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

Gorai.010G157400.1

Common Name

B456_010G157400, LOC105774114

Organism

Gossypium raimondii

Taxonomic ID

29730

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: 741aa MW: 80888.9 Da PI: 6.0955

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.010G157400.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79	5.1e-25	150	251	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F Gorai.010G157400.1 150 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyN-QQRPSQELVAKDLHGSEWRFRHIYRGQPRRHLLTSGWSAFVNKKKLVSGDAVLFL-- 237 99**************************963.3445679********************************************.. PP SSSEE..EEEEE-S CS B3 86 grsefelvvkvfrk 99 + +++el+++v+r+ Gorai.010G157400.1 238 RGEDGELRLGVRRA 251 449999***996 PP
2	Auxin_resp	114.4	1e-37	276	357	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 ++ha+s+ksvF+++YnPras+s+Fv++v+k+ k l+ ++s+GmRfkm+fe ed++err sG+++g+sd++pvrWp+SkWr+L Gorai.010G157400.1 276 VVHAVSMKSVFSIYYNPRASSSDFVIPVHKFWKCLDPSFSIGMRFKMQFEAEDAAERRHSGVITGISDINPVRWPGSKWRCL 357 689******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.58E-41	143	256	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.8E-41	145	257	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.37E-22	148	250	No hit	No description
SMART	SM01019	2.7E-23	150	252	IPR003340	B3 DNA binding domain
Pfam	PF02362	9.1E-23	150	251	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.676	150	252	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.1E-33	276	357	IPR010525	Auxin response factor

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:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 741 aa Download sequence Send to blast
MGGLIDLNST EDDETPLSGS LSPSSSSASV LSAPGSGSSV CLELWHACAG PLISLPKRGN 60 VVVYFPQGHL EQVSDFSGVA AAYDLPSHVF CRVVDVKLHA EGATDEVYAQ VSLVPETEQS 120 EQKLEGGKTE ADGEEEDAET NIKSTTPHMF CKTLTASDTS THGGFSVPRR AAEDCFPPLD 180 YNQQRPSQEL VAKDLHGSEW RFRHIYRGQP RRHLLTSGWS AFVNKKKLVS GDAVLFLRGE 240 DGELRLGVRR AAQIKDGSSF PSSCSQQLNC SNFADVVHAV SMKSVFSIYY NPRASSSDFV 300 IPVHKFWKCL DPSFSIGMRF KMQFEAEDAA ERRHSGVITG ISDINPVRWP GSKWRCLMVR 360 WNDIDANRHG RVSPWEIEPS GSVSGSNSLI SPGSKRNRVG FPSGNSEFMV PDGIRASDFG 420 EFLWSQVLQV QENLGFNTLY DGSDSLNMHW SEIRRCIPGS IGSDFSAIGN IGRGSLVSPD 480 ISRKSVGFGE SFRFRKVLQG QEIFVSPPYR NGSTADENEE NDAFGLPDVG QLSGTRSGWS 540 SLMQRYNTHS RTRPFAPSTQ TSSPSSVLTF LQVSNPILNF SPIYNSNNQK RKQGVNKQSS 600 FHAPEMYEGK LFPSSASEHD SRARDLGSSD LFGHSIGSVQ LGDASPLAAQ PVFRTSQELD 660 SSCKSSCRLF GFSLTEGRHD ASKEEDVVQA TSSLAAGAFL PCVREEFHPK PSSVTDTVGS 720 NYTEASNLYS VRDMVLDIAL *

Sequence ? help Back to Top

Protein Sequence Length: 741 aa Download sequence Send to blast

MGGLIDLNST EDDETPLSGS LSPSSSSASV LSAPGSGSSV CLELWHACAG PLISLPKRGN  60
VVVYFPQGHL EQVSDFSGVA AAYDLPSHVF CRVVDVKLHA EGATDEVYAQ VSLVPETEQS  120
EQKLEGGKTE ADGEEEDAET NIKSTTPHMF CKTLTASDTS THGGFSVPRR AAEDCFPPLD  180
YNQQRPSQEL VAKDLHGSEW RFRHIYRGQP RRHLLTSGWS AFVNKKKLVS GDAVLFLRGE  240
DGELRLGVRR AAQIKDGSSF PSSCSQQLNC SNFADVVHAV SMKSVFSIYY NPRASSSDFV  300
IPVHKFWKCL DPSFSIGMRF KMQFEAEDAA ERRHSGVITG ISDINPVRWP GSKWRCLMVR  360
WNDIDANRHG RVSPWEIEPS GSVSGSNSLI SPGSKRNRVG FPSGNSEFMV PDGIRASDFG  420
EFLWSQVLQV QENLGFNTLY DGSDSLNMHW SEIRRCIPGS IGSDFSAIGN IGRGSLVSPD  480
ISRKSVGFGE SFRFRKVLQG QEIFVSPPYR NGSTADENEE NDAFGLPDVG QLSGTRSGWS  540
SLMQRYNTHS RTRPFAPSTQ TSSPSSVLTF LQVSNPILNF SPIYNSNNQK RKQGVNKQSS  600
FHAPEMYEGK LFPSSASEHD SRARDLGSSD LFGHSIGSVQ LGDASPLAAQ PVFRTSQELD  660
SSCKSSCRLF GFSLTEGRHD ASKEEDVVQA TSSLAAGAFL PCVREEFHPK PSSVTDTVGS  720
NYTEASNLYS VRDMVLDIAL *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-119	39	386	18	361	Auxin response factor 1
4ldy_B	1e-119	39	386	18	361	Auxin response factor 1
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected during gynoecium development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078, ECO:0000269\|PubMed:9409666}.

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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

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_012451921.1	0.0	PREDICTED: auxin response factor 3-like isoform X1
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A0D2STN2	0.0	A0A0D2STN2_GOSRA; Auxin response factor
STRING	Gorai.010G157400.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4924	28	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	Gorai.010G157400.1
Entrez Gene	105774114

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] 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] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] 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] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]