PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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

Family

ARF

Protein Properties

Length: 947aa MW: 103836 Da PI: 6.2679

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa20g032720.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.8	8.5e-23	127	228	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+ ++L +gD+v+F + + + Csa20g032720.1 127 FCKTLTASDTSTHGGFSVPRRAAEKIfpaldfSMQPPCQ-ELVAKDIHDSTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR--DGK 218 99***************************98888885.9**********************************************5..467 PP E..EEEEE-S CS B3 90 felvvkvfrk 99 ++l+++++r+ Csa20g032720.1 219 AQLLLGIRRA 228 8889999997 PP
2	Auxin_resp	117.9	8.6e-39	253	335	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F+++YnPra+++eFvv+++k+ ka++ +vs+GmRf+m fete++ rr++Gtv+g+sdldpvrW+nS+Wr+L+ Csa20g032720.1 253 AAHANANNSPFTIFYNPRAAPAEFVVPLAKYTKAMYAQVSLGMRFRMIFETEECGVRRYMGTVTGISDLDPVRWKNSQWRNLQ 335 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.62E-42	117	256	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.4E-41	121	242	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.51E-19	126	227	No hit	No description
SMART	SM01019	3.1E-22	127	229	IPR003340	B3 DNA binding domain
Pfam	PF02362	4.9E-21	127	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.055	127	229	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.8E-34	253	335	IPR010525	Auxin response factor
Pfam	PF02309	1.3E-9	817	905	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	26.956	819	912	IPR000270	PB1 domain
SuperFamily	SSF54277	7.85E-9	832	897	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009638	Biological Process	phototropism
GO:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0009785	Biological Process	blue light signaling pathway
GO:0010311	Biological Process	lateral root formation
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0048366	Biological Process	leaf development
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: 947 aa Download sequence Send to blast
MKAPSSNGVS PNPVEGERRN INSELWHACA GPLISLPPAG SLVVYFPQGH SEQVAASMQK 60 QTDFIPSYPN LPSKLICMLH NVTLNADPET DEVYAQMTLQ PVNKYDRDAL LASDMGLKLN 120 RQPNEFFCKT LTASDTSTHG GFSVPRRAAE KIFPALDFSM QPPCQELVAK DIHDSTWTFR 180 HIYRGQPKRH LLTTGWSVFV STKRLFAGDS VLFIRDGKAQ LLLGIRRANR QQPALSSSVI 240 SSDSMHIGVL AAAAHANANN SPFTIFYNPR AAPAEFVVPL AKYTKAMYAQ VSLGMRFRMI 300 FETEECGVRR YMGTVTGISD LDPVRWKNSQ WRNLQIGWDE SAAGDRPSRV SVWDIEPVLT 360 PFYICPPPFF RPRFGGQPGM PDDETDMESA LKRAMPWLDN SSEMKDASST IFPGLSLVQW 420 MNMQQQNGQL PSAAAGQPGF FPSMLSPSAA LHNNLGGTDD PSNKSSSNMM SVPPQETQFP 480 RQVEQQQPSG LPSGLKGQNQ QILSQQKAHQ AQAQQIFQQS LLEQPHLQFQ LLQRLQQQQQ 540 QQQQQQFLSP QSQLPHHQMQ SQQLQQLPAL SQGHQFPSSC TNNGLSTLQP PQMLVNRPQE 600 KQNPPVGGGV KAYSGITDGG DAPSSSTSPS TNNCQISSSG FLNRSQSGPA ILMPDPAIDI 660 SGNLVQDLYS KSDMRLKQEL VGQQKSKASL TDHHLEASAS GTSYGLDGGD NNRQQNFLAP 720 TFGLDGDSRN SLLGGANVDN GFVPDTLLSR GYDSQKDLQN MLSNYGGVTN DIGTEMSTSA 780 VRTQSFGVPN VPAISNDLAV NDAGVLGGGL WPAQTQRMRT YTKVQKRGSV GRSIDVNRYR 840 GYDELRHDLA RMFGIEGQLE DPQTSDWKLV YVDHENDILL VGDDPWEEFV NCVQSIKILS 900 SAEVQQMSLD GNFAGVPVTN QACSGGDSGN AWRGHYDDNS ATSFNR*

Sequence ? help Back to Top

Protein Sequence Length: 947 aa Download sequence Send to blast

MKAPSSNGVS PNPVEGERRN INSELWHACA GPLISLPPAG SLVVYFPQGH SEQVAASMQK  60
QTDFIPSYPN LPSKLICMLH NVTLNADPET DEVYAQMTLQ PVNKYDRDAL LASDMGLKLN  120
RQPNEFFCKT LTASDTSTHG GFSVPRRAAE KIFPALDFSM QPPCQELVAK DIHDSTWTFR  180
HIYRGQPKRH LLTTGWSVFV STKRLFAGDS VLFIRDGKAQ LLLGIRRANR QQPALSSSVI  240
SSDSMHIGVL AAAAHANANN SPFTIFYNPR AAPAEFVVPL AKYTKAMYAQ VSLGMRFRMI  300
FETEECGVRR YMGTVTGISD LDPVRWKNSQ WRNLQIGWDE SAAGDRPSRV SVWDIEPVLT  360
PFYICPPPFF RPRFGGQPGM PDDETDMESA LKRAMPWLDN SSEMKDASST IFPGLSLVQW  420
MNMQQQNGQL PSAAAGQPGF FPSMLSPSAA LHNNLGGTDD PSNKSSSNMM SVPPQETQFP  480
RQVEQQQPSG LPSGLKGQNQ QILSQQKAHQ AQAQQIFQQS LLEQPHLQFQ LLQRLQQQQQ  540
QQQQQQFLSP QSQLPHHQMQ SQQLQQLPAL SQGHQFPSSC TNNGLSTLQP PQMLVNRPQE  600
KQNPPVGGGV KAYSGITDGG DAPSSSTSPS TNNCQISSSG FLNRSQSGPA ILMPDPAIDI  660
SGNLVQDLYS KSDMRLKQEL VGQQKSKASL TDHHLEASAS GTSYGLDGGD NNRQQNFLAP  720
TFGLDGDSRN SLLGGANVDN GFVPDTLLSR GYDSQKDLQN MLSNYGGVTN DIGTEMSTSA  780
VRTQSFGVPN VPAISNDLAV NDAGVLGGGL WPAQTQRMRT YTKVQKRGSV GRSIDVNRYR  840
GYDELRHDLA RMFGIEGQLE DPQTSDWKLV YVDHENDILL VGDDPWEEFV NCVQSIKILS  900
SAEVQQMSLD GNFAGVPVTN QACSGGDSGN AWRGHYDDNS ATSFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-168	21	356	51	388	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). Act as a transcriptional activator of several tropic stimulus-induced (TSI) genes, including SAUR50. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Required for differential growth responses of aerial tissues. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF19. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF5. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:16371470, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Csa20g032720.1

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	AF042195	0.0	AF042195.1 Arabidopsis thaliana auxin response factor 7 (ARF7) mRNA, complete cds.
GenBank	AY669789	0.0	AY669789.1 Arabidopsis thaliana clone C105344 ARF7 (At5g20730) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010493184.1	0.0	PREDICTED: auxin response factor 7-like isoform X1
Swissprot	P93022	0.0	ARFG_ARATH; Auxin response factor 7
TrEMBL	A0A2P5VXF9	0.0	A0A2P5VXF9_GOSBA; Auxin response factor
STRING	XP_010493184.1	0.0	(Camelina sativa)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2629	26	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G20730.2	0.0	ARF family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Hu J,Zhang Y,Wang J,Zhou Y Glycerol affects root development through regulation of multiple pathways in Arabidopsis. PLoS ONE, 2014. 9(1): p. e86269 [PMID:24465999] Mellor N, et al. Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis. J. Theor. Biol., 2015. 366: p. 57-70 [PMID:25446711] Gupta A,Singh M,Laxmi A Interaction between glucose and brassinosteroid during the regulation of lateral root development in Arabidopsis. Plant Physiol., 2015. 168(1): p. 307-20 [PMID:25810094] Youn JH, et al. ARF7 increases the endogenous contents of castasterone through suppression of BAS1 expression in Arabidopsis thaliana. Phytochemistry, 2016. 122: p. 34-44 [PMID:26608667] Porco S, et al. Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3. Development, 2016. 143(18): p. 3340-9 [PMID:27578783] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Sheng L, et al. Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture. Development, 2017. 144(17): p. 3126-3133 [PMID:28743799] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Prát T, et al. WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genet., 2018. 14(1): p. e1007177 [PMID:29377885] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609] Orosa-Puente B, et al. Root branching toward water involves posttranslational modification of transcription factor ARF7. Science, 2018. 362(6421): p. 1407-1410 [PMID:30573626]