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

Lsa005365

Organism

Lactuca sativa

Taxonomic ID

4236

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactucinae; Lactuca

Family

ARF

Protein Properties

Length: 838aa MW: 92549.3 Da PI: 4.9881

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-187a-Lactuca_sativa-35504	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	53.3	5.2e-17	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+k+ltpsd++++g +++p++ ae+ ++++++ ++l+ +d++ ++W++++iy + ++++ G + Fv a++Lk+gD v+F ++++ +l++ Lsa005365 146 FCKTLTPSDTSTHGGFSVPRRAAEKLfpqldfSMQPPT-QELIGRDLHDNTWTFRHIYPRAAKTTLTDYGVEMFVGAKRLKAGDAVLFI--RDEKSQLLL 242 99*******************999*9555554.48999**********9999999999*******************..456777899 PP EEE-S CS B3 95 kvfrk 99 +v+r+ Lsa005365 243 GVRRA 247 99997 PP
2	Auxin_resp	109.4	3.8e-36	272	355	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv+++ +++k++ +++svGmRf m+fete+s +rr++Gt+vg+sd+dp+rWp+SkW +L+ Lsa005365 272 AAHAAANRSPFTIFYNPRACPSEFVIPLVRYRKSVFgTQLSVGMRFGMMFETEESGKRRYMGTIVGISDVDPLRWPGSKWHNLQ 355 79******************************988******************************************997 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.05E-37	132	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	9.2E-33	140	260	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.61E-13	145	246	No hit	No description
PROSITE profile	PS50863	9.347	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.3E-15	146	247	IPR003340	B3 DNA binding domain
SMART	SM01019	1.3E-12	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.4E-31	272	355	IPR010525	Auxin response factor
Pfam	PF02309	5.4E-10	711	802	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.738	715	799	IPR000270	PB1 domain
SuperFamily	SSF54277	2.6E-9	728	794	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:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 838 aa Download sequence Send to blast
MAAIEEKLNS SGVNSGSHSL LEEMKLLKEM QDHSAIKKPI NSELWHACAG PLVTLPQVGS 60 LVYYFPQGHS EQVAVSTNRT ATSQVPNYPN LPSQLLCQVL NATLHADKDT DEIYAQMSLR 120 PVNSEKDVLP IPDFGIKPSR HPSEFFCKTL TPSDTSTHGG FSVPRRAAEK LFPQLDFSMQ 180 PPTQELIGRD LHDNTWTFRH IYPRAAKTTL TDYGVEMFVG AKRLKAGDAV LFIRDEKSQL 240 LLGVRRANRQ QTSLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLV 300 RYRKSVFGTQ LSVGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WHNLQVEWDE 360 PGCGDKQSRV SPWDIEAPES LFIFPSLTSS LKRPFNSAFL GAQTEWDNMV TRPFMRAPET 420 INGNFSNPSM SSLWSEQLVK MLMKPQTNHN TPPVIQDTFT TNRPQFHLIQ PNTTTTITAA 480 SPPQSTQNLS GDHQSDQKPP ITVTSDTIKP ESKPMSPFLN QLSPFDSSVL HGQQFDSPQI 540 DSSSLNGLFP YPDTNVLNPY QSLGSETWDP QPNNTSRSFF QQNTGPTNYG FKDLSDENQT 600 HNNVYNCINF EGSNGGSTVV DPSVSSTVLD EFCNLKDIEF QNPSNYLVSN NNFSSSQDVQ 660 SQITSASLVD SQAYSMQELP DNSGGASSSN GEFDDSGGLL QNNSWQQVAV PTRVRTYTKI 720 QKAGSVGRSI DVSSFKNYDE LCCEIEKMFG LEGLLNDSRG SGWKLVYVDF ENDVLLVGDD 780 PWEEFVGCVR CIRILSPSEV QQMGEEGMQL LNSNAALQAG INGGSGSDNG ARTWVGPT

Sequence ? help Back to Top

Protein Sequence Length: 838 aa Download sequence Send to blast

MAAIEEKLNS SGVNSGSHSL LEEMKLLKEM QDHSAIKKPI NSELWHACAG PLVTLPQVGS  60
LVYYFPQGHS EQVAVSTNRT ATSQVPNYPN LPSQLLCQVL NATLHADKDT DEIYAQMSLR  120
PVNSEKDVLP IPDFGIKPSR HPSEFFCKTL TPSDTSTHGG FSVPRRAAEK LFPQLDFSMQ  180
PPTQELIGRD LHDNTWTFRH IYPRAAKTTL TDYGVEMFVG AKRLKAGDAV LFIRDEKSQL  240
LLGVRRANRQ QTSLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLV  300
RYRKSVFGTQ LSVGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WHNLQVEWDE  360
PGCGDKQSRV SPWDIEAPES LFIFPSLTSS LKRPFNSAFL GAQTEWDNMV TRPFMRAPET  420
INGNFSNPSM SSLWSEQLVK MLMKPQTNHN TPPVIQDTFT TNRPQFHLIQ PNTTTTITAA  480
SPPQSTQNLS GDHQSDQKPP ITVTSDTIKP ESKPMSPFLN QLSPFDSSVL HGQQFDSPQI  540
DSSSLNGLFP YPDTNVLNPY QSLGSETWDP QPNNTSRSFF QQNTGPTNYG FKDLSDENQT  600
HNNVYNCINF EGSNGGSTVV DPSVSSTVLD EFCNLKDIEF QNPSNYLVSN NNFSSSQDVQ  660
SQITSASLVD SQAYSMQELP DNSGGASSSN GEFDDSGGLL QNNSWQQVAV PTRVRTYTKI  720
QKAGSVGRSI DVSSFKNYDE LCCEIEKMFG LEGLLNDSRG SGWKLVYVDF ENDVLLVGDD  780
PWEEFVGCVR CIRILSPSEV QQMGEEGMQL LNSNAALQAG INGGSGSDNG ARTWVGPT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	380	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023734807.1	0.0	auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A2J6KDB8	0.0	A0A2J6KDB8_LACSA; Auxin response factor
STRING	XP_009778804.1	0.0	(Nicotiana sylvestris)

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]