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_025907-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: 935aa MW: 102482 Da PI: 5.5702

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
NNU_025907-RA	genome	CAS	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.9	4.7e-24	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+lt sd++++g +++p++ ae+ ++++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD v+F ++++ NNU_025907-RA 146 FCKTLTASDTSTHGGFSVPRRAAEKLfppldySMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGAKRLRAGDAVLFI--RDEKS 238 99*******************999*9555554.49**********************************************..45677 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 +l+++v+r+ NNU_025907-RA 239 QLLLGVRRA 247 789999997 PP
2	Auxin_resp	104.8	1e-34	272	350	1	78
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSk 78 aahaa+++s+F+++YnPra++seFv++++k++ka++ ++vs+GmRf m+fete+s +rr++Gt++g+sdldp+rWp+Sk NNU_025907-RA 272 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYQKAVYgTQVSIGMRFGMMFETEESGKRRYMGTITGISDLDPLRWPGSK 350 79********************************9**************************************98 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.05E-47	133	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.3E-41	140	260	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.55E-22	145	246	No hit	No description
Pfam	PF02362	1.8E-21	146	247	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.042	146	248	IPR003340	B3 DNA binding domain
SMART	SM01019	2.5E-24	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.3E-29	272	350	IPR010525	Auxin response factor
PROSITE profile	PS51745	25.328	816	900	IPR000270	PB1 domain
SuperFamily	SSF54277	1.57E-8	833	895	No hit	No description
Pfam	PF02309	4.8E-8	860	903	IPR033389	AUX/IAA domain

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: 935 aa Download sequence Send to blast
MASVEENVKP GGLANGSSTL MDEMKILKEF QDLSGVRNTI HSELWHACAG PLVSLPQVGS 60 LVYYFPQGHS EQVAVSTKRT VTSHIPNYPC LPSQLMCQVH SVTLHADKET DEIYAQMSLQ 120 PANSEKDVFP IPDFGLKLSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYSMQ 180 PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG AKRLRAGDAV LFIRDEKSQL 240 LLGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA 300 KYQKAVYGTQ VSIGMRFGMM FETEESGKRR YMGTITGISD LDPLRWPGSK VSLWEIETPE 360 SLFVFPSLTS GLKRPLHPGF VGAETEWGNM IRRPFMRVAE GGNDLPWPPI PSAGSEPLIK 420 MLLKSQSVSP TGTFSSSIPP CLVKAAPVPE GETLYQTLVQ QKPNILPSEN SSLQTQNLHQ 480 HMDQTHAADG NLASQTHVSE KEKPSNKLED QLQPKTQPEE LDVAPIIAPD HLTQLTDKLI 540 GSALSPQNLA NQLLLLNQST LQLQSGSRVV KQHLEANTAL SQVNTTQLDA NNLNSILPHP 600 GLLSSQYLDA DDWVLHPFTS QSLASILKSP VPLSGCGKKD TSIVFPETVN PILTPLGQET 660 WGSQLNYPRY PSQADQLPTC TEQDSTALQS ISNPCGLRGI SEDSNSQSEI YNGLHFDASN 720 CGSTVIDPSV SSTVQEKFGT LRDSDFLNPS DCLFSNFSSS QDVQSQITSA SLADSHGYSL 780 QEFPDHSGGT SSSNVDIDEG SLLQKSSWQQ VSAPLRTYTK VQKLGSVGRS IDVTRFKNYE 840 ELRSAIACMF GLEGLLDDPK GSGWKLVYVD YENDVLLVGD DPWEEFVSCV RCIRILSPSE 900 VQQMSKDGIQ LLNSAAIQGT KTLSDDGCNI WDGMT

Sequence ? help Back to Top

Protein Sequence Length: 935 aa Download sequence Send to blast

MASVEENVKP GGLANGSSTL MDEMKILKEF QDLSGVRNTI HSELWHACAG PLVSLPQVGS  60
LVYYFPQGHS EQVAVSTKRT VTSHIPNYPC LPSQLMCQVH SVTLHADKET DEIYAQMSLQ  120
PANSEKDVFP IPDFGLKLSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYSMQ  180
PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG AKRLRAGDAV LFIRDEKSQL  240
LLGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA  300
KYQKAVYGTQ VSIGMRFGMM FETEESGKRR YMGTITGISD LDPLRWPGSK VSLWEIETPE  360
SLFVFPSLTS GLKRPLHPGF VGAETEWGNM IRRPFMRVAE GGNDLPWPPI PSAGSEPLIK  420
MLLKSQSVSP TGTFSSSIPP CLVKAAPVPE GETLYQTLVQ QKPNILPSEN SSLQTQNLHQ  480
HMDQTHAADG NLASQTHVSE KEKPSNKLED QLQPKTQPEE LDVAPIIAPD HLTQLTDKLI  540
GSALSPQNLA NQLLLLNQST LQLQSGSRVV KQHLEANTAL SQVNTTQLDA NNLNSILPHP  600
GLLSSQYLDA DDWVLHPFTS QSLASILKSP VPLSGCGKKD TSIVFPETVN PILTPLGQET  660
WGSQLNYPRY PSQADQLPTC TEQDSTALQS ISNPCGLRGI SEDSNSQSEI YNGLHFDASN  720
CGSTVIDPSV SSTVQEKFGT LRDSDFLNPS DCLFSNFSSS QDVQSQITSA SLADSHGYSL  780
QEFPDHSGGT SSSNVDIDEG SLLQKSSWQQ VSAPLRTYTK VQKLGSVGRS IDVTRFKNYE  840
ELRSAIACMF GLEGLLDDPK GSGWKLVYVD YENDVLLVGD DPWEEFVSCV RCIRILSPSE  900
VQQMSKDGIQ LLNSAAIQGT KTLSDDGCNI WDGMT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	361	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_010246954.1	0.0	PREDICTED: auxin response factor 5-like isoform X3
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1U7Z1N2	0.0	A0A1U7Z1N2_NELNU; Auxin response factor
STRING	XP_010246954.1	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]