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

MDP0000211459

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: 897aa MW: 98618.1 Da PI: 5.7457

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000211459	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.9	1.1e-24	140	241	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 f+k+lt sd++++g +++p++ ae+ ++++ + ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD+v+F ++++ MDP0000211459 140 FCKTLTASDTSTHGGFSVPRRAAEKLfppldftMQPP-T-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSVFVGAKRLRAGDSVLFI--RDEK 231 99*******************999*954444.4.48********************************************..4577 PP E..EEEEE-S CS B3 90 felvvkvfrk 99 +l+++v+r+ MDP0000211459 232 SQLLIGVRRA 241 778**997 PP
2	Auxin_resp	112.9	3.1e-37	266	349	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaas++s F+++YnPra++seFv++++ ++ka++ +++s+GmRf m+fete+s +rr++Gt+vg+ dldp+rWp+SkWr+L+ MDP0000211459 266 AAHAASNRSSFTIFYNPRACPSEFVIPLATFQKAVYgTQLSIGMRFGMMFETEESGKRRYMGTIVGIXDLDPLRWPGSKWRNLQ 349 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.32E-47	128	269	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	6.9E-42	132	254	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.30E-23	139	240	No hit	No description
Pfam	PF02362	2.2E-22	140	241	IPR003340	B3 DNA binding domain
SMART	SM01019	7.9E-25	140	242	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.155	140	242	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.6E-32	266	349	IPR010525	Auxin response factor
SuperFamily	SSF54277	3.34E-9	775	862	No hit	No description
Pfam	PF02309	1.4E-9	781	869	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.219	783	867	IPR000270	PB1 domain

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: 897 aa Download sequence Send to blast
MMGSVEEKLK TGCLLDEMKL LKELQDHSGS RKAINSELWH ACAGPLVCLP QVGSLSYYFP 60 QGHSEQVAVS TKRTATSQIP NYPNLPSQLL CQVQNVTLHA DKETDEIYAQ MILKPVNSEK 120 DVFPVSDFRM KPSKHPSEFF CKTLTASDTS THGGFSVPRR AAEKLFPPLD FTMQPPTQEL 180 VVRDLHDNTW TFRHIYRGQP KRHLLTTGWS VFVGAKRLRA GDSVLFIRDE KSQLLIGVRR 240 ANRQQTTLPS SVLSADSMHI GVLAAAAHAA SNRSSFTIFY NPRACPSEFV IPLATFQKAV 300 YGTQLSIGMR FGMMFETEES GKRRYMGTIV GIXDLDPLRW PGSKWRNLQV EWDEPGCCDK 360 QNRVSSWEIE TPESLFIFPS LTSSLKRPMH SGFLGAETEW GNMIKRPFIR VPEIGNGNXX 420 PYPISNLCSE QLVNMLMKPQ LANHAGTXAA LQRESASNAD SVVDMKAMYA KINQKNLADG 480 VNANAPSHEL PPGRLNVAAK FGSQTPVGNG TEKTKLEPEF SADQLSQLNS VGHGIEDKLA 540 TGFASPYSXV NQLTFANQNQ DAAQLQTSPR PMQPPLESLL FHSQTDLPHS DFNGMNSSLP 600 FLDNDECMFY SSCQSFSGAL RSPGPLSAFG LQESSAVLTE ANNSSLTSIG QDMWDNTLIN 660 SSSLRDLSDE SNNQSGIYGC PSIDVGSCLS TVVDPSVSST ILNDFSTLKN SNFQNSSDCL 720 VRNLSSSQDL QSQITSASLG DSQAFSRXDL ADXSGGTSSS NVDLDESSLL KNSSWHKVVA 780 PVRTYTKVQK TGSVGRSIDV TNFKNYEELC SAIECMFGLK GLLNDPRGSG WKLVYVDYEN 840 DVLLVGDDPW EEFVGCVRCI RILSPTEVQQ MSEEGMKLLN SAAMQGMNGT MSEXGRP

Sequence ? help Back to Top

Protein Sequence Length: 897 aa Download sequence Send to blast

MMGSVEEKLK TGCLLDEMKL LKELQDHSGS RKAINSELWH ACAGPLVCLP QVGSLSYYFP  60
QGHSEQVAVS TKRTATSQIP NYPNLPSQLL CQVQNVTLHA DKETDEIYAQ MILKPVNSEK  120
DVFPVSDFRM KPSKHPSEFF CKTLTASDTS THGGFSVPRR AAEKLFPPLD FTMQPPTQEL  180
VVRDLHDNTW TFRHIYRGQP KRHLLTTGWS VFVGAKRLRA GDSVLFIRDE KSQLLIGVRR  240
ANRQQTTLPS SVLSADSMHI GVLAAAAHAA SNRSSFTIFY NPRACPSEFV IPLATFQKAV  300
YGTQLSIGMR FGMMFETEES GKRRYMGTIV GIXDLDPLRW PGSKWRNLQV EWDEPGCCDK  360
QNRVSSWEIE TPESLFIFPS LTSSLKRPMH SGFLGAETEW GNMIKRPFIR VPEIGNGNXX  420
PYPISNLCSE QLVNMLMKPQ LANHAGTXAA LQRESASNAD SVVDMKAMYA KINQKNLADG  480
VNANAPSHEL PPGRLNVAAK FGSQTPVGNG TEKTKLEPEF SADQLSQLNS VGHGIEDKLA  540
TGFASPYSXV NQLTFANQNQ DAAQLQTSPR PMQPPLESLL FHSQTDLPHS DFNGMNSSLP  600
FLDNDECMFY SSCQSFSGAL RSPGPLSAFG LQESSAVLTE ANNSSLTSIG QDMWDNTLIN  660
SSSLRDLSDE SNNQSGIYGC PSIDVGSCLS TVVDPSVSST ILNDFSTLKN SNFQNSSDCL  720
VRNLSSSQDL QSQITSASLG DSQAFSRXDL ADXSGGTSSS NVDLDESSLL KNSSWHKVVA  780
PVRTYTKVQK TGSVGRSIDV TNFKNYEELC SAIECMFGLK GLLNDPRGSG WKLVYVDYEN  840
DVLLVGDDPW EEFVGCVRCI RILSPTEVQQ MSEEGMKLLN SAAMQGMNGT MSEXGRP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	374	1	392	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.8554	0.0	bud\| fruit\| stem

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: In early embryo and during organ development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant with a lower expression in leaves. Detected in embryo axis, provascular tissues, procambium and some differentiated vascular regions of mature organs. {ECO:0000269\|PubMed:10476078}.

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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

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_008357134.2	0.0	auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A498JBE7	0.0	A0A498JBE7_MALDO; Auxin response factor
STRING	XP_008357134.1	0.0	(Malus domestica)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8991	32	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	MDP0000211459

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]