWRNLQ 322 ****************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	8.24E-30	139	241	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.0E-19	146	215	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.10E-9	151	213	No hit	No description
Pfam	PF02362	1.2E-7	152	218	IPR003340	B3 DNA binding domain
SMART	SM01019	0.0089	152	255	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.2E-32	239	322	IPR010525	Auxin response factor
Pfam	PF02309	6.9E-9	801	888	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.774	801	885	IPR000270	PB1 domain
SuperFamily	SSF54277	3.73E-8	819	879	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:0009733	Biological Process	response to auxin
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: 915 aa Download sequence Send to blast
MGCVEEKVKA GGSGFMGGSG AHTTCLLEEM KLLKEMQDQS GARKTINSEL WHACAGPLVS 60 LPQLGSLVYY FPQGHSEQVA ASTKRTVTSQ IPNYPNLPSQ LMCQLQNVTL HADKDTDEIY 120 AQMSLQPVNT EKDIFPVPDF GLKPNKHPSE FFCKTLTASD TSTHGGFSVP RRAAEKLFPP 180 LDYTMQPPTQ ELVVRDLHDN TWTFRHIYRG VRRANRQQTT LPSSVLSADS MHIGVLAAAA 240 HAAANRSPFT IFYNPRACPS EFVIPLSRFR KSVFGTQLSV GMRFGMMFET EESGKRRYMG 300 TIVGISDLDP LRWPGSKWRN LQVEWDEPGC CDKQNRVSPW EVETPESLFI FPSLTSGLKR 360 PFHSGFLGTE TEWGNMVKRP LVRVPDNGNG DLPYPIPNIC SEQLIKMLLK PQHMNHPGNF 420 YPPAQQESAT KVDPLRDMKT MQQGTTNQKS HLICSEGTPP IQPQSCLDQP DAMNLNPSSK 480 AMPPGKFNSL AECENRTLAG INTEKPIIEP EISTDELSQL TSTGECNEEK LVACPVTQNL 540 VNQPTFINQN QEPLQSQTSS WPMQPQLESL IYHPQQLDVP QSDCSNPNGF LPSLDPDEWK 600 FYPSCQPLGG MFRSPGPLSM FGLQDSSALF PEAVNPALPP MGQEMWDHQL NNLRILSQAD 660 QLTSFSHQDS RNLSCISNSS GLRDLSDESY NQSGIYSCAN VDVNNGGSTA VDPSVSSTIL 720 DDLCTVKNTG FQNPSDCLVG NFSSSQDVQS QITSASLGDS QAFSRQELPD SSGGTSSSNV 780 DFDEGSLLQN SSWQQVVPLV RTYTKVQKKG SVGRSIDVTG FRNYDELCAA IECMFGLEGL 840 LNDPRGSGWK LVYVDYENDV LLVGDDPWEQ FVRCVRCIKI LSPSEVQKMS EEGMQLLNSA 900 AMQGTNGPMS EGGYA

Sequence ? help Back to Top

Protein Sequence Length: 915 aa Download sequence Send to blast

MGCVEEKVKA GGSGFMGGSG AHTTCLLEEM KLLKEMQDQS GARKTINSEL WHACAGPLVS  60
LPQLGSLVYY FPQGHSEQVA ASTKRTVTSQ IPNYPNLPSQ LMCQLQNVTL HADKDTDEIY  120
AQMSLQPVNT EKDIFPVPDF GLKPNKHPSE FFCKTLTASD TSTHGGFSVP RRAAEKLFPP  180
LDYTMQPPTQ ELVVRDLHDN TWTFRHIYRG VRRANRQQTT LPSSVLSADS MHIGVLAAAA  240
HAAANRSPFT IFYNPRACPS EFVIPLSRFR KSVFGTQLSV GMRFGMMFET EESGKRRYMG  300
TIVGISDLDP LRWPGSKWRN LQVEWDEPGC CDKQNRVSPW EVETPESLFI FPSLTSGLKR  360
PFHSGFLGTE TEWGNMVKRP LVRVPDNGNG DLPYPIPNIC SEQLIKMLLK PQHMNHPGNF  420
YPPAQQESAT KVDPLRDMKT MQQGTTNQKS HLICSEGTPP IQPQSCLDQP DAMNLNPSSK  480
AMPPGKFNSL AECENRTLAG INTEKPIIEP EISTDELSQL TSTGECNEEK LVACPVTQNL  540
VNQPTFINQN QEPLQSQTSS WPMQPQLESL IYHPQQLDVP QSDCSNPNGF LPSLDPDEWK  600
FYPSCQPLGG MFRSPGPLSM FGLQDSSALF PEAVNPALPP MGQEMWDHQL NNLRILSQAD  660
QLTSFSHQDS RNLSCISNSS GLRDLSDESY NQSGIYSCAN VDVNNGGSTA VDPSVSSTIL  720
DDLCTVKNTG FQNPSDCLVG NFSSSQDVQS QITSASLGDS QAFSRQELPD SSGGTSSSNV  780
DFDEGSLLQN SSWQQVVPLV RTYTKVQKKG SVGRSIDVTG FRNYDELCAA IECMFGLEGL  840
LNDPRGSGWK LVYVDYENDV LLVGDDPWEQ FVRCVRCIKI LSPSEVQKMS EEGMQLLNSA  900
AMQGTNGPMS EGGYA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	347	5	392	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	Download

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023900074.1	0.0	auxin response factor 5 isoform X1
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A2N9EDJ7	0.0	A0A2N9EDJ7_FAGSY; Auxin response factor
STRING	XP_008221297.1	0.0	(Prunus mume)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8991	32	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

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] 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]