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

Gh_A05G1607

Organism

Gossypium hirsutum

Taxonomic ID

3635

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: 949aa MW: 105290 Da PI: 6.0568

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_A05G1607	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.6	1.2e-23	149	249	1	98
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 +++L++gD+++F ++++ +l Gh_A05G1607 149 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldyTMQPPS-QELVMRDIHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSILFI--RDEKSQL 243 99*******************99999555544.59**********************************************..4567778 PP EEEEE- CS B3 93 vvkvfr 98 +v+++ Gh_A05G1607 244 LVGIRH 249 999986 PP
2	Auxin_resp	111.7	7e-37	275	358	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aa+aa+++++F+++YnPr+++seFv++++k+ k+++ +++s+GmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+L+ Gh_A05G1607 275 AAQAAANRTPFTIFYNPRSCPSEFVIPMAKYCKSVYaTQISAGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 358 789******************************989******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.49E-44	138	277	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.1E-40	142	263	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.67E-22	148	248	No hit	No description
SMART	SM01019	3.2E-23	149	251	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.943	149	251	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.5E-21	149	250	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.2E-32	275	358	IPR010525	Auxin response factor
Pfam	PF02309	7.3E-10	828	916	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	23.673	830	914	IPR000270	PB1 domain
SuperFamily	SSF54277	3.53E-8	843	909	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: 949 aa Download sequence Send to blast
MGSFVEEKMK TGVFGNGWAE ATLLEEMKLL KEMQHQSGSR KVINTELWHA CAGPLVSLPQ 60 VGSLVYYFPQ GHSEQVWVST KRMMTSQVPN YPNIQSQLMC QVHNVTLNAD TETDEVYAQM 120 SLQPVNSEKD VFHIPHFGVN PNKHPNEIFC KTLTASDTST HGGFSVPRRA AEKLFPQLDY 180 TMQPPSQELV MRDIHDNTWT FRHIYRGQPK RHLLTTGWSL FVGSKRLRAG DSILFIRDEK 240 SQLLVGIRHA NRHQAPLPSS VLSADSMHIG VLAAAAQAAA NRTPFTIFYN PRSCPSEFVI 300 PMAKYCKSVY ATQISAGMRF GMMFETEESG KRRYMGTIVG ISDLDPLRWP GSKWRNLQVE 360 WDEPGCHDKQ NRVSPWEVET PESLFIFPSI TSGLKRSYPW ILGAESERGN LINRPLLQFP 420 ENVSGNLPSS ISNSYSEQLM KMMLKPHLVN HPGTFASTSQ QISAAKGSPL KEMKNVQYTS 480 NQEPELMQSE NLLIEKPNPS QLALDQPDPI NSNLLKINAN GNPHPANEFE GQTQARSNNK 540 KLKSEPEHST DQLSQLNSTL ECIEEKLAAN TISPTICNKL SFPNNNQTPS QLQNNPCAIQ 600 SQFEPSLIQA HQMQVSQADI SSLSSYLPFF NTNEWATILP SFQSIAGVYG SPGPIPLVGL 660 QDSSAAFPEA TNPTLTTRSE VTWDSQLYNC RSSSQANELC SFTQQDPCSF NSGGIRDLSD 720 DSNSKSGIYS CLSNGGSTVI DPSVSNVILE ELCSLKDAKF QKPSDSLVGN FSCSQDVQSQ 780 ITSASLADSR VFSRQDLPDS SGVTSSSNVD FDENGLLHNT SWQHITPRVR TYTKVQKAGS 840 VGRSIDVTSY KNYDELLSAI ECMFGLKGLL KDPRGSGWKL VYVDYENDVL LVGDDPWEQF 900 VGCVRCIRIL SPTEVQQMSE EGMKLLNRVG STVQGPISEV CNAPPKNEP

Sequence ? help Back to Top

Protein Sequence Length: 949 aa Download sequence Send to blast

MGSFVEEKMK TGVFGNGWAE ATLLEEMKLL KEMQHQSGSR KVINTELWHA CAGPLVSLPQ  60
VGSLVYYFPQ GHSEQVWVST KRMMTSQVPN YPNIQSQLMC QVHNVTLNAD TETDEVYAQM  120
SLQPVNSEKD VFHIPHFGVN PNKHPNEIFC KTLTASDTST HGGFSVPRRA AEKLFPQLDY  180
TMQPPSQELV MRDIHDNTWT FRHIYRGQPK RHLLTTGWSL FVGSKRLRAG DSILFIRDEK  240
SQLLVGIRHA NRHQAPLPSS VLSADSMHIG VLAAAAQAAA NRTPFTIFYN PRSCPSEFVI  300
PMAKYCKSVY ATQISAGMRF GMMFETEESG KRRYMGTIVG ISDLDPLRWP GSKWRNLQVE  360
WDEPGCHDKQ NRVSPWEVET PESLFIFPSI TSGLKRSYPW ILGAESERGN LINRPLLQFP  420
ENVSGNLPSS ISNSYSEQLM KMMLKPHLVN HPGTFASTSQ QISAAKGSPL KEMKNVQYTS  480
NQEPELMQSE NLLIEKPNPS QLALDQPDPI NSNLLKINAN GNPHPANEFE GQTQARSNNK  540
KLKSEPEHST DQLSQLNSTL ECIEEKLAAN TISPTICNKL SFPNNNQTPS QLQNNPCAIQ  600
SQFEPSLIQA HQMQVSQADI SSLSSYLPFF NTNEWATILP SFQSIAGVYG SPGPIPLVGL  660
QDSSAAFPEA TNPTLTTRSE VTWDSQLYNC RSSSQANELC SFTQQDPCSF NSGGIRDLSD  720
DSNSKSGIYS CLSNGGSTVI DPSVSNVILE ELCSLKDAKF QKPSDSLVGN FSCSQDVQSQ  780
ITSASLADSR VFSRQDLPDS SGVTSSSNVD FDENGLLHNT SWQHITPRVR TYTKVQKAGS  840
VGRSIDVTSY KNYDELLSAI ECMFGLKGLL KDPRGSGWKL VYVDYENDVL LVGDDPWEQF  900
VGCVRCIRIL SPTEVQQMSE EGMKLLNRVG STVQGPISEV CNAPPKNEP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	3	383	6	392	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Ghi.12466	0.0	boll

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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_016749043.1	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]