PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

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: 1030aa MW: 114423 Da PI: 6.1906

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gh_D05G1792	genome	NAU-NBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.1	1.5e-22	201	302	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_D05G1792 201 FCKTLTASDTSTHGGFSVPRRAAEKLfpqldyTMQPPS-QELVMRDIHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSILFIRHA-IKSQL 296 99*******************99999555544.59*********************************************9544.44457 PP EEEEE- CS B3 93 vvkvfr 98 +v+++ Gh_D05G1792 297 LVGIRH 302 888875 PP
2	Auxin_resp	112	5.9e-37	328	411	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aa+aa+++++F+++YnPr+++seFv++++k+ k+++ ++vs+GmRf m+fete+s +rr++Gt+vg+sdldp+rWp+SkWr+L+ Gh_D05G1792 328 AAQAAANRTPFTIFYNPRSCPSEFVIPMAKYCKSVYaTQVSAGMRFGMMFETEESGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 411 789******************************989******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-44	189	330	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.6E-38	194	316	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.56E-22	200	301	No hit	No description
SMART	SM01019	8.4E-21	201	304	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.167	201	304	IPR003340	B3 DNA binding domain
Pfam	PF02362	7.3E-20	201	302	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.2E-32	328	411	IPR010525	Auxin response factor
PROSITE profile	PS51745	22.554	911	995	IPR000270	PB1 domain
SuperFamily	SSF54277	2.49E-8	925	990	No hit	No description
Pfam	PF02309	2.3E-7	956	997	IPR033389	AUX/IAA domain

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: 1030 aa Download sequence Send to blast
MGYLFLIIFQ AEVFTSEHVN VESLLCVILV RVDCKASLKG TSLLEDTPVR VMGSFVEEKM 60 KTGVFGNGWA EATLLEEMKL LKEMQHQSGF RKAINSELWH ACAGPLVSLP QVGNLVYYFP 120 QGHSEQQVSV STKRMMTSQV PSYPNLQSQL MCQVHNVTLH ADTETDEVYA QMSLQPVNSE 180 KDVFNIPDFG VNPNKHPNEI FCKTLTASDT STHGGFSVPR RAAEKLFPQL DYTMQPPSQE 240 LVMRDIHDNT WTFRHIYRGQ PKRHLLTTGW SLFVGSKRLR AGDSILFIRH AIKSQLLVGI 300 RHANRHQATL PSSVLSADSM HIGVLAAAAQ AAANRTPFTI FYNPRSCPSE FVIPMAKYCK 360 SVYATQVSAG MRFGMMFETE ESGKRRYMGT IVGISDLDPL RWPGSKWRNL QVEWDEPGCH 420 DKQNRISPWE VETPESLFIF PSINSGLKRP YPWILGKLMV VILIGLHFAT FFDTCIFLFF 480 VLTGAESEWG NLINRPLLQF PENGSGNLPY PISNSYSKQL MKMMLKPHLV NHPGTFSSTS 540 QQISAAKGSP LNEMKNVQYT SNQEPQLMQS ENLLIEKPNP SQLALDQPDP INSNLLKINA 600 NGNPHPANEF EGQTQARCNN KKLKSEPEHS TDQLSQLNST LECTEEKLVA NTISPTICNK 660 LSFPNNNQTP SQLQNNPCPI QSQFEPSLLQ AHQMQVSQAD ISSLSSYLPF FNTDEWATIL 720 PSCQSIAGVY GSPGPIPLVG LQDSSAAFPE ATNPTLTTRS EVTWDSQLYN CRSSSQANEL 780 CSFAQEDPCS FNSGGIRDLS DDSNSKSGIY SCFSNNGSTV IDPSVSNVIL EELCSLKDAK 840 FQKPSDSLVG NFSCSQDVQS QITSASLADS RVFSRQDLPD SSGVTSSSNV DFDENGLLQK 900 TSWQQITPRL RTYTKVQKAG SVGRSIDVTS YKNYDKLLSA IECMFGLKGL LKDPRGSGWK 960 LVYVDHENDV LLVGDDPWEQ FVGCVRCIRI LSPTEVQQMS EEGMKLLNRV GSTVQGPISE 1020 VCNAPPKNEP

Sequence ? help Back to Top

Protein Sequence Length: 1030 aa Download sequence Send to blast

MGYLFLIIFQ AEVFTSEHVN VESLLCVILV RVDCKASLKG TSLLEDTPVR VMGSFVEEKM  60
KTGVFGNGWA EATLLEEMKL LKEMQHQSGF RKAINSELWH ACAGPLVSLP QVGNLVYYFP  120
QGHSEQQVSV STKRMMTSQV PSYPNLQSQL MCQVHNVTLH ADTETDEVYA QMSLQPVNSE  180
KDVFNIPDFG VNPNKHPNEI FCKTLTASDT STHGGFSVPR RAAEKLFPQL DYTMQPPSQE  240
LVMRDIHDNT WTFRHIYRGQ PKRHLLTTGW SLFVGSKRLR AGDSILFIRH AIKSQLLVGI  300
RHANRHQATL PSSVLSADSM HIGVLAAAAQ AAANRTPFTI FYNPRSCPSE FVIPMAKYCK  360
SVYATQVSAG MRFGMMFETE ESGKRRYMGT IVGISDLDPL RWPGSKWRNL QVEWDEPGCH  420
DKQNRISPWE VETPESLFIF PSINSGLKRP YPWILGKLMV VILIGLHFAT FFDTCIFLFF  480
VLTGAESEWG NLINRPLLQF PENGSGNLPY PISNSYSKQL MKMMLKPHLV NHPGTFSSTS  540
QQISAAKGSP LNEMKNVQYT SNQEPQLMQS ENLLIEKPNP SQLALDQPDP INSNLLKINA  600
NGNPHPANEF EGQTQARCNN KKLKSEPEHS TDQLSQLNST LECTEEKLVA NTISPTICNK  660
LSFPNNNQTP SQLQNNPCPI QSQFEPSLLQ AHQMQVSQAD ISSLSSYLPF FNTDEWATIL  720
PSCQSIAGVY GSPGPIPLVG LQDSSAAFPE ATNPTLTTRS EVTWDSQLYN CRSSSQANEL  780
CSFAQEDPCS FNSGGIRDLS DDSNSKSGIY SCFSNNGSTV IDPSVSNVIL EELCSLKDAK  840
FQKPSDSLVG NFSCSQDVQS QITSASLADS RVFSRQDLPD SSGVTSSSNV DFDENGLLQK  900
TSWQQITPRL RTYTKVQKAG SVGRSIDVTS YKNYDKLLSA IECMFGLKGL LKDPRGSGWK  960
LVYVDHENDV LLVGDDPWEQ FVGCVRCIRI LSPTEVQQMS EEGMKLLNRV GSTVQGPISE  1020
VCNAPPKNEP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	54	436	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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JX577731	8e-62	JX577731.1 Gossypium hirsutum clone NBRI_GE9609 microsatellite sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012444848.1	0.0	PREDICTED: auxin response factor 5 isoform X2
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A0D2TMS8	0.0	A0A0D2TMS8_GOSRA; 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]