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

DCAR_022437

Organism

Daucus carota

Taxonomic ID

4039

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Apiineae; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus

Family

ARF

Protein Properties

Length: 940aa MW: 104025 Da PI: 5.4239

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
DCAR_022437	genome	ARS-USDA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.7	5.4e-24	146	247	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 a++Lk+gD v+F ++++ +l DCAR_022437 146 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldfSMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSMFVGAKRLKAGDAVLFI--RDEKSQL 240 99*******************999*9555544.49**********************************************..4566667 PP EEEEE-S CS B3 93 vvkvfrk 99 +++++r+ DCAR_022437 241 LLGLRRA 247 9999886 PP
2	Auxin_resp	116.5	2.3e-38	272	355	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++++F+++YnPra++seFv++++k++k+++ +++svGmRf m+fetedss+rr++Gt+v++sdld +rWp SkWr+L+ DCAR_022437 272 AAHAAANRTPFTIFYNPRACPSEFVIPLAKYRKSVYgTQLSVGMRFGMMFETEDSSKRRYMGTIVSISDLDAIRWPSSKWRNLQ 355 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	5.89E-46	133	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.5E-41	139	260	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.66E-22	145	246	No hit	No description
PROSITE profile	PS50863	13.211	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.9E-22	146	247	IPR003340	B3 DNA binding domain
SMART	SM01019	1.4E-22	146	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.6E-33	272	355	IPR010525	Auxin response factor
Pfam	PF02309	1.8E-9	823	914	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.228	827	911	IPR000270	PB1 domain
SuperFamily	SSF54277	7.36E-9	840	906	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: 940 aa Download sequence Send to blast
MSCVEDAHKP AGLINGAHTL LDEIRLLKEM QDHPGVKKPI SSELWHACAG PLVSLPQVGS 60 LVYYFPQGHS EQVAVSTNRT ATSHIPNYPN LPSQLLCQVH NVTLHADKET DEIYAQMSLQ 120 PVNSEKDVFP IPDLGLKTSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPQLDFSMQ 180 PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSMFVG AKRLKAGDAV LFIRDEKSQL 240 LLGLRRAKRQ QAALPSSVLS ADSMHIGVLA AAAHAAANRT PFTIFYNPRA CPSEFVIPLA 300 KYRKSVYGTQ LSVGMRFGMM FETEDSSKRR YMGTIVSISD LDAIRWPSSK WRNLQVEWDE 360 PMCGDKQNRV SPWEIETPES LFIFPTLTSS LKRPFQSGFL GTQNEWEMLN RPIMRVPEPI 420 NPDFSNLPIS GQWSEQLIKM LMKPQAAGYS GSLASAAHDS ANNGVPSQRT KFLTQATVDQ 480 KTQATEHMLT QAENCAQFHR IQPEGIDSNS LQSRLQERLQ SQNVIETKAP HISDEMTKPE 540 IAISPEQLHR FNSERQCSEN IAEIRQSNPN ILVNEPTHVS ESHNSAQLQS NSWLMQSQFN 600 SNPFQPSQIE AATLNALLPN LDNSEWISNS SNSQNISGCL RSPGSAGLFS ETTNPTLPSS 660 SHEMWDQQIN DSKPLSETSQ FQSSCPQDLC KAYSISSTYN LKNISEESNT QSDLYSCLNF 720 ETSNGGSTVL DPSVSVLDPS VSSTAIDEFC SFKSGHFQNP SAYLVNNFGS NQDLQSQITS 780 ASLAESQAFS LQEFPDSSGG ASSSNGEFDE SSLLQNSSWQ QVAPRVRTYT KIQKAGSVGR 840 SIDVSSFKNY DELCCEIERM FGLGGLLSDT RGSGWKLVYV DYENDVLLVG DDPWEEFVGC 900 VRCIRILSPS EVQQMGEEGM QYLNSTAAQG INGSEGGHA*

Sequence ? help Back to Top

Protein Sequence Length: 940 aa Download sequence Send to blast

MSCVEDAHKP AGLINGAHTL LDEIRLLKEM QDHPGVKKPI SSELWHACAG PLVSLPQVGS  60
LVYYFPQGHS EQVAVSTNRT ATSHIPNYPN LPSQLLCQVH NVTLHADKET DEIYAQMSLQ  120
PVNSEKDVFP IPDLGLKTSK HPSEFFCKTL TASDTSTHGG FSVPRRAAEK LFPQLDFSMQ  180
PPTQELVVRD LHDNTWTFRH IYRGQPKRHL LTTGWSMFVG AKRLKAGDAV LFIRDEKSQL  240
LLGLRRAKRQ QAALPSSVLS ADSMHIGVLA AAAHAAANRT PFTIFYNPRA CPSEFVIPLA  300
KYRKSVYGTQ LSVGMRFGMM FETEDSSKRR YMGTIVSISD LDAIRWPSSK WRNLQVEWDE  360
PMCGDKQNRV SPWEIETPES LFIFPTLTSS LKRPFQSGFL GTQNEWEMLN RPIMRVPEPI  420
NPDFSNLPIS GQWSEQLIKM LMKPQAAGYS GSLASAAHDS ANNGVPSQRT KFLTQATVDQ  480
KTQATEHMLT QAENCAQFHR IQPEGIDSNS LQSRLQERLQ SQNVIETKAP HISDEMTKPE  540
IAISPEQLHR FNSERQCSEN IAEIRQSNPN ILVNEPTHVS ESHNSAQLQS NSWLMQSQFN  600
SNPFQPSQIE AATLNALLPN LDNSEWISNS SNSQNISGCL RSPGSAGLFS ETTNPTLPSS  660
SHEMWDQQIN DSKPLSETSQ FQSSCPQDLC KAYSISSTYN LKNISEESNT QSDLYSCLNF  720
ETSNGGSTVL DPSVSVLDPS VSSTAIDEFC SFKSGHFQNP SAYLVNNFGS NQDLQSQITS  780
ASLAESQAFS LQEFPDSSGG ASSSNGEFDE SSLLQNSSWQ QVAPRVRTYT KIQKAGSVGR  840
SIDVSSFKNY DELCCEIERM FGLGGLLSDT RGSGWKLVYV DYENDVLLVG DDPWEEFVGC  900
VRCIRILSPS EVQQMGEEGM QYLNSTAAQG INGSEGGHA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	380	5	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}.

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_017257770.1	0.0	PREDICTED: auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A164VDX2	0.0	A0A164VDX2_DAUCS; Auxin response factor
STRING	XP_009778804.1	0.0	(Nicotiana sylvestris)

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

Link Out ? help Back to Top
Phytozome	DCAR_022437

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]