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

AHYPO_017867-RA

Organism

Amaranthus hypochondriacus

Taxonomic ID

28502

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Amaranthaceae; Amaranthus

Family

ARF

Protein Properties

Length: 957aa MW: 106079 Da PI: 6.0064

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AHYPO_017867-RA	genome	BYU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	32.2	1.9e-10	122	183	1	57
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETT CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksg 57 f+k+lt sd++++g +++p++ ae++ + +++ ++l+ +d++g++W++++iyr+ ++ AHYPO_017867-RA 122 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QELMAKDLHGQTWTFRHIYRGIRR 183 99***************************954.5444.48***************54433 PP
2	Auxin_resp	122.5	3.1e-40	209	291	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras++eFvv+++k++ka++++ s+GmRf+m+fete++ rr++Gt++g+sdldpvrW+nS+Wr+L+ AHYPO_017867-RA 209 AAHAANNNSPFTIFYNPRASPAEFVVPLAKYNKAMYTQASLGMRFRMMFETEECGVRRYMGTITGISDLDPVRWKNSQWRNLQ 291 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.84E-28	111	184	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.9E-20	114	180	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.09E-8	121	183	No hit	No description
SMART	SM01019	0.002	122	225	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-8	122	182	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.5E-35	209	291	IPR010525	Auxin response factor
PROSITE profile	PS51745	22.145	830	922	IPR000270	PB1 domain
SuperFamily	SSF54277	1.23E-8	839	907	No hit	No description
Pfam	PF02309	1.7E-7	841	915	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: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: 957 aa Download sequence Send to blast
MKAPTNGLMP NSGEELWHAC AGPLVAVPPV GSLVVYFPQG HSEQVAASMQ KETDGIPSYP 60 NLPSKLICML HNITLHADLE TDEVYAQMTL QPVNKVRPSY DREALLQSEL ALKQSRQPAE 120 FFCKTLTASD TSTHGGFSVP RRAAEKIFPP LDFSMQPPAQ ELMAKDLHGQ TWTFRHIYRG 180 IRRANRQQPA LASSVISSDS MHIGILAAAA HAANNNSPFT IFYNPRASPA EFVVPLAKYN 240 KAMYTQASLG MRFRMMFETE ECGVRRYMGT ITGISDLDPV RWKNSQWRNL QVGWDESTTG 300 ERPSRVSIWD IEPVVTPFYI CPPPFFRPKF PKQPGMPDDD SDMENMFKRG MPWLGDDFGM 360 KDVPNSIFPG LSLVQWMSMQ QNNQFPGTQA GIFPSMLTAS ALQGSLGTDD PSKLQSLPQP 420 QMYGQLHHQQ MIGGNNQTPP NFPVNKDSVL TSLAPDMQFQ QQTEQQTNVF QRLQQQQQQQ 480 QQQQQPIQLQ PPSQQLLQES LSQRPSVLQS LSEHQLQLQL LQKLQQPQAQ HQQPQPQLNQ 540 QQPQQSHPLL SPISQVHPQV TSQLHVAQQN QVLQHRPLTQ YPPQVGVSTI STSPLMNSTP 600 ITVQHQGMQK TSGLVRSLSG PTDGDAPSCS TSPSSNNCQI PNSNFLNRNQ LGRNLLVDHS 660 VEPNSNLVQD LQEKPDVRLK NEIPSSKVIE PPRINGIIAD PLEASSSITS FGLDASGLQQ 720 NLSLPSFGLD GDVQSHPRNN LPLSTGMDAL TPDTLLSRGF DSGKELHNLL SNYNSTPRDI 780 ETELSAAAMS SQSFGVPDMP FKSGCSNDVA AINDPAVLSG GIWPNQTQQR MRTYTKRGSV 840 GRSIDVTRYK GYDDLRRDLA RMFGIEGQLE DPQRTEWKLV YVDHENDILL VGDDPWDEFV 900 NCVQSIKILS SVEVQQMSLD GDLGNGPIPN QASSGTDSGN AWRGHYDDHS AASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 957 aa Download sequence Send to blast

MKAPTNGLMP NSGEELWHAC AGPLVAVPPV GSLVVYFPQG HSEQVAASMQ KETDGIPSYP  60
NLPSKLICML HNITLHADLE TDEVYAQMTL QPVNKVRPSY DREALLQSEL ALKQSRQPAE  120
FFCKTLTASD TSTHGGFSVP RRAAEKIFPP LDFSMQPPAQ ELMAKDLHGQ TWTFRHIYRG  180
IRRANRQQPA LASSVISSDS MHIGILAAAA HAANNNSPFT IFYNPRASPA EFVVPLAKYN  240
KAMYTQASLG MRFRMMFETE ECGVRRYMGT ITGISDLDPV RWKNSQWRNL QVGWDESTTG  300
ERPSRVSIWD IEPVVTPFYI CPPPFFRPKF PKQPGMPDDD SDMENMFKRG MPWLGDDFGM  360
KDVPNSIFPG LSLVQWMSMQ QNNQFPGTQA GIFPSMLTAS ALQGSLGTDD PSKLQSLPQP  420
QMYGQLHHQQ MIGGNNQTPP NFPVNKDSVL TSLAPDMQFQ QQTEQQTNVF QRLQQQQQQQ  480
QQQQQPIQLQ PPSQQLLQES LSQRPSVLQS LSEHQLQLQL LQKLQQPQAQ HQQPQPQLNQ  540
QQPQQSHPLL SPISQVHPQV TSQLHVAQQN QVLQHRPLTQ YPPQVGVSTI STSPLMNSTP  600
ITVQHQGMQK TSGLVRSLSG PTDGDAPSCS TSPSSNNCQI PNSNFLNRNQ LGRNLLVDHS  660
VEPNSNLVQD LQEKPDVRLK NEIPSSKVIE PPRINGIIAD PLEASSSITS FGLDASGLQQ  720
NLSLPSFGLD GDVQSHPRNN LPLSTGMDAL TPDTLLSRGF DSGKELHNLL SNYNSTPRDI  780
ETELSAAAMS SQSFGVPDMP FKSGCSNDVA AINDPAVLSG GIWPNQTQQR MRTYTKRGSV  840
GRSIDVTRYK GYDDLRRDLA RMFGIEGQLE DPQRTEWKLV YVDHENDILL VGDDPWDEFV  900
NCVQSIKILS SVEVQQMSLD GDLGNGPIPN QASSGTDSGN AWRGHYDDHS AASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-132	10	312	49	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}.

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_024964050.1	0.0	auxin response factor 19-like isoform X1
Refseq	XP_024964051.1	0.0	auxin response factor 19-like isoform X2
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A4P1R007	0.0	A0A4P1R007_LUPAN; Uncharacterized protein
STRING	XP_004168159.1	0.0	(Cucumis sativus)

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	AHYPO_017867-RA

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]