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

AA39G00205

Organism

Aethionema arabicum

Taxonomic ID

228871

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1088aa MW: 120458 Da PI: 6.8369

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AA39G00205	genome	VEGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.1	3.3e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ +l AA39G00205 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RDEKSQL 220 99***************************954.4444.48********************************************..4567778 PP EEEEE-S CS B3 93 vvkvfrk 99 +++++r+ AA39G00205 221 MLGIRRA 227 **997 PP
2	Auxin_resp	118.8	4.3e-39	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+gvsdldpvrW++S+Wr+L+ AA39G00205 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGVSDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.92E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.9E-42	119	240	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.80E-21	125	226	No hit	No description
SMART	SM01019	1.0E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.534	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	6.0E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	6.3E-10	972	1061	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.747	975	1068	IPR000270	PB1 domain
SuperFamily	SSF54277	2.16E-8	990	1053	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: 1088 aa Download sequence Send to blast
MKTPSHGFQP NSTEGETKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKFDREALL ASDMGLKMNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVMS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGVSDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP 360 FYICPPPFFR PKYPRQPGMP DDELDIENAF KRAMPWMGED FGMKDAQSSM FPGLSLVQWM 420 SMQQNNPLSA ATQLPSALSG YNLPSSFVSN DPSKLLNFQS PTLSSANAQF NKPYAVNHPV 480 QAPVKSQQQL QQQVQMSQQQ QQQHQQQHQQ QQQQQHQQQV VYNTGSVNNG VGVANQIPSQ 540 NPHQSTAFSQ SQLQQHQQQV VYNTGSVNNG VGVASQNPHQ STAFPQSQLQ QQQAMLPNGA 600 KSHQNTISGN KGSSQMASFA QELQFQQQLE LQNNSHLMRN QQEQAQSQQA SLHSLQQTLS 660 QNPQQSQMQQ SSKPSPSQQL QLQLLQKLQQ QQQSIPPVSS SLQPQPLQTQ NHQLQQLLSS 720 QNQQPVLHGN NSFSSSTFMQ PPQVQVTQPQ GQINKPLVTG RSQSGHTEGE APSCSTSPSA 780 NNTGHVSPSN FLSRNQPGQA MSTSDSVFER ASNPVQELYT KTESRINQGL VNLKSSPSQF 840 KFKGTATDHM DASTAGTTYC PDVATAQQQT FPLPAFGFDG DCQSHSRNNL AFAGNLEAVT 900 SDALYSQKDF QNLVPNYGGA PRDIETELSS AAISSQSFGI PSITFKSGCS NEVGINDSGI 960 MNNGGLWTNQ TQRMRTYTKV QKRGSVGRSI DVTRYRGYDE LRHDLARMFG IEGQLEDPQT 1020 SDWKLVYTDH ENDILLVGDD PWEEFVNCVQ NIKILSSAEV QQMSLDGDLA AIPIPNQACS 1080 ETESGNAW

Sequence ? help Back to Top

Protein Sequence Length: 1088 aa Download sequence Send to blast

MKTPSHGFQP NSTEGETKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKFDREALL ASDMGLKMNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVMS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGVSDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDELDIENAF KRAMPWMGED FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSA ATQLPSALSG YNLPSSFVSN DPSKLLNFQS PTLSSANAQF NKPYAVNHPV  480
QAPVKSQQQL QQQVQMSQQQ QQQHQQQHQQ QQQQQHQQQV VYNTGSVNNG VGVANQIPSQ  540
NPHQSTAFSQ SQLQQHQQQV VYNTGSVNNG VGVASQNPHQ STAFPQSQLQ QQQAMLPNGA  600
KSHQNTISGN KGSSQMASFA QELQFQQQLE LQNNSHLMRN QQEQAQSQQA SLHSLQQTLS  660
QNPQQSQMQQ SSKPSPSQQL QLQLLQKLQQ QQQSIPPVSS SLQPQPLQTQ NHQLQQLLSS  720
QNQQPVLHGN NSFSSSTFMQ PPQVQVTQPQ GQINKPLVTG RSQSGHTEGE APSCSTSPSA  780
NNTGHVSPSN FLSRNQPGQA MSTSDSVFER ASNPVQELYT KTESRINQGL VNLKSSPSQF  840
KFKGTATDHM DASTAGTTYC PDVATAQQQT FPLPAFGFDG DCQSHSRNNL AFAGNLEAVT  900
SDALYSQKDF QNLVPNYGGA PRDIETELSS AAISSQSFGI PSITFKSGCS NEVGINDSGI  960
MNNGGLWTNQ TQRMRTYTKV QKRGSVGRSI DVTRYRGYDE LRHDLARMFG IEGQLEDPQT  1020
SDWKLVYTDH ENDILLVGDD PWEEFVNCVQ NIKILSSAEV QQMSLDGDLA AIPIPNQACS  1080
ETESGNAW

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-171	19	355	50	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	AA39G00205

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_010477125.1	0.0	PREDICTED: auxin response factor 19
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A178WP07	0.0	A0A178WP07_ARATH; Auxin response factor
STRING	Bostr.7128s0527.1.p	0.0	(Boechera stricta)

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
AT1G19220.1	0.0	auxin response factor 19

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]