PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Cotton_A_27669_BGI-A2_v1.0

Common Name

F383_03094

Organism

Gossypium arboreum

Taxonomic ID

29729

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

ARF

Protein Properties

Length: 950aa MW: 104464 Da PI: 5.0477

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_27669_BGI-A2_v1.0	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.1	2e-24	154	255	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkeg 77 f+k+lt sd++++g +++p++ ae+ ++++++ ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++g Cotton_A_27669_BGI-A2_v1.0 154 FCKTLTASDTSTHGGFSVPRRAAEKLfpsldySMQPPT-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAG 235 99*******************999*9555554.49************************************** PP -EEEEEE-SSSEE..EEEEE-S CS B3 78 DfvvFkldgrsefelvvkvfrk 99 D+v+F ++++ +l+v+v+r+ Cotton_A_27669_BGI-A2_v1.0 236 DSVLFI--RDEKSQLLVGVRRA 255 **..4577778***97 PP
2	Auxin_resp	114.5	9.5e-38	280	363	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 aahaa+++s+F+++YnPra++seFv+++ +++k+++ ++vsvGmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+L Cotton_A_27669_BGI-A2_v1.0 280 AAHAAANRSPFTIFYNPRACPSEFVIPLPRYRKSVYgSQVSVGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNL 362 79********************************99******************************************9 PP Auxin_resp 83 k 83 + Cotton_A_27669_BGI-A2_v1.0 363 Q 363 7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.68E-47	141	283	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	4.0E-42	148	268	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.50E-22	153	254	No hit	No description
PROSITE profile	PS50863	13.183	154	256	IPR003340	B3 DNA binding domain
Pfam	PF02362	7.1E-22	154	255	IPR003340	B3 DNA binding domain
SMART	SM01019	4.6E-24	154	256	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.4E-32	280	363	IPR010525	Auxin response factor
Pfam	PF02309	2.7E-9	829	919	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.573	833	917	IPR000270	PB1 domain
SuperFamily	SSF54277	6.28E-9	835	912	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: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: 950 aa Download sequence Send to blast
MGSVVEEKIK QGGLVNVGAQ STLLEEMKLL KEMQDQSGSS FVGTRKAINS ELWHACAGPL 60 VSLPQVGSLV YYFPQGHSEQ VAVSTKRMAT SQIPNYPNLP SQLMCQVHNV TLHADRDTDE 120 IYAQMSLQPV NSEKDVFPIP DFGLKLSKHP NEFFCKTLTA SDTSTHGGFS VPRRAAEKLF 180 PSLDYSMQPP TQELVVRDLH DNTWTFRHIY RGQPKRHLLT TGWSLFVGSK RLRAGDSVLF 240 IRDEKSQLLV GVRRANRQQT TLPSSVLSAD SMHIGVLAAA AHAAANRSPF TIFYNPRACP 300 SEFVIPLPRY RKSVYGSQVS VGMRFGMMFE TEESGKRRYM GTIVGISDLD PLRWPGSKWR 360 NLQVEWDEPG CNDKQNRVSA WEIETPESLF IFPSLTSSLK RPLYPGFSGA ESEWGSLMKR 420 PLLQFPENGN GNLPYSMSNL CSEQLMKMML KPQLVNHPGI FASPLQQIAD VKIPPLEEMK 480 NLQSKSHPKP QVIQSENMLI ENQNLSHPVP DHPDPITSNM SKINANGNPH PANILTQAGT 540 GSSNEKLKLE SKHSAEQLTS TSECNEEKLV ASTVNTTMSN QLSFPTQPQI PLHVQNNPWS 600 IQSQLDSSVL QAHQMLVSQA DISTLNSFLP FSDTDEWTSN LSSCQPLSGA YKSPGPIPMV 660 GLQDSSAVFP VETDDSLTTV GEEIWDPKLN SCRVSSQADQ LASFTQQDPC SLNSGGVRDL 720 SDDSNNQSGI YSSCLNIDVS NGCSTVIDPF VSSAILDEFC SLKDADFQNP SDCLVGNFGS 780 CQDVQSQITS ASLADSQAFS RQDLPDSSGG NIDFDDSGLL QNNSWKQTAP RVRTYTKVQK 840 AGSVGRSIDV TSFKNYDELI SAIECMFGLK GLLDDPRGSG WKLVYVDYEN DVLLVGDDPW 900 EEFVGCVRCI RILSPTEVQQ MSEEGMKLLN SAATVQGING SNSDGSNANA

Sequence ? help Back to Top

Protein Sequence Length: 950 aa Download sequence Send to blast

MGSVVEEKIK QGGLVNVGAQ STLLEEMKLL KEMQDQSGSS FVGTRKAINS ELWHACAGPL  60
VSLPQVGSLV YYFPQGHSEQ VAVSTKRMAT SQIPNYPNLP SQLMCQVHNV TLHADRDTDE  120
IYAQMSLQPV NSEKDVFPIP DFGLKLSKHP NEFFCKTLTA SDTSTHGGFS VPRRAAEKLF  180
PSLDYSMQPP TQELVVRDLH DNTWTFRHIY RGQPKRHLLT TGWSLFVGSK RLRAGDSVLF  240
IRDEKSQLLV GVRRANRQQT TLPSSVLSAD SMHIGVLAAA AHAAANRSPF TIFYNPRACP  300
SEFVIPLPRY RKSVYGSQVS VGMRFGMMFE TEESGKRRYM GTIVGISDLD PLRWPGSKWR  360
NLQVEWDEPG CNDKQNRVSA WEIETPESLF IFPSLTSSLK RPLYPGFSGA ESEWGSLMKR  420
PLLQFPENGN GNLPYSMSNL CSEQLMKMML KPQLVNHPGI FASPLQQIAD VKIPPLEEMK  480
NLQSKSHPKP QVIQSENMLI ENQNLSHPVP DHPDPITSNM SKINANGNPH PANILTQAGT  540
GSSNEKLKLE SKHSAEQLTS TSECNEEKLV ASTVNTTMSN QLSFPTQPQI PLHVQNNPWS  600
IQSQLDSSVL QAHQMLVSQA DISTLNSFLP FSDTDEWTSN LSSCQPLSGA YKSPGPIPMV  660
GLQDSSAVFP VETDDSLTTV GEEIWDPKLN SCRVSSQADQ LASFTQQDPC SLNSGGVRDL  720
SDDSNNQSGI YSSCLNIDVS NGCSTVIDPF VSSAILDEFC SLKDADFQNP SDCLVGNFGS  780
CQDVQSQITS ASLADSQAFS RQDLPDSSGG NIDFDDSGLL QNNSWKQTAP RVRTYTKVQK  840
AGSVGRSIDV TSFKNYDELI SAIECMFGLK GLLDDPRGSG WKLVYVDYEN DVLLVGDDPW  900
EEFVGCVRCI RILSPTEVQQ MSEEGMKLLN SAATVQGING SNSDGSNANA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	3	388	6	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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017619239.1	0.0	PREDICTED: auxin response factor 5-like isoform X1
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A0B0Q0F7	0.0	A0A0B0Q0F7_GOSAR; Auxin response factor
STRING	Gorai.002G124400.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46

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]