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

CA04g23050

Organism

Capsicum annuum

Taxonomic ID

4072

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Capsiceae; Capsicum

Family

ARF

Protein Properties

Length: 938aa MW: 103204 Da PI: 5.0991

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
CA04g23050	genome	PEP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.5	1.5e-24	148	249	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 f+k+lt sd++++g +++p++ ae+ ++++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv a++L++gD+v+F ++++ +l+ CA04g23050 148 FCKTLTASDTSTHGGFSVPRRAAEKLfppldySMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGAKRLRAGDSVLFI--RDEKSQLL 243 99*******************999*9555554.49**********************************************..45677789 PP EEEE-S CS B3 94 vkvfrk 99 ++v+r+ CA04g23050 244 LGVRRA 249 999997 PP
2	Auxin_resp	116.2	2.9e-38	274	357	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv+++ k++k+++ +++svGmRf m+fete+s +rr++Gt+ g+sd+dp+rWp+SkWr+L+ CA04g23050 274 AAHAAANRSTFTIFYNPRACPSEFVIPLTKYRKSVYsTQLSVGMRFGMMFETEESGKRRYMGTIGGISDVDPLRWPGSKWRCLQ 357 79*******************************989*******************************************7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.4E-47	135	277	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.9E-42	141	262	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.30E-22	147	248	No hit	No description
PROSITE profile	PS50863	13.211	148	250	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.4E-22	148	249	IPR003340	B3 DNA binding domain
SMART	SM01019	2.7E-24	148	250	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.0E-33	274	357	IPR010525	Auxin response factor
Pfam	PF02309	2.9E-8	814	910	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	26.465	824	908	IPR000270	PB1 domain
SuperFamily	SSF54277	5.43E-9	843	903	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:0009733	Biological Process	response to auxin
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: 938 aa Download sequence Send to blast
MGSAEEKSKP GSLVSGGHTL LEEMKLLKEM QDHTGARKLI NSELWHACAG PLVTLPQVGS 60 LVYYFPQGHS EQVAVSTNRT ATSQIPNYPN LAPQLLCQVH NVTLHADKET DEIYAQMSLQ 120 PVNSVSFRDV FPIPDFGLKP NKHPTEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYS 180 MQPPTQELVV RDLHDNTWTF RHIYRGQPKR HLLTTGWSMF VGAKRLRAGD SVLFIRDEKS 240 QLLLGVRRAN RQQTSLPSSV LSADSMHIGV LAAAAHAAAN RSTFTIFYNP RACPSEFVIP 300 LTKYRKSVYS TQLSVGMRFG MMFETEESGK RRYMGTIGGI SDVDPLRWPG SKWRCLQVEW 360 DEPGCGDKQS RVSPWEVETP ESLFIFPSLT AGLKRPYQST FLGAQPEWDS LMHRPFMRVP 420 ENVYGDLQSS SISNLWSEQL MKMLVRPPGV TGLQCGIPTV QDIKVVLPQE AQRNVIQAAG 480 NLKPDLTTVE ATPAQSETNS EVILNQPGVV NSISSMQAKS QPPEKVGIDT VGKSSEQVKE 540 TSTSSGKLDQ FESVEQCTED KVTVKPASTP NLPTDASATA SNHNSLSQLQ ASPWLIQAQL 600 ESQIPPNTQI YSAGSNNILH CSTNNEWNPS SVQSAAGLLR CPVSTSTLTK HDNSFILPDT 660 VGTGLAPIGQ DLWDHQLNDV KCFSQTNLPV PLDITNMQFL PDSYGFKDLS EESHNQSDIY 720 SCLNFDSNSG STVIDNSVSS TVLDEFCTLK HTDFQNPSDF LLGNISSSQD VQSQITSASL 780 ADSQNFSVQE FADNSGGASS SNVNFDECNL LQNNSWQQVA PRVRTYTKIQ KAGSVGRSID 840 VSGFRTYDEL RAEIERMFGL EGLLNDSRGS GWKLVYVDFE NDVLLVGDDP WEEFVGCVRC 900 IRILSPTEVQ QMGEEGMQLL NSAGLQGING STSEYPN*

Sequence ? help Back to Top

Protein Sequence Length: 938 aa Download sequence Send to blast

MGSAEEKSKP GSLVSGGHTL LEEMKLLKEM QDHTGARKLI NSELWHACAG PLVTLPQVGS  60
LVYYFPQGHS EQVAVSTNRT ATSQIPNYPN LAPQLLCQVH NVTLHADKET DEIYAQMSLQ  120
PVNSVSFRDV FPIPDFGLKP NKHPTEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYS  180
MQPPTQELVV RDLHDNTWTF RHIYRGQPKR HLLTTGWSMF VGAKRLRAGD SVLFIRDEKS  240
QLLLGVRRAN RQQTSLPSSV LSADSMHIGV LAAAAHAAAN RSTFTIFYNP RACPSEFVIP  300
LTKYRKSVYS TQLSVGMRFG MMFETEESGK RRYMGTIGGI SDVDPLRWPG SKWRCLQVEW  360
DEPGCGDKQS RVSPWEVETP ESLFIFPSLT AGLKRPYQST FLGAQPEWDS LMHRPFMRVP  420
ENVYGDLQSS SISNLWSEQL MKMLVRPPGV TGLQCGIPTV QDIKVVLPQE AQRNVIQAAG  480
NLKPDLTTVE ATPAQSETNS EVILNQPGVV NSISSMQAKS QPPEKVGIDT VGKSSEQVKE  540
TSTSSGKLDQ FESVEQCTED KVTVKPASTP NLPTDASATA SNHNSLSQLQ ASPWLIQAQL  600
ESQIPPNTQI YSAGSNNILH CSTNNEWNPS SVQSAAGLLR CPVSTSTLTK HDNSFILPDT  660
VGTGLAPIGQ DLWDHQLNDV KCFSQTNLPV PLDITNMQFL PDSYGFKDLS EESHNQSDIY  720
SCLNFDSNSG STVIDNSVSS TVLDEFCTLK HTDFQNPSDF LLGNISSSQD VQSQITSASL  780
ADSQNFSVQE FADNSGGASS SNVNFDECNL LQNNSWQQVA PRVRTYTKIQ KAGSVGRSID  840
VSGFRTYDEL RAEIERMFGL EGLLNDSRGS GWKLVYVDFE NDVLLVGDDP WEEFVGCVRC  900
IRILSPTEVQ QMGEEGMQLL NSAGLQGING STSEYPN*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	19	382	32	392	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). 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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HM195248	0.0	HM195248.1 Solanum lycopersicum auxin response factor 5 (ARF5) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016568464.1	0.0	PREDICTED: auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1U8GK35	0.0	A0A1U8GK35_CAPAN; Auxin response factor
TrEMBL	A0A2G2ZSE7	0.0	A0A2G2ZSE7_CAPAN; Auxin response factor
STRING	Solyc04g081240.2.1	0.0	(Solanum lycopersicum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA5859	23	34

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

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]