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_16408_BGI-A2_v1.0

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: 942aa MW: 104299 Da PI: 5.8817

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_16408_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	73.2	3.1e-23	141	242	1	98
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_16408_BGI-A2_v1.0 141 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldyTMQPPS-QELVMRDIHDNAWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAG 222 99*******************99999555544.59************************************** PP -EEEEEE-SSSEE..EEEEE- CS B3 78 DfvvFkldgrsefelvvkvfr 98 D+++F +++ ++ +l+v+++ Cotton_A_16408_BGI-A2_v1.0 223 DSILFIRQD-EKSQLLVGIRH 242 ****655.77778999986 PP
2	Auxin_resp	111.8	6.8e-37	268	351	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 aa+aa+++++F+++YnPr+++seFv++++k+ k+++ ++vs+GmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+L Cotton_A_16408_BGI-A2_v1.0 268 AAQAAANRTPFTIFYNPRSCPSEFVIPMAKYCKSVYaSQVSAGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNL 350 789******************************989******************************************9 PP Auxin_resp 83 k 83 + Cotton_A_16408_BGI-A2_v1.0 351 Q 351 7 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.66E-44	130	270	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	9.2E-39	134	256	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.05E-22	140	241	No hit	No description
Pfam	PF02362	9.6E-21	141	243	IPR003340	B3 DNA binding domain
SMART	SM01019	7.5E-21	141	244	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.76	141	244	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.0E-32	268	351	IPR010525	Auxin response factor
Pfam	PF02309	5.2E-10	820	909	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	23.673	823	907	IPR000270	PB1 domain
SuperFamily	SSF54277	3.43E-8	836	902	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: 942 aa Download sequence Send to blast
MKTGVFGNGW AEATLLEEMK LLKEMQHQSG SRKVINTELW HACAGPLVSL PQVGSLVYYF 60 PQGHSEQVSV STKRMMTSQV PNYPNIQSQL MCQVHNVTLN ADTETDEVYA QMSLQPVNSE 120 KDVFHIPHFG VNPNKHPNEI FCKTLTASDT STHGGFSVPR RAAEKLFPQL DYTMQPPSQE 180 LVMRDIHDNA WTFRHIYRGQ PKRHLLTTGW SLFVGSKRLR AGDSILFIRQ DEKSQLLVGI 240 RHANRHQAPL PSSVLSADSM HIGVLAAAAQ AAANRTPFTI FYNPRSCPSE FVIPMAKYCK 300 SVYASQVSAG MRFGMMFETE ESGKRRYMGT IVGISDLDPL RWPGSKWRNL QVEWDEPGCH 360 DKQNRVSPWE VETPESLFIF PSITSGLKRS YPWILGAESE WGNLINRPLL QFPENVSGNL 420 PSSISNSYSE QLMKMMLKPH LVNHPGTFAS TSQQISAAKG SPLKEMKNVQ YTSNQEPELM 480 QSENLLIEKP NPSQLALDQP DPINSNLLKI NANGNPHPAN EFEGQTQARS NNKKLKSEPE 540 HSNDQLSQLN STLECIEEKL AANTISPTIC NKLSFPNNNQ TPSQLQNNPC AIQSQFEPSL 600 IQAHQMQVSQ ADISSLSSYL PFFNTDEWAT ILPSCQSIAG VYGSPGPIPL VGLQDSSAAF 660 PEATNPTLTT RSEVTWDSQL YNCRSSSQAN ELCSFTQQDP CSFNSGGIRD LSDDSNSKSG 720 IYSCLSNGGS TVIDPSVSNV ILEELCSLKD AKFQKPSDSL VGNFSCSQDV QSQITSASLA 780 DSQVFSRQDL PDSSGVTSSS NVDFDENGLL HNTSWQHITA RVRTYTKVQK AGSVGRSIDV 840 TSYKNYDELL SAIECMFGLK GLLKDPRGSG WKLVYVDYEN DVLLVGDDPW EQFVGCVRCI 900 RILSPTEVQQ MSEEGMKLLN RVGSTVQGPI SEVCNAPPKN EP

Sequence ? help Back to Top

Protein Sequence Length: 942 aa Download sequence Send to blast

MKTGVFGNGW AEATLLEEMK LLKEMQHQSG SRKVINTELW HACAGPLVSL PQVGSLVYYF  60
PQGHSEQVSV STKRMMTSQV PNYPNIQSQL MCQVHNVTLN ADTETDEVYA QMSLQPVNSE  120
KDVFHIPHFG VNPNKHPNEI FCKTLTASDT STHGGFSVPR RAAEKLFPQL DYTMQPPSQE  180
LVMRDIHDNA WTFRHIYRGQ PKRHLLTTGW SLFVGSKRLR AGDSILFIRQ DEKSQLLVGI  240
RHANRHQAPL PSSVLSADSM HIGVLAAAAQ AAANRTPFTI FYNPRSCPSE FVIPMAKYCK  300
SVYASQVSAG MRFGMMFETE ESGKRRYMGT IVGISDLDPL RWPGSKWRNL QVEWDEPGCH  360
DKQNRVSPWE VETPESLFIF PSITSGLKRS YPWILGAESE WGNLINRPLL QFPENVSGNL  420
PSSISNSYSE QLMKMMLKPH LVNHPGTFAS TSQQISAAKG SPLKEMKNVQ YTSNQEPELM  480
QSENLLIEKP NPSQLALDQP DPINSNLLKI NANGNPHPAN EFEGQTQARS NNKKLKSEPE  540
HSNDQLSQLN STLECIEEKL AANTISPTIC NKLSFPNNNQ TPSQLQNNPC AIQSQFEPSL  600
IQAHQMQVSQ ADISSLSSYL PFFNTDEWAT ILPSCQSIAG VYGSPGPIPL VGLQDSSAAF  660
PEATNPTLTT RSEVTWDSQL YNCRSSSQAN ELCSFTQQDP CSFNSGGIRD LSDDSNSKSG  720
IYSCLSNGGS TVIDPSVSNV ILEELCSLKD AKFQKPSDSL VGNFSCSQDV QSQITSASLA  780
DSQVFSRQDL PDSSGVTSSS NVDFDENGLL HNTSWQHITA RVRTYTKVQK AGSVGRSIDV  840
TSYKNYDELL SAIECMFGLK GLLKDPRGSG WKLVYVDYEN DVLLVGDDPW EQFVGCVRCI  900
RILSPTEVQQ MSEEGMKLLN RVGSTVQGPI SEVCNAPPKN EP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	11	376	29	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017645543.1	0.0	PREDICTED: auxin response factor 5-like isoform X2
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A1U8PFI5	0.0	A0A1U8PFI5_GOSHI; Auxin response factor
STRING	Gorai.009G196100.1	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]