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

Sp_094480_jsmt.t1

Common Name

SOVF_094480

Organism

Spinacia oleracea

Taxonomic ID

3562

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia

Family

ARF

Protein Properties

Length: 1137aa MW: 127111 Da PI: 6.9535

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sp_094480_jsmt.t1	genome	TBVR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.9	1.9e-23	125	226	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++p++ ae++ +++++++ +l+ +d+++++W++++iyr++++r++lt+GW+ Fv++++L +gD+v+F + Sp_094480_jsmt.t1 125 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPCQ-ELMAKDLHNQTWTFRHIYRGQPKRHLLTTGWSVFVSSKRLFAGDSVLFI--R 213 99***************************98888885.***********************************************..5 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++ +l+++++r+ Sp_094480_jsmt.t1 214 DEKSHLLLGIRRA 226 5778889999997 PP
2	Auxin_resp	120.7	1.1e-39	251	333	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras++eFvv+++k++ka++++vs+GmRf+m+fete++ rr++Gt++g++dld+ rW+nS+Wr+L+ Sp_094480_jsmt.t1 251 AAHAATNNSPFTIFYNPRASPAEFVVPLAKYNKAMYTQVSLGMRFRMMFETEECGVRRYMGTITGINDLDSARWKNSQWRNLQ 333 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	7.06E-44	114	254	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.1E-42	116	240	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.31E-20	124	225	No hit	No description
PROSITE profile	PS50863	12.139	125	227	IPR003340	B3 DNA binding domain
SMART	SM01019	4.4E-23	125	227	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.1E-21	125	226	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.4E-35	251	333	IPR010525	Auxin response factor
PROSITE profile	PS51745	22.882	1069	1137	IPR000270	PB1 domain
SuperFamily	SSF54277	3.92E-5	1084	1137	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: 1137 aa Download sequence Send to blast
MKAPSNGLVA NPGEEGRAIN SELWHACAGP LVAVPPVGSL VVYFPQGHSE QVAASMQKET 60 DGIPSYPNLP SKLICVLHSV TLHADPETDE VYAQMTLQPV NKYDRDALLA SEMALKQNRQ 120 PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI FPPLDFSMQP PCQELMAKDL HNQTWTFRHI 180 YRGQPKRHLL TTGWSVFVSS KRLFAGDSVL FIRDEKSHLL LGIRRANRQQ PALASSVISS 240 DSMHIGILAA AAHAATNNSP FTIFYNPRAS PAEFVVPLAK YNKAMYTQVS LGMRFRMMFE 300 TEECGVRRYM GTITGINDLD SARWKNSQWR NLQVGWDEST AGDRPGRVSI WDIEPVVTPF 360 YICPPPFFRP KFPKQPGMPD DDSDMDSIFK RGMPWLGDEY GMKDVPSSIF PGLSLVQWMN 420 MQHNNQVPGA QPGIFPSMLT ASAMNGGLGT DDPSKLLNFQ APNMSMPNLQ FSKAVQQNQV 480 GQLQQQSANW SQQQQQQLQQ LLQNPLNSQQ QQQQQQPQQQ PQQQQSLQQQ LQKQQIQQQQ 540 QHQQQQHHHQ QLQQQQQQQQ QQQLQQQQQH QQQLQQQQQH QHQQQQQHQQ HQQQQQQQQQ 600 QQHQQQQAQP ASHPAPQKQQ IPQSTFVNSG LISPNQNINQ NLPQSPMFSQ LHHQQLLGGN 660 TQGPPNLPAD SLHLTSLTPD MQFQQQTEQQ SNVLQRLQQQ QQQQQAQMQQ SSQQLLQESL 720 SHRSSPALQS LSEHQLQLQL LQKLQQQPQQ HSQQQQHQQH SQQSHPMLSP ISSHSHPQVT 780 TQQHTAQSNQ HLQQRPSSQY QPTQQVGVGV GVGVGVGVSS ISTSPLMNSP AVSAVQLQGM 840 QKTGGIVRSL SGPTDGDAPS CSTSPSTNNC QIPHSNFLNR NQQARNMLVE HSITEPSSNM 900 VQDLQQEKSD MRIKNEISTS KVIEPPRING GIITDPLEAS SSVTSYGLDA SGLHQNLSLP 960 SFGLDGDVQS HPRHNSLPIS TAMDDLTTDS FLSRGFDSGK ELHNLLSSYN GAPTPRDIET 1020 ELSAAGMSPQ SFGVPNIPFK SGCSNDVAAI NDPAGLGGGM WPSQAPRMRT YTKVQKRGSV 1080 GRSIDVTRYK GYDELRLDLA RMFGIEGQLE DPQRTDWKLV YVDHENDILL VGDDPWE

Sequence ? help Back to Top

Protein Sequence Length: 1137 aa Download sequence Send to blast

MKAPSNGLVA NPGEEGRAIN SELWHACAGP LVAVPPVGSL VVYFPQGHSE QVAASMQKET  60
DGIPSYPNLP SKLICVLHSV TLHADPETDE VYAQMTLQPV NKYDRDALLA SEMALKQNRQ  120
PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI FPPLDFSMQP PCQELMAKDL HNQTWTFRHI  180
YRGQPKRHLL TTGWSVFVSS KRLFAGDSVL FIRDEKSHLL LGIRRANRQQ PALASSVISS  240
DSMHIGILAA AAHAATNNSP FTIFYNPRAS PAEFVVPLAK YNKAMYTQVS LGMRFRMMFE  300
TEECGVRRYM GTITGINDLD SARWKNSQWR NLQVGWDEST AGDRPGRVSI WDIEPVVTPF  360
YICPPPFFRP KFPKQPGMPD DDSDMDSIFK RGMPWLGDEY GMKDVPSSIF PGLSLVQWMN  420
MQHNNQVPGA QPGIFPSMLT ASAMNGGLGT DDPSKLLNFQ APNMSMPNLQ FSKAVQQNQV  480
GQLQQQSANW SQQQQQQLQQ LLQNPLNSQQ QQQQQQPQQQ PQQQQSLQQQ LQKQQIQQQQ  540
QHQQQQHHHQ QLQQQQQQQQ QQQLQQQQQH QQQLQQQQQH QHQQQQQHQQ HQQQQQQQQQ  600
QQHQQQQAQP ASHPAPQKQQ IPQSTFVNSG LISPNQNINQ NLPQSPMFSQ LHHQQLLGGN  660
TQGPPNLPAD SLHLTSLTPD MQFQQQTEQQ SNVLQRLQQQ QQQQQAQMQQ SSQQLLQESL  720
SHRSSPALQS LSEHQLQLQL LQKLQQQPQQ HSQQQQHQQH SQQSHPMLSP ISSHSHPQVT  780
TQQHTAQSNQ HLQQRPSSQY QPTQQVGVGV GVGVGVGVSS ISTSPLMNSP AVSAVQLQGM  840
QKTGGIVRSL SGPTDGDAPS CSTSPSTNNC QIPHSNFLNR NQQARNMLVE HSITEPSSNM  900
VQDLQQEKSD MRIKNEISTS KVIEPPRING GIITDPLEAS SSVTSYGLDA SGLHQNLSLP  960
SFGLDGDVQS HPRHNSLPIS TAMDDLTTDS FLSRGFDSGK ELHNLLSSYN GAPTPRDIET  1020
ELSAAGMSPQ SFGVPNIPFK SGCSNDVAAI NDPAGLGGGM WPSQAPRMRT YTKVQKRGSV  1080
GRSIDVTRYK GYDELRLDLA RMFGIEGQLE DPQRTDWKLV YVDHENDILL VGDDPWE

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-167	13	354	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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A0K9R8I5	0.0	A0A0K9R8I5_SPIOL; Auxin response factor

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]