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

Csa03g023040.1

Organism

Camelina sativa

Taxonomic ID

90675

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1253aa MW: 138697 Da PI: 7.3599

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Csa03g023040.1	genome	CSGP	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.9	4e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F +++ Csa03g023040.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfpplefsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RDE 216 99***************************954.4444.48********************************************..456 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 + +l+++++r+ Csa03g023040.1 217 KSQLMLGIRRA 227 7778**997 PP
2	B3	52.4	9.7e-17	340	406	30	99
..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 30 keesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 ++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ +l+++++r+ Csa03g023040.1 340 PPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RDEKSQLMLGIRRA 406 333.48**********************************************..4567778**997 PP
3	Auxin_resp	118.3	6.4e-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+ Csa03g023040.1 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP
4	Auxin_resp	118.3	6.4e-39	431	513	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+ Csa03g023040.1 431 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 513 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.96E-43	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.5E-41	120	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.41E-21	125	226	No hit	No description
SMART	SM01019	1.1E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.534	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	9.0E-34	252	334	IPR010525	Auxin response factor
SMART	SM01019	4.4E-8	310	407	IPR003340	B3 DNA binding domain
SuperFamily	SSF101936	1.28E-23	325	434	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.7E-25	335	420	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.63E-12	335	405	No hit	No description
Pfam	PF02362	1.5E-14	338	406	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.63	344	407	IPR003340	B3 DNA binding domain
Pfam	PF06507	9.0E-34	431	513	IPR010525	Auxin response factor
Pfam	PF02309	1.6E-9	1122	1210	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.801	1124	1217	IPR000270	PB1 domain
SuperFamily	SSF54277	1.9E-8	1138	1202	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: 1253 aa Download sequence Send to blast
MKAPSNGFLP NSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMALQP VNKYDREALL ASDMGLKLNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLEFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQEFSMQP PAQEIVAKDL HDTTWTFRHI 360 YRGQPKRHLL TTGWSVFVST KRLFAGDSVL FVRDEKSQLM LGIRRANRQT PTLSSSVISS 420 DSMHIGILAA AAHANANSSP FTIFFNPRAS PSEFVVPLAK YNKALYAQVS LGMRFRMMFE 480 TEDCGVRRYM GTVTGISDLD PVRWKGSQWR NLQVGWDEST AGDRPSRVSI WEIEPVITPF 540 YICPPPFFRP KYPRQPGMPD DELDMENAFK RAMPWMGEEF GMKDAQSSMF PGLSLVQWMS 600 MQQNNPLSGS ATPQLPAALS SYNLPNNFAS NDPSKLLNFQ SPNLSSANSQ FNKPNTANHI 660 SQQMQTQPAN AKSQQQQLQM SHQQLQQQGI YNTGSINNGV NAVANQVSSQ NPHQSTGFSQ 720 SQLQQQSMLP NGAKMTHPNI NSAGNKGSSQ MTSFAQELQF QQQLELHNSS QLLRNQQEQS 780 SLHSLQQSLS QNPQQLQMQQ QSPKPSPSQQ LQLQLLQKLQ QQQQQQQSIP PVSSSLQPQL 840 SALQQTQSHQ LQQLLSSQNQ QPLAHGNNSF SASTFMQPPQ IQVNHQQQGQ MNNKPLVAPG 900 RSHSGHTDGE APSCSTSPSA NNTGHDNVSP TNFLSRNQQQ GQGVSVSASD SVFERASNPV 960 QELYAKNDSR INQGLVNLKS AGEQFKFKGA VTDQIDVSTA GTTYCPDVVG SAQQQQTFPL 1020 PSFGFDGDCQ SHHPRNNLAF ASNLEAVTPD ALYSQKDFQN LVPNYGNAPR DIETELSSAA 1080 ISSQSFGIPS IPFKSGCSNE VGGINDSGIM NGGGLWPNQT QRMRTYTKVQ KRGSVGRSID 1140 VTRYSGYDEL RHDLARMFGI EGQLEDPLTS DWKLVYTDHE NDILLVGDDP WEEFVNCVQN 1200 IKILSSAEVQ QMSLDGDLAA IPATNQACSE TDSGNAWKVH YEDTSAAASF NR*

Sequence ? help Back to Top

Protein Sequence Length: 1253 aa Download sequence Send to blast

MKAPSNGFLP NSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMALQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLEFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQEFSMQP PAQEIVAKDL HDTTWTFRHI  360
YRGQPKRHLL TTGWSVFVST KRLFAGDSVL FVRDEKSQLM LGIRRANRQT PTLSSSVISS  420
DSMHIGILAA AAHANANSSP FTIFFNPRAS PSEFVVPLAK YNKALYAQVS LGMRFRMMFE  480
TEDCGVRRYM GTVTGISDLD PVRWKGSQWR NLQVGWDEST AGDRPSRVSI WEIEPVITPF  540
YICPPPFFRP KYPRQPGMPD DELDMENAFK RAMPWMGEEF GMKDAQSSMF PGLSLVQWMS  600
MQQNNPLSGS ATPQLPAALS SYNLPNNFAS NDPSKLLNFQ SPNLSSANSQ FNKPNTANHI  660
SQQMQTQPAN AKSQQQQLQM SHQQLQQQGI YNTGSINNGV NAVANQVSSQ NPHQSTGFSQ  720
SQLQQQSMLP NGAKMTHPNI NSAGNKGSSQ MTSFAQELQF QQQLELHNSS QLLRNQQEQS  780
SLHSLQQSLS QNPQQLQMQQ QSPKPSPSQQ LQLQLLQKLQ QQQQQQQSIP PVSSSLQPQL  840
SALQQTQSHQ LQQLLSSQNQ QPLAHGNNSF SASTFMQPPQ IQVNHQQQGQ MNNKPLVAPG  900
RSHSGHTDGE APSCSTSPSA NNTGHDNVSP TNFLSRNQQQ GQGVSVSASD SVFERASNPV  960
QELYAKNDSR INQGLVNLKS AGEQFKFKGA VTDQIDVSTA GTTYCPDVVG SAQQQQTFPL  1020
PSFGFDGDCQ SHHPRNNLAF ASNLEAVTPD ALYSQKDFQN LVPNYGNAPR DIETELSSAA  1080
ISSQSFGIPS IPFKSGCSNE VGGINDSGIM NGGGLWPNQT QRMRTYTKVQ KRGSVGRSID  1140
VTRYSGYDEL RHDLARMFGI EGQLEDPLTS DWKLVYTDHE NDILLVGDDP WEEFVNCVQN  1200
IKILSSAEVQ QMSLDGDLAA IPATNQACSE TDSGNAWKVH YEDTSAAASF NR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-159	15	534	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	Csa03g023040.1

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	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_010498333.1	0.0	PREDICTED: auxin response factor 19-like isoform X2
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	R0GUD5	0.0	R0GUD5_9BRAS; Auxin response factor
STRING	XP_010498333.1	0.0	(Camelina sativa)

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]