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

MDP0000876321

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1150aa MW: 128483 Da PI: 6.833

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000876321	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	69.2	5.7e-22	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+lt sd++++g +++p++ ae++ +++++ ++l+ +d++ W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ MDP0000876321 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVAKDLHDSAWTFRHIYRGQPKRHLLTTGWSIFVSTKRLFAGDSVLFI--RDEKS 218 99***************************9445444.38**********************************************..45677 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 +l+++++r+ MDP0000876321 219 QLLLGIRRA 227 789999997 PP
2	Auxin_resp	124.2	9.2e-41	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFvv+++k++ka++++vs+GmRf+m+fete++ rr++Gt++g+sdldpvrW++S+Wr+L+ MDP0000876321 252 AAHAAANNSPFTIFYNPRASPSEFVVPLAKYNKAMYTQVSLGMRFRMMFETEEAGVRRYMGTITGISDLDPVRWKGSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	5.1E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.5E-40	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.88E-19	125	226	No hit	No description
Pfam	PF02362	3.0E-20	126	227	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.125	126	228	IPR003340	B3 DNA binding domain
SMART	SM01019	9.9E-22	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	8.9E-36	252	334	IPR010525	Auxin response factor
Pfam	PF02309	1.3E-8	1019	1107	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.519	1022	1115	IPR000270	PB1 domain
SuperFamily	SSF54277	1.37E-8	1035	1100	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: 1150 aa Download sequence Send to blast
MKVPTNGFME NSGEGEQKRI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDFIPNYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYEKEALL ASDMGLKQSK 120 QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELVAKD LHDSAWTFRH 180 IYRGQPKRHL LTTGWSIFVS TKRLFAGDSV LFIRDEKSQL LLGIRRANRQ QPAICSSVIS 240 SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVVPLA KYNKAMYTQV SLGMRFRMMF 300 ETEEAGVRRY MGTITGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVVTP 360 FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWLGDE FGMKNSPSSV FPGLSLMQWM 420 NMQQNNQFSA SQSGFFPSMV PPTGLQNNLG TDDPSKLLNF QAPVLSAPGL QSNKSAPQNQ 480 ASQMQQPNVT WAQQQQLQQL MHNPMSQQQQ SNPQQQQLHQ LLNSSANQHQ QNHPQQQLQQ 540 LLQTPTNQQL QNYSHQQQRE PQQQQDPQNL LQHQQLHQQQ PQRQQHQQQQ LSQPNPVNNG 600 SVAPNQVPGQ NLQQPVMFSQ HQQQQLLTGN TQSQQAVHSS SKNSFQVPTG QQNSQLQQQQ 660 LEPQPGVLQR QQQVSQLQPS PQQFLQQNMS QKVQQQPQVQ QSSQQGISEQ QLQLQLLQKF 720 QQQQQPQLLS PSSSLLQPQL LQQQLAHQQN QQLQQLPMTQ HHQQQLSGNS FSTDRLLNNF 780 AAPSVMQSHH MPSIQPQNQH KPLTAIRSHS GLTEGDGPSC STSPSTNNCQ MSPSKYSNRN 840 QQGTAMLLGD SVAEPAHNLV QELQSKSDIR IKNELPSSKG PDQIKYKGTI TDQLEASSSG 900 TSYCLDASTI HQNYALPTFC LDGDVQSNPR SSLPFSANID GLAPDTLLSR GYDSQKDLQN 960 LLSNYGGTPR DIEIELSTAA ISSQSFGAPN LPFKTGCSSD IPITDTGVLG NGLWANQAQR 1020 MRTYTKVQKR GSVGRCIDVT RYKGYDELRH DLARMFGIEG QLEDPHRTDW KLVYVDHEND 1080 ILLVGDDPWE EFVSCVQSIK ILSSVEVRQM SLDGDLGNIP VPNQASSGTD SGNAWRPQYD 1140 DNSAASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1150 aa Download sequence Send to blast

MKVPTNGFME NSGEGEQKRI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDFIPNYPNL PSKLICMLHN VTLHADTETD EVYAQMTLQP VNKYEKEALL ASDMGLKQSK  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELVAKD LHDSAWTFRH  180
IYRGQPKRHL LTTGWSIFVS TKRLFAGDSV LFIRDEKSQL LLGIRRANRQ QPAICSSVIS  240
SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPSEFVVPLA KYNKAMYTQV SLGMRFRMMF  300
ETEEAGVRRY MGTITGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVVTP  360
FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWLGDE FGMKNSPSSV FPGLSLMQWM  420
NMQQNNQFSA SQSGFFPSMV PPTGLQNNLG TDDPSKLLNF QAPVLSAPGL QSNKSAPQNQ  480
ASQMQQPNVT WAQQQQLQQL MHNPMSQQQQ SNPQQQQLHQ LLNSSANQHQ QNHPQQQLQQ  540
LLQTPTNQQL QNYSHQQQRE PQQQQDPQNL LQHQQLHQQQ PQRQQHQQQQ LSQPNPVNNG  600
SVAPNQVPGQ NLQQPVMFSQ HQQQQLLTGN TQSQQAVHSS SKNSFQVPTG QQNSQLQQQQ  660
LEPQPGVLQR QQQVSQLQPS PQQFLQQNMS QKVQQQPQVQ QSSQQGISEQ QLQLQLLQKF  720
QQQQQPQLLS PSSSLLQPQL LQQQLAHQQN QQLQQLPMTQ HHQQQLSGNS FSTDRLLNNF  780
AAPSVMQSHH MPSIQPQNQH KPLTAIRSHS GLTEGDGPSC STSPSTNNCQ MSPSKYSNRN  840
QQGTAMLLGD SVAEPAHNLV QELQSKSDIR IKNELPSSKG PDQIKYKGTI TDQLEASSSG  900
TSYCLDASTI HQNYALPTFC LDGDVQSNPR SSLPFSANID GLAPDTLLSR GYDSQKDLQN  960
LLSNYGGTPR DIEIELSTAA ISSQSFGAPN LPFKTGCSSD IPITDTGVLG NGLWANQAQR  1020
MRTYTKVQKR GSVGRCIDVT RYKGYDELRH DLARMFGIEG QLEDPHRTDW KLVYVDHEND  1080
ILLVGDDPWE EFVSCVQSIK ILSSVEVRQM SLDGDLGNIP VPNQASSGTD SGNAWRPQYD  1140
DNSAASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-173	20	355	51	388	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.24725	0.0	leaf

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_008337824.2	0.0	LOW QUALITY PROTEIN: auxin response factor 19-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A498HXG3	0.0	A0A498HXG3_MALDO; Auxin response factor
STRING	XP_008337824.1	0.0	(Malus domestica)

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	MDP0000876321

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]