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

PGSC0003DMP400004261

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

ARF

Protein Properties

Length: 1107aa MW: 124625 Da PI: 6.5096

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400004261	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70.9	1.7e-22	75	175	1	98
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvF 82 f+k+lt sd++++g +++p++ ae++ ++++++ +l+ +d++ + W++++iyr++++r++lt+GW+ F ++++L++gD+v+F PGSC0003DMP400004261 75 FCKTLTASDTSTHGGFSVPRRAAEKIfppldyaMQPPAQ--ELMARDLHDQAWTFRHIYRGQPKRHLLTTGWSVFISSKRLCAGDSVLF 161 99****************************5444444..8********************************************* PP EE-SSSEE..EEEEE- CS B3 83 kldgrsefelvvkvfr 98 +d ++ +l++++ r PGSC0003DMP400004261 162 IRD--DKSQLLLGIKR 175 *54..45556888776 PP
2	Auxin_resp	123.6	1.4e-40	201	283	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFv++++k++ka++ +vs+GmRf+m+fete+s rr++Gt++gvsdldp+rW+ S+Wr+L+ PGSC0003DMP400004261 201 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYAQVSLGMRFRMMFETEESGVRRYMGTITGVSDLDPIRWKSSEWRNLQ 283 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-42	63	204	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.7E-39	67	190	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.60E-17	74	175	No hit	No description
SMART	SM01019	1.0E-20	75	177	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.5E-19	75	175	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.899	75	177	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.2E-35	201	283	IPR010525	Auxin response factor
Pfam	PF02309	2.2E-9	969	1065	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	27.484	979	1072	IPR000270	PB1 domain
SuperFamily	SSF54277	1.23E-9	980	1057	No hit	No description
CDD	cd05992	1.41E-4	983	1065	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:0009734	Biological Process	auxin-activated signaling pathway
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: 1107 aa Download sequence Send to blast
MNSELWHACA GPLVSLPPVG SLVVYFPQGH SEQADTETDE VYAQMTLQPV NKYDQEALLL 60 SDMGLKQNRQ PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI FPPLDYAMQP PAQELMARDL 120 HDQAWTFRHI YRGQPKRHLL TTGWSVFISS KRLCAGDSVL FIRDDKSQLL LGIKRTNRQQ 180 PALSSSVISS DSMHIGILAA AAHAAANNSP FTIFYNPRAS PSEFVIPLAK YNKAMYAQVS 240 LGMRFRMMFE TEESGVRRYM GTITGVSDLD PIRWKSSEWR NLQVGWDEST AGERPSRVSI 300 WDIEPVVTPF YICPPPFFRP KFPKQPNFPG DESDIENVLK RGMPWINDEL GLKDSQNSIF 360 PGLSLVQWMS MQQNNHVPVA QSGLPSVLHS NIGSDDHSKL LNFQSPTLAT PGLQFNKPNQ 420 LNQPFGQIQQ PPLAWAQQQQ QSLQSPVSAQ QQQPTLQQQQ QQHTLQQQQP TLQQQQHTLQ 480 QQQHTLQQQQ QQQQQQQHTL QQQQQQQHTL QQQQQQHTLQ QQQQQQHTLQ HQQQHTLQQS 540 QQHMLQQQPQ LHQQAQQQLQ QQQRPSQQQQ LTGNSSPVNR CVSPNQIPNQ TFPQAAVYGQ 600 LQQQQVLSAS TQSQQNVPVN RNPFPSTSLA QDFQFQQQVE QQSNLLQKSQ QQQTIPQQVP 660 LQLLQQSLMQ RPQVQPSSQQ SLTEQQLQLQ LLNKLQQQQQ QQQQQAQLLS PVSSTLEPRM 720 PQQQQNRQPQ ELQIAHQQLS SNIVTTATHL QSTHHAFNQL QSQHKSPITI KALSGGTDGD 780 APSCSTSPST NNFQVSPPNF LTKNQGQAIL VDESVVDPSQ EQNKSEFRIK HELVFSKGSE 840 QSKYKGNNTE NLEAASSTTS YGLDSSGFNF SLPALCVDGD VQSHSRNSLP SAANNIDGLN 900 PDALLSRDYD SGKDMQNLFS PFGNAPRDIE TELSDAGINS QQFGVPNMAY KPRCTNDLAV 960 NDNGVLNNNA WTNQTQRMRT YTKVQKRGSV GRTIDVTRYI GYDELRHDLA RMFGIEGQLE 1020 DPQRTEWKLV YVDHENDMLL VGDDPWEEFV SCVQSIKILS SAEVQQMSLD GDLGNVPVPN 1080 QASSGTDSGN AWKGHYDDNS AASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1107 aa Download sequence Send to blast

MNSELWHACA GPLVSLPPVG SLVVYFPQGH SEQADTETDE VYAQMTLQPV NKYDQEALLL  60
SDMGLKQNRQ PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI FPPLDYAMQP PAQELMARDL  120
HDQAWTFRHI YRGQPKRHLL TTGWSVFISS KRLCAGDSVL FIRDDKSQLL LGIKRTNRQQ  180
PALSSSVISS DSMHIGILAA AAHAAANNSP FTIFYNPRAS PSEFVIPLAK YNKAMYAQVS  240
LGMRFRMMFE TEESGVRRYM GTITGVSDLD PIRWKSSEWR NLQVGWDEST AGERPSRVSI  300
WDIEPVVTPF YICPPPFFRP KFPKQPNFPG DESDIENVLK RGMPWINDEL GLKDSQNSIF  360
PGLSLVQWMS MQQNNHVPVA QSGLPSVLHS NIGSDDHSKL LNFQSPTLAT PGLQFNKPNQ  420
LNQPFGQIQQ PPLAWAQQQQ QSLQSPVSAQ QQQPTLQQQQ QQHTLQQQQP TLQQQQHTLQ  480
QQQHTLQQQQ QQQQQQQHTL QQQQQQQHTL QQQQQQHTLQ QQQQQQHTLQ HQQQHTLQQS  540
QQHMLQQQPQ LHQQAQQQLQ QQQRPSQQQQ LTGNSSPVNR CVSPNQIPNQ TFPQAAVYGQ  600
LQQQQVLSAS TQSQQNVPVN RNPFPSTSLA QDFQFQQQVE QQSNLLQKSQ QQQTIPQQVP  660
LQLLQQSLMQ RPQVQPSSQQ SLTEQQLQLQ LLNKLQQQQQ QQQQQAQLLS PVSSTLEPRM  720
PQQQQNRQPQ ELQIAHQQLS SNIVTTATHL QSTHHAFNQL QSQHKSPITI KALSGGTDGD  780
APSCSTSPST NNFQVSPPNF LTKNQGQAIL VDESVVDPSQ EQNKSEFRIK HELVFSKGSE  840
QSKYKGNNTE NLEAASSTTS YGLDSSGFNF SLPALCVDGD VQSHSRNSLP SAANNIDGLN  900
PDALLSRDYD SGKDMQNLFS PFGNAPRDIE TELSDAGINS QQFGVPNMAY KPRCTNDLAV  960
NDNGVLNNNA WTNQTQRMRT YTKVQKRGSV GRTIDVTRYI GYDELRHDLA RMFGIEGQLE  1020
DPQRTEWKLV YVDHENDMLL VGDDPWEEFV SCVQSIKILS SAEVQQMSLD GDLGNVPVPN  1080
QASSGTDSGN AWKGHYDDNS AASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-150	1	304	51	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	PGSC0003DMP400004261

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	EF121545	0.0	EF121545.1 Solanum lycopersicum auxin response factor mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006353789.1	0.0	PREDICTED: auxin response factor 7-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	M0ZQW9	0.0	M0ZQW9_SOLTU; Auxin response factor
STRING	PGSC0003DMT400006151	0.0	(Solanum tuberosum)

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	PGSC0003DMP400004261

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] Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] 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]