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

RrC8501_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

ARF

Protein Properties

Length: 834aa MW: 92323 Da PI: 6.5552

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC8501_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	60	4.2e-19	149	232	1	79
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDf 79 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+ RrC8501_p2 149 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDS 232 99***************************954.4444.48****************************************97 PP
2	Auxin_resp	119	3.8e-39	268	350	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+g+sdldpvrW++S+Wr+L+ RrC8501_p2 268 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 350 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	8.76E-40	139	271	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.6E-34	143	257	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.22E-17	148	242	No hit	No description
PROSITE profile	PS50863	10.109	149	258	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.0E-17	149	232	IPR003340	B3 DNA binding domain
SMART	SM01019	5.6E-16	149	244	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.3E-34	268	350	IPR010525	Auxin response factor
PROSITE profile	PS51745	23.609	766	834	IPR000270	PB1 domain
SuperFamily	SSF54277	1.67E-5	780	834	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:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0010311	Biological Process	lateral root formation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 834 aa Download sequence Send to blast
MPQIFDKASD FLHEYREKKA INSQLWHACA GPLVSLPPVG SLVVYFPQGH SEQVMVPKQQ 60 FFSVAASMQK QTDFIPNYPN LPSKLICLLH SVTLHADTET DEVYAQMTLQ PVNKLNLCLI 120 TQNVYQYDRE ALLASDMGLK INRQPTEFFC KTLTASDTST HGGFSVPRRA AEKIFPPLDF 180 SMQPPAQEIV AKDLHDTTWT FRHIYRGQPK RHLLTTGWSV FVSTKRLFAG DSKSQLTLGI 240 RRANRQTPTL SSSVISSDSM HIGILAAAAH ANANSSPFTI FFNPRASPSE FVVPLAKYNK 300 ALYAQVSLGM RFRMMFETED CGVRRYMGTV TGISDLDPVR WKGSQWRNLQ VMCSILIISS 360 ESFAEKAFVR LFEQVGWDES TAGDRPSRVS IWEIEPVITP FYICPPPFFR PKYPRQPGMP 420 DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLSQLQ QQLMLSNGLV SNDSARIAVS 480 AATGVAQQYP IIEKPAGTVV YASATTKSPL PQSNNSFMQP PQIQVSHHQQ QGYMNNNNKP 540 VVAAGRSQSG HIDGEAPSCS TSPSANNTGG HDNVSPTNFL SRNQQQGQAV SVSVPVPVPA 600 SDSVFERASN PVQQGMVNLK SATEQFKFKG AVTDQIDVTT VGTTYCPDVV GPGQQQQQQQ 660 QTFPLPSFGF DGDLQTHHPR NNLAYAGNLE AVNPDALYSQ KDFQNLVPNY GNAPRDIETE 720 LSSASQSFGI PSIPFKSGGS NEIGGINDSG IMNGGGIWPN QAQRMRTYTK VQKRGSVGRS 780 IDVTRYSGYE ELRHDLARMF GIEGQLEDPQ TSDWKLVYTD HENDILLVGD DPWE

Sequence ? help Back to Top

Protein Sequence Length: 834 aa Download sequence Send to blast

MPQIFDKASD FLHEYREKKA INSQLWHACA GPLVSLPPVG SLVVYFPQGH SEQVMVPKQQ  60
FFSVAASMQK QTDFIPNYPN LPSKLICLLH SVTLHADTET DEVYAQMTLQ PVNKLNLCLI  120
TQNVYQYDRE ALLASDMGLK INRQPTEFFC KTLTASDTST HGGFSVPRRA AEKIFPPLDF  180
SMQPPAQEIV AKDLHDTTWT FRHIYRGQPK RHLLTTGWSV FVSTKRLFAG DSKSQLTLGI  240
RRANRQTPTL SSSVISSDSM HIGILAAAAH ANANSSPFTI FFNPRASPSE FVVPLAKYNK  300
ALYAQVSLGM RFRMMFETED CGVRRYMGTV TGISDLDPVR WKGSQWRNLQ VMCSILIISS  360
ESFAEKAFVR LFEQVGWDES TAGDRPSRVS IWEIEPVITP FYICPPPFFR PKYPRQPGMP  420
DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLSQLQ QQLMLSNGLV SNDSARIAVS  480
AATGVAQQYP IIEKPAGTVV YASATTKSPL PQSNNSFMQP PQIQVSHHQQ QGYMNNNNKP  540
VVAAGRSQSG HIDGEAPSCS TSPSANNTGG HDNVSPTNFL SRNQQQGQAV SVSVPVPVPA  600
SDSVFERASN PVQQGMVNLK SATEQFKFKG AVTDQIDVTT VGTTYCPDVV GPGQQQQQQQ  660
QTFPLPSFGF DGDLQTHHPR NNLAYAGNLE AVNPDALYSQ KDFQNLVPNY GNAPRDIETE  720
LSSASQSFGI PSIPFKSGGS NEIGGINDSG IMNGGGIWPN QAQRMRTYTK VQKRGSVGRS  780
IDVTRYSGYE ELRHDLARMF GIEGQLEDPQ TSDWKLVYTD HENDILLVGD DPWE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-154	17	395	47	388	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). 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 ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	JN979484	0.0	JN979484.1 Brassica rapa subsp. pekinensis auxin response factor 19-2 (ARF19-2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013586633.1	0.0	PREDICTED: auxin response factor 19 isoform X1
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A103Y265	0.0	A0A103Y265_CYNCS; Auxin response factor
STRING	Lus10033635	0.0	(Linum usitatissimum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2629	26	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	0.0	auxin response factor 19

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290]