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

NNU_016552-RA

Organism

Nelumbo nucifera

Taxonomic ID

4432

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; stem eudicotyledons; Proteales; Nelumbonaceae; Nelumbo

Family

ARF

Protein Properties

Length: 950aa MW: 104859 Da PI: 5.6661

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_016552-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.6	5.9e-24	146	247	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+ ++++ + ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD v+F ++++ NNU_016552-RA 146 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytMQPP-T-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGAKRLRAGDAVLFI--RDEK 237 99*******************999*954444.4.38**********************************************..4567 PP E..EEEEE-S CS B3 90 felvvkvfrk 99 +l+++v+r+ NNU_016552-RA 238 SQLLLGVRRA 247 7789999997 PP
2	Auxin_resp	117.2	1.3e-38	272	355	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++ka++ ++vs+GmRf m+fete+s +rr++Gt++g+sdldp+rWp+SkWr+L+ NNU_016552-RA 272 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYQKAVYgTQVSIGMRFGMMFETEESGKRRYMGTIIGISDLDPLRWPGSKWRNLQ 355 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.45E-47	133	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.9E-41	139	260	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.68E-22	145	246	No hit	No description
SMART	SM01019	3.0E-24	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.8E-21	146	247	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.014	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.1E-33	272	355	IPR010525	Auxin response factor
PROSITE profile	PS51745	25.019	831	915	IPR000270	PB1 domain
Pfam	PF02309	4.1E-9	831	918	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.9E-8	849	910	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: 950 aa Download sequence Send to blast
MASVEEKIKP GGLINGTATL MEEMKILKEF QDQSGVKKTI NSELWHACAG PLVSLPQVGS 60 LVYYFPQGHS EQVAVSTKRT ITSHIPNYPS LPSQLMCQVH NVTLHADKDT DEIYAQMSLQ 120 PVNSEKDVFP IPDFGLKPSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYTMQ 180 PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG AKRLRAGDAV LFIRDEKSQL 240 LLGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA 300 KYQKAVYGTQ VSIGMRFGMM FETEESGKRR YMGTIIGISD LDPLRWPGSK WRNLQVEWDE 360 PGCVEKHNRV SLWEIETPES LFIFPSFPSG LKRPLHPGFV GAETEWGNLI KRPFTRVAGG 420 NDFPCPPIPS IGSESLMKML LKSQSVNHTG AFSSVIPPCV VKAAPVPEAE TLKQTLIQQK 480 PHVVPSENSL LQTRNPHQQC LHQTQIADRN FALQTRISEK EQSLDKFENQ LPPKIHTEEL 540 EVAPVVATDQ LSQLTASGKC SEDKFSGSAL NPQNLANQLL LLNQATLQLQ SGTLPHIDAP 600 PLDTNNLNNL LPYPGLLSSQ HLDADDWMLQ ASNSQSLAGI FKSPGPPLSG CDKQDTSVIF 660 PEAVNPILPP LGQEMWGTQL NYLRYLSQGD QLTTCTHQDM TALPSISNSC GLRDFSEESN 720 NQSELYNGFH FDVSNCGSTV MDPSVSSSVL EQFNTLKDAN FQNPSDCQVG NLSSSQDVQS 780 QITSASLADS HGYSLQELPD NSGGTSSSNV DFDEGSLMQK SSWQQVSAPL RTYTKIQKLG 840 SVGRSIDVTR FKNYEELRSA IACMFGLEGL LDDPKGSGWK LVYVDYENDV LLVGDDPWEE 900 FVSCVRCIRI LSPSEVQQMS EDGMQLFNNT TCQGTKNLSD GGHVWDGTTS

Sequence ? help Back to Top

Protein Sequence Length: 950 aa Download sequence Send to blast

MASVEEKIKP GGLINGTATL MEEMKILKEF QDQSGVKKTI NSELWHACAG PLVSLPQVGS  60
LVYYFPQGHS EQVAVSTKRT ITSHIPNYPS LPSQLMCQVH NVTLHADKDT DEIYAQMSLQ  120
PVNSEKDVFP IPDFGLKPSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYTMQ  180
PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG AKRLRAGDAV LFIRDEKSQL  240
LLGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA  300
KYQKAVYGTQ VSIGMRFGMM FETEESGKRR YMGTIIGISD LDPLRWPGSK WRNLQVEWDE  360
PGCVEKHNRV SLWEIETPES LFIFPSFPSG LKRPLHPGFV GAETEWGNLI KRPFTRVAGG  420
NDFPCPPIPS IGSESLMKML LKSQSVNHTG AFSSVIPPCV VKAAPVPEAE TLKQTLIQQK  480
PHVVPSENSL LQTRNPHQQC LHQTQIADRN FALQTRISEK EQSLDKFENQ LPPKIHTEEL  540
EVAPVVATDQ LSQLTASGKC SEDKFSGSAL NPQNLANQLL LLNQATLQLQ SGTLPHIDAP  600
PLDTNNLNNL LPYPGLLSSQ HLDADDWMLQ ASNSQSLAGI FKSPGPPLSG CDKQDTSVIF  660
PEAVNPILPP LGQEMWGTQL NYLRYLSQGD QLTTCTHQDM TALPSISNSC GLRDFSEESN  720
NQSELYNGFH FDVSNCGSTV MDPSVSSSVL EQFNTLKDAN FQNPSDCQVG NLSSSQDVQS  780
QITSASLADS HGYSLQELPD NSGGTSSSNV DFDEGSLMQK SSWQQVSAPL RTYTKIQKLG  840
SVGRSIDVTR FKNYEELRSA IACMFGLEGL LDDPKGSGWK LVYVDYENDV LLVGDDPWEE  900
FVSCVRCIRI LSPSEVQQMS EDGMQLFNNT TCQGTKNLSD GGHVWDGTTS

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}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010271412.1	0.0	PREDICTED: auxin response factor 5-like
Refseq	XP_010271413.1	0.0	PREDICTED: auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1U8B6A0	0.0	A0A1U8B6A0_NELNU; Auxin response factor
STRING	XP_010271412.1	0.0	(Nelumbo nucifera)

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]