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

Rsa1.0_00015.1_g00006.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

ARF

Protein Properties

Length: 819aa MW: 90717.9 Da PI: 5.6976

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00015.1_g00006.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	59.1	7.7e-19	133	201	28	99
--..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 28 gkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 ++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++gD+v+F ++++ +l+v+v+r+ Rsa1.0_00015.1_g00006.1 133 AQPPT-QELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSVLFI--RDEKSQLMVGVRRA 201 34433.48**********************************************..4577778***97 PP
2	Auxin_resp	108.3	8e-36	227	310	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha++++++F +++nPra+++eFv++++k++ka+ +++svGmRf m+feteds +rr++Gt+vg+sd+dp+rW++SkWr+L+ Rsa1.0_00015.1_g00006.1 227 AAHATANRTPFLIFFNPRACPAEFVIPLAKYRKAICgSQLSVGMRFGMMFETEDSGKRRYMGTIVGISDIDPLRWSGSKWRNLQ 310 79******************************9989******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SMART	SM01019	2.8E-10	108	202	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	3.14E-24	126	230	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.0E-24	130	208	IPR015300	DNA-binding pseudobarrel domain
Pfam	PF02362	3.2E-16	130	201	IPR003340	B3 DNA binding domain
CDD	cd10017	1.66E-13	135	200	No hit	No description
PROSITE profile	PS50863	11.251	139	202	IPR003340	B3 DNA binding domain
Pfam	PF06507	8.9E-31	227	310	IPR010525	Auxin response factor
PROSITE profile	PS51745	22.081	710	794	IPR000270	PB1 domain
SuperFamily	SSF54277	1.37E-6	724	788	No hit	No description
Pfam	PF02309	2.9E-6	754	795	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: 819 aa Download sequence Send to blast
MMASVEDKMK TNSWANGGTK TTSQSTLLEE MKLLKDQSGT RKPVINSELW HACAGPLVCL 60 PQVGSLVYYF SQGHSEQVAV STRRSATTQV PNYPNLPSQL MCQVHNVTLH ADKDSDEIYA 120 QMSLQPVHSD YTAQPPTQEL VVRDLHENTW TFRHIYRGQP KRHLLTTGWS LFVGSKRLRA 180 GDSVLFIRDE KSQLMVGVRR ANRHQQTALP SSVLSADSMH IGVLAAAAHA TANRTPFLIF 240 FNPRACPAEF VIPLAKYRKA ICGSQLSVGM RFGMMFETED SGKRRYMGTI VGISDIDPLR 300 WSGSKWRNLQ VEWDEPGCND KPTRVSPWDI ETPESLFIFP SLTSGLKRQL HPSYFAGETE 360 WGSLIKRPLI RVSDSTNGIL PYASFPNMAS EQLMKMMMRP HNNNNNNNQN ATSSFMSEML 420 QQNVLMGHGG GLLGDMNMQQ PMVTSQKPEM VQQPESKITL NPSTAFNTTG QEQNLSQNMT 480 APPESEHHGN EQKSVEQASQ ARTVTVCNED ALSPLQAEPC PDTSQQIYPP QSDPINGFSF 540 LETEELTSFH SLAGSSLLSS QEDSSAVVLP DSTNSSLFHD VWDNQLSGLK FDQFSPLMQQ 600 DLYGCQDSTT SNILDPPPLS NTVLDDFCAI QNHHPSSDCL VGNSNTSFAQ DVQSSQITTA 660 GFADSKAFSR QDNSGGTTVT SSSNVDFDDS TLLQQNSKGS WQKLATPRVR TYTKVQKTGS 720 VGRSIDVTSF RDYKELKTAI ECMFGLEGLL TRPQSSGWKL VYVDYESDVL LVGDDPWKEF 780 VGCVRCIKIL SPAEVEQMSE EGMKLLNSAC INDLKTSVS

Sequence ? help Back to Top

Protein Sequence Length: 819 aa Download sequence Send to blast

MMASVEDKMK TNSWANGGTK TTSQSTLLEE MKLLKDQSGT RKPVINSELW HACAGPLVCL  60
PQVGSLVYYF SQGHSEQVAV STRRSATTQV PNYPNLPSQL MCQVHNVTLH ADKDSDEIYA  120
QMSLQPVHSD YTAQPPTQEL VVRDLHENTW TFRHIYRGQP KRHLLTTGWS LFVGSKRLRA  180
GDSVLFIRDE KSQLMVGVRR ANRHQQTALP SSVLSADSMH IGVLAAAAHA TANRTPFLIF  240
FNPRACPAEF VIPLAKYRKA ICGSQLSVGM RFGMMFETED SGKRRYMGTI VGISDIDPLR  300
WSGSKWRNLQ VEWDEPGCND KPTRVSPWDI ETPESLFIFP SLTSGLKRQL HPSYFAGETE  360
WGSLIKRPLI RVSDSTNGIL PYASFPNMAS EQLMKMMMRP HNNNNNNNQN ATSSFMSEML  420
QQNVLMGHGG GLLGDMNMQQ PMVTSQKPEM VQQPESKITL NPSTAFNTTG QEQNLSQNMT  480
APPESEHHGN EQKSVEQASQ ARTVTVCNED ALSPLQAEPC PDTSQQIYPP QSDPINGFSF  540
LETEELTSFH SLAGSSLLSS QEDSSAVVLP DSTNSSLFHD VWDNQLSGLK FDQFSPLMQQ  600
DLYGCQDSTT SNILDPPPLS NTVLDDFCAI QNHHPSSDCL VGNSNTSFAQ DVQSSQITTA  660
GFADSKAFSR QDNSGGTTVT SSSNVDFDDS TLLQQNSKGS WQKLATPRVR TYTKVQKTGS  720
VGRSIDVTSF RDYKELKTAI ECMFGLEGLL TRPQSSGWKL VYVDYESDVL LVGDDPWKEF  780
VGCVRCIKIL SPAEVEQMSE EGMKLLNSAC INDLKTSVS

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	335	1	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00015.1_g00006.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JN979465	0.0	JN979465.1 Brassica rapa subsp. pekinensis auxin response factor 5-1 (ARF5-1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018439086.1	0.0	PREDICTED: auxin response factor 5-like isoform X1
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A078GW89	0.0	A0A078GW89_BRANA; Auxin response factor
TrEMBL	A0A397YXN3	0.0	A0A397YXN3_BRACM; Auxin response factor
STRING	Bo5g027930.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46

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]