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

Thhalv10006635m

Common Name

EUTSA_v10006635mg

Organism

Eutrema salsugineum

Taxonomic ID

72664

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1084aa MW: 119803 Da PI: 6.6526

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thhalv10006635m	genome	JGI	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-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++ Thhalv10006635m 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RD 215 99***************************954.4444.48********************************************..45 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 ++ +l+++++r+ Thhalv10006635m 216 EKSQLMLGIRRA 227 67778**997 PP
2	Auxin_resp	118.5	5.4e-39	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+g+sdldpvrW++S+Wr+L+ Thhalv10006635m 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.4E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	8.0E-42	120	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.76E-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	7.5E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	5.3E-10	953	1041	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.665	955	1048	IPR000270	PB1 domain
SuperFamily	SSF54277	1.77E-8	969	1033	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:0009734	Biological Process	auxin-activated signaling pathway
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: 1084 aa Download sequence Send to blast
MKAPSNGFHP NSTEGEKKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP 360 FYICPPPFFR PKYPRQPGMP DDDLDIENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM 420 SMQQNNPLSA TTQLPSALSS YNLPNNFASN DPSKLLNFQS PNLSPANSQF NKPNMVNHIS 480 QQMQAQPAIV KSQQQQQQQQ QQLQQQVQMS HQQLQQHHQQ QQGIYNIGSV NNGVTVVSNQ 540 ASCQNQSTGF SQAQLQQQSM LSNGATMTQQ NIVSGGIKGS SQMTSLAQEL QFQQQLELHN 600 SSQLLRNQQE QSSMHTLQQT LSQNPQQLQM QQQSSKQSPS QQLQLQLLQK LQQQQQQQSI 660 PPVSSSIQPQ LSALQQAQSH QLQQLLSSQN QQPLAHGNNS FSASTFMQPP QIQVSHQQQG 720 QMNNKPLVTT GRSHSGHTDG EAPSCSTSPS ANNTGHDNVS PTNFLSRNLQ QGQGVSVSPS 780 DSVFERASNQ GQELYAKTES RVNQGMVNLK SAPEHFKFKG AVTDQLDVST AGATYCPDVV 840 GPAQQQQTFP LPSFGFDGDC QSQHPRNSLG FAGNLEAVTS DALYSQKDFH NLVPNYGNAP 900 RDIETELSSA AISSQSFGIP SIPFKSGGSN EIGGINDSGI MNGGGLWPNQ TQRMRTYTKV 960 QKRGSVGRSI DVTRYSGYEE LRHDLARMFG IEGQLEDPQT SDWKLVYTDH ENDILLVGDD 1020 PWEEFVNCVQ NIKILSSAEV QQMSLDGDLA AIPATNQACS ETDSGNAWKV HYEDTSAAAS 1080 FNR*

Sequence ? help Back to Top

Protein Sequence Length: 1084 aa Download sequence Send to blast

MKAPSNGFHP NSTEGEKKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDDLDIENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSA TTQLPSALSS YNLPNNFASN DPSKLLNFQS PNLSPANSQF NKPNMVNHIS  480
QQMQAQPAIV KSQQQQQQQQ QQLQQQVQMS HQQLQQHHQQ QQGIYNIGSV NNGVTVVSNQ  540
ASCQNQSTGF SQAQLQQQSM LSNGATMTQQ NIVSGGIKGS SQMTSLAQEL QFQQQLELHN  600
SSQLLRNQQE QSSMHTLQQT LSQNPQQLQM QQQSSKQSPS QQLQLQLLQK LQQQQQQQSI  660
PPVSSSIQPQ LSALQQAQSH QLQQLLSSQN QQPLAHGNNS FSASTFMQPP QIQVSHQQQG  720
QMNNKPLVTT GRSHSGHTDG EAPSCSTSPS ANNTGHDNVS PTNFLSRNLQ QGQGVSVSPS  780
DSVFERASNQ GQELYAKTES RVNQGMVNLK SAPEHFKFKG AVTDQLDVST AGATYCPDVV  840
GPAQQQQTFP LPSFGFDGDC QSQHPRNSLG FAGNLEAVTS DALYSQKDFH NLVPNYGNAP  900
RDIETELSSA AISSQSFGIP SIPFKSGGSN EIGGINDSGI MNGGGLWPNQ TQRMRTYTKV  960
QKRGSVGRSI DVTRYSGYEE LRHDLARMFG IEGQLEDPQT SDWKLVYTDH ENDILLVGDD  1020
PWEEFVNCVQ NIKILSSAEV QQMSLDGDLA AIPATNQACS ETDSGNAWKV HYEDTSAAAS  1080
FNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-172	16	355	47	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	Thhalv10006635m

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JN979484	0.0	JN979484.1 Brassica rapa subsp. pekinensis auxin response factor 19-2 (ARF19-2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006416527.1	0.0	auxin response factor 19
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	V4KB06	0.0	V4KB06_EUTSA; Auxin response factor
STRING	XP_006416527.1	0.0	(Eutrema salsugineum)

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

Link Out ? help Back to Top
Phytozome	Thhalv10006635m
Entrez Gene	18993000

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]