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

mrna12917.1-v1.0-hybrid

Organism

Fragaria vesca

Taxonomic ID

57918

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Rosoideae; Potentilleae; Fragariinae; Fragaria

Family

ARF

Protein Properties

Length: 1162aa MW: 130113 Da PI: 6.7193

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
mrna12917.1-v1.0-hybrid	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	69.1	5.9e-22	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 f+k+lt sd++++g +++p++ ae++ +++++ ++l+ +d++ W++++iyr++++r++lt+GW+ Fv+ ++L +gD v mrna12917.1-v1.0-hybrid 126 FCKTLTASDTSTHGGFSVPRRAAEKIfpaldfSMQPPA-QELVAKDLHDSAWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDAV 210 99***************************9445444.38***************************************** PP EEEE-SSSEE..EEEEE-S CS B3 81 vFkldgrsefelvvkvfrk 99 +F ++++ +l+++++r+ mrna12917.1-v1.0-hybrid 211 LFI--RDEKSQLLLGIRRA 227 *..45677789999997 PP
2	Auxin_resp	122.1	4.1e-40	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFvv+++k++ka++++vs+GmRf+m+fete+s rr++Gt++g+s+ld+vrW+nS+Wr+L+ mrna12917.1-v1.0-hybrid 252 AAHAAANNSAFTIFYNPRASPSEFVVPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITGISELDSVRWKNSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.68E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.2E-41	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.06E-18	125	226	No hit	No description
PROSITE profile	PS50863	12.139	126	228	IPR003340	B3 DNA binding domain
SMART	SM01019	1.9E-20	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.3E-20	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.4E-35	252	334	IPR010525	Auxin response factor
Pfam	PF02309	1.0E-8	1032	1120	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.074	1034	1127	IPR000270	PB1 domain
SuperFamily	SSF54277	1.18E-8	1048	1112	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:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0010311	Biological Process	lateral root formation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 1162 aa Download sequence Send to blast
MKAPTNGFLA TSVEGEQKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDFIPNYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDKEAIL ASDMGLKQSR 120 QPSEFFCKTL TASDTSTHGG FSVPRRAAEK IFPALDFSMQ PPAQELVAKD LHDSAWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDAV LFIRDEKSQL LLGIRRANRQ QPALSSSVIS 240 SDSMHIGILA AAAHAAANNS AFTIFYNPRA SPSEFVVPLA KYNKAMYTQV SLGMRFRMMF 300 ETEESGVRRY MGTITGISEL DSVRWKNSQW RNLQVGWDES TAGDRPSRVS IWEIEPVVTP 360 FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWLGDE FGMKNSTSSI FPGLSLVQWM 420 NMQQNNQFSA AQSGFFPSMV PPTTLHNGID DPSKLLNFQA PGLTAPSQLN KAALQNQVGQ 480 VQQPTVTWPQ QQQLQQLMQN PMNQQQQNHS QQQQLQQLMH TPLNQQQQNL PQQQQLQQLM 540 QTPANQQLQN YSQQQQQQRE QQQRQEPQGH QPLQNLHQIH QQQPQRQQPQ QQQLGQPTSV 600 SNGLITPNQI PSQNSQQPMM FTQLQQQHSL TSSAQSQQTV HTPNKNSFQL AAGTQDSQIQ 660 QQLEPQPSLL QRQQQAQLQQ SPLQLLQQSQ KAQQQPQVQP SPQQGLSEQQ IHLQLLQKLQ 720 QQQQQHQQQQ QQQQQLFSPS SPLLQQQMLQ QQLAHQQNQQ LQQLQLPLSQ HHQQQLSSNG 780 FAADKLLNSN NFSASPLLQP QHVSSIQQQN QHKQVTAIRS HSNLTEGDGP SCSTSPSTNN 840 CHVSPSNLLN RNQQGTAMLI ADPVPEPSSN LVHEFQSKSD IRIKHELPIS KGPDQIKYKG 900 TITDQLEASS SGTSYCLDAS TMQQNYALPS FCLDGDVQSH PRNNLPFSAN IDGLAPDTLL 960 SRGYDSQKDL QNLLANYGGT PRDIETELST AAISSQSFGA PNMPFKPGCS SDVALNDAGV 1020 LNNGLWGSQP QRMRTYTKVQ KRGLVGRCID VTRYKGYDEL RHDLARMFGI EGQLEDPQRT 1080 EWKLVYVDHE NDILLVGDDP WEEFVSCVQS IKILSSVEVQ QMSLDGDLGN VPVPNQACSG 1140 TDSGNAWRPP YDDNSAASFN R*

Sequence ? help Back to Top

Protein Sequence Length: 1162 aa Download sequence Send to blast

MKAPTNGFLA TSVEGEQKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDFIPNYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYDKEAIL ASDMGLKQSR  120
QPSEFFCKTL TASDTSTHGG FSVPRRAAEK IFPALDFSMQ PPAQELVAKD LHDSAWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDAV LFIRDEKSQL LLGIRRANRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS AFTIFYNPRA SPSEFVVPLA KYNKAMYTQV SLGMRFRMMF  300
ETEESGVRRY MGTITGISEL DSVRWKNSQW RNLQVGWDES TAGDRPSRVS IWEIEPVVTP  360
FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWLGDE FGMKNSTSSI FPGLSLVQWM  420
NMQQNNQFSA AQSGFFPSMV PPTTLHNGID DPSKLLNFQA PGLTAPSQLN KAALQNQVGQ  480
VQQPTVTWPQ QQQLQQLMQN PMNQQQQNHS QQQQLQQLMH TPLNQQQQNL PQQQQLQQLM  540
QTPANQQLQN YSQQQQQQRE QQQRQEPQGH QPLQNLHQIH QQQPQRQQPQ QQQLGQPTSV  600
SNGLITPNQI PSQNSQQPMM FTQLQQQHSL TSSAQSQQTV HTPNKNSFQL AAGTQDSQIQ  660
QQLEPQPSLL QRQQQAQLQQ SPLQLLQQSQ KAQQQPQVQP SPQQGLSEQQ IHLQLLQKLQ  720
QQQQQHQQQQ QQQQQLFSPS SPLLQQQMLQ QQLAHQQNQQ LQQLQLPLSQ HHQQQLSSNG  780
FAADKLLNSN NFSASPLLQP QHVSSIQQQN QHKQVTAIRS HSNLTEGDGP SCSTSPSTNN  840
CHVSPSNLLN RNQQGTAMLI ADPVPEPSSN LVHEFQSKSD IRIKHELPIS KGPDQIKYKG  900
TITDQLEASS SGTSYCLDAS TMQQNYALPS FCLDGDVQSH PRNNLPFSAN IDGLAPDTLL  960
SRGYDSQKDL QNLLANYGGT PRDIETELST AAISSQSFGA PNMPFKPGCS SDVALNDAGV  1020
LNNGLWGSQP QRMRTYTKVQ KRGLVGRCID VTRYKGYDEL RHDLARMFGI EGQLEDPQRT  1080
EWKLVYVDHE NDILLVGDDP WEEFVSCVQS IKILSSVEVQ QMSLDGDLGN VPVPNQACSG  1140
TDSGNAWRPP YDDNSAASFN R*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-168	20	355	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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	mrna12917.1-v1.0-hybrid

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_004287660.1	0.0	PREDICTED: auxin response factor 19-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A251NDW3	0.0	A0A251NDW3_PRUPE; Auxin response factor
STRING	XP_004287660.1	0.0	(Fragaria vesca)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4918	33	52

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	0.0	auxin response factor 19

Link Out ? help Back to Top
Phytozome	mrna12917.1-v1.0-hybrid

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] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] 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] 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] 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] 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]