PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Pyrus

Family

ARF

Protein Properties

Length: 1155aa MW: 128902 Da PI: 6.8314

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Pbr027725.1	genome	CPETR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70.8	1.8e-22	127	228	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++ +++++ ++l+ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ +l Pbr027725.1 127 FCKTLTASDTSTHGGFSVPRRAAEKIlppldfSMQPPA-QELVAKDLHDSVWTFRHIYRGQPKRHLLTTGWSVFVSNKRLFAGDSVLFI--RDEKSQL 221 99***************************9445444.38**********************************************..4567778 PP EEEEE-S CS B3 93 vvkvfrk 99 +++++r+ Pbr027725.1 222 LLGIRRA 228 9999997 PP
2	Auxin_resp	124.4	7.8e-41	253	335	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFvv+++k++ka++++vs+GmRf+m+fete+s rr++Gtv+g+sdldpvrW++S+Wr+L+ Pbr027725.1 253 AAHAAANNSPFTIFYNPRASPSEFVVPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 335 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	7.85E-43	117	256	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.6E-41	119	242	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.76E-19	126	227	No hit	No description
Pfam	PF02362	9.8E-21	127	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.196	127	229	IPR003340	B3 DNA binding domain
SMART	SM01019	1.5E-22	127	229	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.9E-36	253	335	IPR010525	Auxin response factor
Pfam	PF02309	3.1E-8	1039	1128	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.383	1042	1135	IPR000270	PB1 domain
SuperFamily	SSF54277	4.32E-8	1044	1120	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:0009725	Biological Process	response to hormone
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: 1155 aa Download sequence Send to blast
MKVPTNGFLA NSGEAGEQKR INSELWHACA GPLVSLPPVG SLVVYFPQGH SEQVAASMQK 60 ETDFIPNYTN LPSKLICMLH NVTLHADTET DEVYAQMTLQ PVNKYEKEAL LASDMGLRQS 120 RQPAEFFCKT LTASDTSTHG GFSVPRRAAE KILPPLDFSM QPPAQELVAK DLHDSVWTFR 180 HIYRGQPKRH LLTTGWSVFV SNKRLFAGDS VLFIRDEKSQ LLLGIRRANR QQPALSSSVI 240 SSDSMHIGIL AAAAHAAANN SPFTIFYNPR ASPSEFVVPL AKYNKAMYTQ VSLGMRFRMM 300 FETEESGVRR YMGTVTGISD LDPVRWKGSQ WRNLQVGWDE STAGDRPSRV SIWEIEPVIT 360 PFYICPPPFF RPKFPKQPGM PDDVSDVDNA FRRAMPWLGD EFGMKNSPSS FFPGLSLVQW 420 MNMQQNNQFS AAQSGFFPSM VPPTGLQNNL GTDDPSKLLS FQAPVLSLPS LQSNKSAPQN 480 HASQMQQPNV TWAQQQQLQQ LMYNPMNQQQ QSDPQQQQLQ QLLNSSASQH QQNQPQQQQQ 540 LQQLLNSSAN QHQQNHPQQQ QQLLQTPTNQ QLHNFSHQQQ QREPQQQQEP QNLLQHQQLH 600 QQQAQRHQHQ QQQLSQPNPV NDGSVAPNQV PGQNSQQPVM LSQHQQQQLL TGNTQQAVPS 660 SSKNSFQLPT GQQNSQLQQQ QLEPQPSLLQ RQQQAAQLQS SPHQLLQQSV SQKVQQQPQV 720 QQSSPQGISE QQLQLQLLQK FQQRQQPQLL SSSSSLLQPQ LLQQQLARQQ NQQLQQLPMT 780 QHHQQQLSGN SFSTDKLLNN FAAPSMMQSQ HMPSIQPQNQ HKPLTAIRSH SGLTEGDGPS 840 CSTSPSTNCQ MSPSNFLNRN QQGMAMLLGD SVAEPAHNLV QELQSKSDVW VKHEPPSSKG 900 PDHIKYKGTI TDQLEASSSG TSYCLDTSTI HQNYALPTFC LDGDVQSNPR SSLPFSANID 960 GLAPDTLLSR EYDSQKDLQN LLSNYGGTPR DIETELSTAA ISSQSFGAPN IPFKAGCSSD 1020 IPITDAGVLG NGSWANQAQR MRTYTKVQKR GSVGRCIDVN RYKGYDELRH DLARMFGIEG 1080 QLEDPHRTDW KLVYVDHENE ILLVGDDPWE EFVSCVQSIK ILSSVEVQQM SLDGDLGNIP 1140 VPNQASSGTH SGNA*

Sequence ? help Back to Top

Protein Sequence Length: 1155 aa Download sequence Send to blast

MKVPTNGFLA NSGEAGEQKR INSELWHACA GPLVSLPPVG SLVVYFPQGH SEQVAASMQK  60
ETDFIPNYTN LPSKLICMLH NVTLHADTET DEVYAQMTLQ PVNKYEKEAL LASDMGLRQS  120
RQPAEFFCKT LTASDTSTHG GFSVPRRAAE KILPPLDFSM QPPAQELVAK DLHDSVWTFR  180
HIYRGQPKRH LLTTGWSVFV SNKRLFAGDS VLFIRDEKSQ LLLGIRRANR QQPALSSSVI  240
SSDSMHIGIL AAAAHAAANN SPFTIFYNPR ASPSEFVVPL AKYNKAMYTQ VSLGMRFRMM  300
FETEESGVRR YMGTVTGISD LDPVRWKGSQ WRNLQVGWDE STAGDRPSRV SIWEIEPVIT  360
PFYICPPPFF RPKFPKQPGM PDDVSDVDNA FRRAMPWLGD EFGMKNSPSS FFPGLSLVQW  420
MNMQQNNQFS AAQSGFFPSM VPPTGLQNNL GTDDPSKLLS FQAPVLSLPS LQSNKSAPQN  480
HASQMQQPNV TWAQQQQLQQ LMYNPMNQQQ QSDPQQQQLQ QLLNSSASQH QQNQPQQQQQ  540
LQQLLNSSAN QHQQNHPQQQ QQLLQTPTNQ QLHNFSHQQQ QREPQQQQEP QNLLQHQQLH  600
QQQAQRHQHQ QQQLSQPNPV NDGSVAPNQV PGQNSQQPVM LSQHQQQQLL TGNTQQAVPS  660
SSKNSFQLPT GQQNSQLQQQ QLEPQPSLLQ RQQQAAQLQS SPHQLLQQSV SQKVQQQPQV  720
QQSSPQGISE QQLQLQLLQK FQQRQQPQLL SSSSSLLQPQ LLQQQLARQQ NQQLQQLPMT  780
QHHQQQLSGN SFSTDKLLNN FAAPSMMQSQ HMPSIQPQNQ HKPLTAIRSH SGLTEGDGPS  840
CSTSPSTNCQ MSPSNFLNRN QQGMAMLLGD SVAEPAHNLV QELQSKSDVW VKHEPPSSKG  900
PDHIKYKGTI TDQLEASSSG TSYCLDTSTI HQNYALPTFC LDGDVQSNPR SSLPFSANID  960
GLAPDTLLSR EYDSQKDLQN LLSNYGGTPR DIETELSTAA ISSQSFGAPN IPFKAGCSSD  1020
IPITDAGVLG NGSWANQAQR MRTYTKVQKR GSVGRCIDVN RYKGYDELRH DLARMFGIEG  1080
QLEDPHRTDW KLVYVDHENE ILLVGDDPWE EFVSCVQSIK ILSSVEVQQM SLDGDLGNIP  1140
VPNQASSGTH SGNA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-172	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). 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	Pbr027725.1

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_009337178.1	0.0	PREDICTED: auxin response factor 7
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A498KLI9	0.0	A0A498KLI9_MALDO; Auxin response factor
STRING	XP_009337178.1	0.0	(Pyrus x bretschneideri)

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

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]