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

Carubv10008159m

Common Name

CARUB_v10008159mg

Organism

Capsella rubella

Taxonomic ID

81985

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1068aa MW: 118124 Da PI: 6.6006

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Carubv10008159m	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.2	3.2e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++ Carubv10008159m 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RD 215 99***************************954.4444.48********************************************..45 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 ++ +l+++++r+ Carubv10008159m 216 EKSQLMLGIRRA 227 67778**997 PP
2	Auxin_resp	118.5	5.3e-39	252	334	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+ Carubv10008159m 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.27E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.9E-42	120	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.60E-21	125	226	No hit	No description
SMART	SM01019	1.0E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.534	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.5E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.4E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	1.3E-9	937	1025	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.801	939	1032	IPR000270	PB1 domain
SuperFamily	SSF54277	1.57E-8	953	1017	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:0009734	Biological Process	auxin-activated signaling pathway
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: 1068 aa Download sequence Send to blast
MKAPSNGFLP NSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP 360 FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM 420 SMQQNNPLSG SATPQLPSAL SSYNLPNNFA SNDPSKLLNF QSPNLSSANS QFNKLNTLNH 480 ISQQMQAQPA MVKSQQQQQQ LQMSHQQLQQ QGIYNTGSDV SAVANQVSCQ NPHQSTTQSQ 540 LQQQSMLPNG VKMTHQNIHS GNKGSSQMTS FAQELQFQQQ LELHNSSQSL RNQQEQSSLH 600 SLQQSLSQNP QQLQMQQQSP KPSPSQQLQL QLLQKLQQQQ QQQSIPPVTS SLQPQFSALQ 660 QPQSHQLQQL LSSQNQQPLA HGNNSFSAST FMQPPQIQVN HQQQGQMNNK PLVAAGRSHS 720 GHTDGEAPSC STSPSTNNTG HDNVSPTNFL SRNQQGQAVS VSASESVFER ASNPVQELYA 780 KTDNRINQGM VNLKSAGEQF KFKGAVTDQI DVSTAGTTYC PDVVGSAQQQ QTFPLPSFGF 840 DGDCQSHQPR NNLAFASNLE AVTSDALYSQ KDFQNLVPNY GNAPRDIETE LSSAAISSQS 900 FGIPSIPFKS GCSNEVGGIN DSGIMNGGGL WPNQTQRMRT YTKVQKRGSV GRSIDVTRYS 960 GYDELRHDLA RMFGIEGQLE DPLTSDWKLV YTDHENDILL VGDDPWEEFV NCVQNIKILS 1020 SAEVQQMSLD GDLAAIPATN QACSETDSGN AWKVHYEDTS AAASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1068 aa Download sequence Send to blast

MKAPSNGFLP NSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSG SATPQLPSAL SSYNLPNNFA SNDPSKLLNF QSPNLSSANS QFNKLNTLNH  480
ISQQMQAQPA MVKSQQQQQQ LQMSHQQLQQ QGIYNTGSDV SAVANQVSCQ NPHQSTTQSQ  540
LQQQSMLPNG VKMTHQNIHS GNKGSSQMTS FAQELQFQQQ LELHNSSQSL RNQQEQSSLH  600
SLQQSLSQNP QQLQMQQQSP KPSPSQQLQL QLLQKLQQQQ QQQSIPPVTS SLQPQFSALQ  660
QPQSHQLQQL LSSQNQQPLA HGNNSFSAST FMQPPQIQVN HQQQGQMNNK PLVAAGRSHS  720
GHTDGEAPSC STSPSTNNTG HDNVSPTNFL SRNQQGQAVS VSASESVFER ASNPVQELYA  780
KTDNRINQGM VNLKSAGEQF KFKGAVTDQI DVSTAGTTYC PDVVGSAQQQ QTFPLPSFGF  840
DGDCQSHQPR NNLAFASNLE AVTSDALYSQ KDFQNLVPNY GNAPRDIETE LSSAAISSQS  900
FGIPSIPFKS GCSNEVGGIN DSGIMNGGGL WPNQTQRMRT YTKVQKRGSV GRSIDVTRYS  960
GYDELRHDLA RMFGIEGQLE DPLTSDWKLV YTDHENDILL VGDDPWEEFV NCVQNIKILS  1020
SAEVQQMSLD GDLAAIPATN QACSETDSGN AWKVHYEDTS AAASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-172	15	355	45	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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Carubv10008159m

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	AB493467	0.0	AB493467.1 Arabidopsis thaliana At1g19220 mRNA for hypothetical protein, partial cds, clone: RAAt1g19220.
GenBank	ATU53672	0.0	U53672.2 Arabidopsis thaliana early auxin-induced IAA22 mRNA, complete cds.
GenBank	AY669794	0.0	AY669794.1 Arabidopsis thaliana clone C105352 ARF19 (At1g19220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006306645.1	0.0	auxin response factor 19
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	R0IQP5	0.0	R0IQP5_9BRAS; Auxin response factor
STRING	XP_006306645.1	0.0	(Capsella rubella)

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

Link Out ? help Back to Top
Phytozome	Carubv10008159m
Entrez Gene	17898551

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]