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

Medtr1g024025.1

Common Name

MTR_1g024025

Organism

Medicago truncatula

Taxonomic ID

3880

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Medicago

Family

ARF

Protein Properties

Length: 1266aa MW: 141164 Da PI: 5.111

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Medtr1g024025.1	genome	Mt	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.5	6.2e-24	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae+ +++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++gD+v+F +++ Medtr1g024025.1 146 FCKTLTASDTSTHGGFSVPRRAAEKLfppldyTIQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSVLFI--RDE 236 99*******************999*9555555.49********************************************..457 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 + +l+v+v+r+ Medtr1g024025.1 237 KSQLRVGVRRA 247 7778**997 PP
2	Auxin_resp	112.8	3.2e-37	272	355	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++s+Fv++++k++k+++ +++s+GmRf m+fete+s +rr++Gt+vg+sd+dp+rWp+SkWr+++ Medtr1g024025.1 272 AAHAAANRSPFTIFYNPRACPSDFVIPLAKYRKSVYgTQLSAGMRFGMMFETEESGKRRYMGTIVGISDVDPLRWPGSKWRNIQ 355 79********************************9******************************************986 PP
3	Auxin_resp	36.3	2.5e-13	898	940	1	45
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRf 45 aahaa+++ +F+++YnPra+ s+Fv++++k + + ++svGmRf Medtr1g024025.1 898 AAHAAANRIPFTIFYNPRACLSDFVIPLAKSVYGT--QLSVGMRF 940 79************************9877665..9****9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.62E-46	136	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.4E-41	138	260	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.66E-23	145	246	No hit	No description
SMART	SM01019	6.3E-25	146	248	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.056	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.1E-21	146	247	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.0E-32	272	355	IPR010525	Auxin response factor
Pfam	PF02309	5.4E-11	743	841	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	23.746	754	838	IPR000270	PB1 domain
SuperFamily	SSF54277	6.57E-8	755	833	No hit	No description
Pfam	PF06507	1.1E-7	898	940	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 1266 aa Download sequence Send to blast
MASLDEKAKS VGGVVGGQTL VAEMKLLKEM QEHCGVRKTL NSELWHACAG PLVSLPQVGG 60 LVYYFPQGHS EQVAASTRRI ATSQIPNYPS LPSQLLCQVQ NVTLHADKET DEIYAQMTLQ 120 PLNSEKEVFP VSEFGLSKSK HPTEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYTIQ 180 PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG SKRLRAGDSV LFIRDEKSQL 240 RVGVRRANRQ QTTLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSDFVIPLA 300 KYRKSVYGTQ LSAGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WRNIQAEWDE 360 PGCGDKQNRV SVWEIETPES LFIFPSLTSS LKRPLQSGYL ENEWGTLIRR PFIKVPENGG 420 TVEISSSMQN LYQENMKMFY KPQVINNSGA FLPIMQQDYS PTRVPFQDMK STQALENPKV 480 HLSSTESIPN NTFNMHSLLK NDQPEKLQPL AKTDNSKLES EVLPDHIFDF PSFESCSNIE 540 KVNTANQLTY HNQNQSQNPL LAHTSPWTMQ QPQLESSMSH PQLIDMVQPD SSIVNSMLPQ 600 LDVDEWMMYS SCQPQVVNPS IPSMNQEVWD QYVKNFNLRD LSAESNNQSE ICVNVDASNS 660 VSTTVVDPST SNTIFDDFCS MKDKDFQHPQ DCMVGNLSSS QDGQSQITSA SLAESHAFSL 720 RDNSGGTSSS HVDFDESSFL QNNNSWKQVA APIRTYTKVQ KAGSVGRSID VTTFKNYEEL 780 IRAIECMFGL DGLLNDTKGS GWKLVYVDYE SDVLLVGDDP WEEFVGCVRC IRILSPSEVK 840 EMSEEGMKLL NSGALQGINV DEKSPLRVGV RRANRQQTTL PSSVLSADSM HIGVLAAAAH 900 AAANRIPFTI FYNPRACLSD FVIPLAKSVY GTQLSVGMRF GCLRPRNRAE WDEPGCGDKQ 960 NRLQPLAKTD NSKLESEVLP DHMFDFPSFE SCSNIEKLES SMSHPQLIDM VQPDSSIANS 1020 MLPQLDVDEW MMYSSCQPQV VNPSIPSMNQ EMWDQYVKNF NLRDLSAESN NQSEICVNVD 1080 ATNSVSTTMV DPSTTNTIFD EFCSMKDKDF QHPQDCAVGN LSSSQDGQSQ ITSASLAESH 1140 AFSLRDNSGG TSSSHVDFDE SIFLQNNNSW KQVAAPIRTY TKLEKAGSVG RSIDVTTFKN 1200 YEELIRAIEY MFGLDGLLND TKDDPWKEFV GCVRRIRILS PSEVKEMSEE GMKLLNSGAL 1260 QGINV*

Sequence ? help Back to Top

Protein Sequence Length: 1266 aa Download sequence Send to blast

MASLDEKAKS VGGVVGGQTL VAEMKLLKEM QEHCGVRKTL NSELWHACAG PLVSLPQVGG  60
LVYYFPQGHS EQVAASTRRI ATSQIPNYPS LPSQLLCQVQ NVTLHADKET DEIYAQMTLQ  120
PLNSEKEVFP VSEFGLSKSK HPTEFFCKTL TASDTSTHGG FSVPRRAAEK LFPPLDYTIQ  180
PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSLFVG SKRLRAGDSV LFIRDEKSQL  240
RVGVRRANRQ QTTLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSDFVIPLA  300
KYRKSVYGTQ LSAGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WRNIQAEWDE  360
PGCGDKQNRV SVWEIETPES LFIFPSLTSS LKRPLQSGYL ENEWGTLIRR PFIKVPENGG  420
TVEISSSMQN LYQENMKMFY KPQVINNSGA FLPIMQQDYS PTRVPFQDMK STQALENPKV  480
HLSSTESIPN NTFNMHSLLK NDQPEKLQPL AKTDNSKLES EVLPDHIFDF PSFESCSNIE  540
KVNTANQLTY HNQNQSQNPL LAHTSPWTMQ QPQLESSMSH PQLIDMVQPD SSIVNSMLPQ  600
LDVDEWMMYS SCQPQVVNPS IPSMNQEVWD QYVKNFNLRD LSAESNNQSE ICVNVDASNS  660
VSTTVVDPST SNTIFDDFCS MKDKDFQHPQ DCMVGNLSSS QDGQSQITSA SLAESHAFSL  720
RDNSGGTSSS HVDFDESSFL QNNNSWKQVA APIRTYTKVQ KAGSVGRSID VTTFKNYEEL  780
IRAIECMFGL DGLLNDTKGS GWKLVYVDYE SDVLLVGDDP WEEFVGCVRC IRILSPSEVK  840
EMSEEGMKLL NSGALQGINV DEKSPLRVGV RRANRQQTTL PSSVLSADSM HIGVLAAAAH  900
AAANRIPFTI FYNPRACLSD FVIPLAKSVY GTQLSVGMRF GCLRPRNRAE WDEPGCGDKQ  960
NRLQPLAKTD NSKLESEVLP DHMFDFPSFE SCSNIEKLES SMSHPQLIDM VQPDSSIANS  1020
MLPQLDVDEW MMYSSCQPQV VNPSIPSMNQ EMWDQYVKNF NLRDLSAESN NQSEICVNVD  1080
ATNSVSTTMV DPSTTNTIFD EFCSMKDKDF QHPQDCAVGN LSSSQDGQSQ ITSASLAESH  1140
AFSLRDNSGG TSSSHVDFDE SIFLQNNNSW KQVAAPIRTY TKLEKAGSVG RSIDVTTFKN  1200
YEELIRAIEY MFGLDGLLND TKDDPWKEFV GCVRRIRILS PSEVKEMSEE GMKLLNSGAL  1260
QGINV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	19	965	32	392	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mtr.25092	0.0	root

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Medtr1g024025.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024631194.1	0.0	auxin response factor 5
Refseq	XP_024631195.1	0.0	auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A072VFI0	0.0	A0A072VFI0_MEDTR; Auxin response factor
STRING	XP_004499235.1	0.0	(Cicer arietinum)

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	Medtr1g024025.1
Entrez Gene	25482193

Publications ? help Back to Top
Young ND, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 2011. 480(7378): p. 520-4 [PMID:22089132] 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]