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

cra_locus_5267_iso_9

Organism

Catharanthus roseus

Taxonomic ID

4058

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthinae; Catharanthus

Family

ARF

Protein Properties

Length: 969aa MW: 106255 Da PI: 6.8535

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
cra_locus_5267_iso_9	genome	MPGR	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70	3.1e-22	13	114	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHH CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeF 68 f+k+lt sd++++g +++p++ ae+ +++++ ++l+ +d++ +sW++++iyr++++r++lt+GW+ F cra_locus_5267_iso_9_len_3880_ver_3 13 FCKTLTASDTSNHGGFSVPRRVAETSsppldvSMQPPA-QELVGRDLHDQSWTFRHIYRGQPKRHLLTTGWSVF 85 99*******************999*9445444.38***************************** PP HHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 69 vkangLkegDfvvFkldgrsefelvvkvfrk 99 v++++L +gD+v+F ++++ +l+++++r+ cra_locus_5267_iso_9_len_3880_ver_3 86 VSSKRLIAGDSVLFI--RDEKSQLLLGIRRA 114 *************..45677789999997 PP
2	Auxin_resp	125.3	4.2e-41	139	221	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrW 74 aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s rr++Gtv+g+sdldpvrW cra_locus_5267_iso_9_len_3880_ver_3 139 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTVTGISDLDPVRW 212 79********************************************************************** PP Auxin_resp 75 pnSkWrsLk 83 +nS+Wr+L+ cra_locus_5267_iso_9_len_3880_ver_3 213 KNSQWRNLQ 221 *****97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.1E-38	4	142	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.8E-38	6	128	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.52E-18	12	113	No hit	No description
PROSITE profile	PS50863	12.478	13	115	IPR003340	B3 DNA binding domain
SMART	SM01019	1.4E-21	13	115	IPR003340	B3 DNA binding domain
Pfam	PF02362	4.7E-20	13	114	IPR003340	B3 DNA binding domain
Pfam	PF06507	6.4E-36	139	221	IPR010525	Auxin response factor
Pfam	PF02309	2.0E-9	839	928	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.638	842	935	IPR000270	PB1 domain
SuperFamily	SSF54277	3.97E-9	846	920	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:0009725	Biological Process	response to hormone
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: 969 aa Download sequence Send to blast
MGLKQSRQPG EFFCKTLTAS DTSNHGGFSV PRRVAETSSP PLDVSMQPPA QELVGRDLHD 60 QSWTFRHIYR GQPKRHLLTT GWSVFVSSKR LIAGDSVLFI RDEKSQLLLG IRRANRQQPA 120 LSSSVISSDS MHIGILAAAA HAAANNSPFT IFYNPRASPS EFVIPLAKYN KAMYTQVSLG 180 MRFRMMFETE ESGVRRYMGT VTGISDLDPV RWKNSQWRNL QVGWDESTAG ERPGRVSLWE 240 IEPVVTPFYI CPPPFFRPKF PKHPGFPDDE SDMENLFKRG MPWLGEEFGL KDATNSVFPG 300 LSLVQWMNMQ QNGQFSSAQS GIFPSALNGN MNTEDRSKLL SFQSPGFAAT NLQFGKANQL 360 NQQVNPXPTV ISGWATTAAA AATAAVFCKF TAAAATAAAS STTTAATTSA TASSTDAAAA 420 TATAPQMMNL ASVSMANAAS LSSSQITNQN LQQQSSYPQL QQHQILAGNP QLQQNVSSTN 480 KTSFPMTSLP QDLPFQQQIE QQPSLLQKSQ QQHTQLQQAP LQLLQQSLTQ RQQVQQTSQQ 540 SFAEQQLQLQ LLQKLQQQQQ QQMLSPVGSH LESQLPHQHQ SLQQNRQYQH QQTPLAQQQP 600 SGNSFSTSTL LQSPQHPVNQ LQSQNKSPIA IKAHSGPTDG DAPSCSTSPS TNNCQVSSSK 660 FLNRSQTGPT TLGGDSVIDP SRILVQELQS RSDIRMKHEL SSSKVAEQPK FRSNGTDHLE 720 AASSATSYCL DTSGLQQNFS LPNLCLDNDV QSQSRSTLPF TSTIDSLAPD ALLSRGYDSG 780 KDIQNVLTNY GGTSGDIETE LSAAGFGVPS MSFKPGCSND VPINDSGVLN NGLWPNQTQR 840 MRTYTKVQKR GSVGRTIDVT RYKGYDELKH DLARMFGIEG QLDDPQRNEW KLVYVDHEND 900 ILLVGDDPWE EFVSCVQSIK ILSSAEVQQM SLDGDLGNVP VPNQACSGTD SGNAWRGHYD 960 DNSAASFNR

Sequence ? help Back to Top

Protein Sequence Length: 969 aa Download sequence Send to blast

MGLKQSRQPG EFFCKTLTAS DTSNHGGFSV PRRVAETSSP PLDVSMQPPA QELVGRDLHD  60
QSWTFRHIYR GQPKRHLLTT GWSVFVSSKR LIAGDSVLFI RDEKSQLLLG IRRANRQQPA  120
LSSSVISSDS MHIGILAAAA HAAANNSPFT IFYNPRASPS EFVIPLAKYN KAMYTQVSLG  180
MRFRMMFETE ESGVRRYMGT VTGISDLDPV RWKNSQWRNL QVGWDESTAG ERPGRVSLWE  240
IEPVVTPFYI CPPPFFRPKF PKHPGFPDDE SDMENLFKRG MPWLGEEFGL KDATNSVFPG  300
LSLVQWMNMQ QNGQFSSAQS GIFPSALNGN MNTEDRSKLL SFQSPGFAAT NLQFGKANQL  360
NQQVNPXPTV ISGWATTAAA AATAAVFCKF TAAAATAAAS STTTAATTSA TASSTDAAAA  420
TATAPQMMNL ASVSMANAAS LSSSQITNQN LQQQSSYPQL QQHQILAGNP QLQQNVSSTN  480
KTSFPMTSLP QDLPFQQQIE QQPSLLQKSQ QQHTQLQQAP LQLLQQSLTQ RQQVQQTSQQ  540
SFAEQQLQLQ LLQKLQQQQQ QQMLSPVGSH LESQLPHQHQ SLQQNRQYQH QQTPLAQQQP  600
SGNSFSTSTL LQSPQHPVNQ LQSQNKSPIA IKAHSGPTDG DAPSCSTSPS TNNCQVSSSK  660
FLNRSQTGPT TLGGDSVIDP SRILVQELQS RSDIRMKHEL SSSKVAEQPK FRSNGTDHLE  720
AASSATSYCL DTSGLQQNFS LPNLCLDNDV QSQSRSTLPF TSTIDSLAPD ALLSRGYDSG  780
KDIQNVLTNY GGTSGDIETE LSAAGFGVPS MSFKPGCSND VPINDSGVLN NGLWPNQTQR  840
MRTYTKVQKR GSVGRTIDVT RYKGYDELKH DLARMFGIEG QLDDPQRNEW KLVYVDHEND  900
ILLVGDDPWE EFVSCVQSIK ILSSAEVQQM SLDGDLGNVP VPNQACSGTD SGNAWRGHYD  960
DNSAASFNR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-121	3	242	148	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027175099.1	0.0	auxin response factor 19-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A068U4G5	0.0	A0A068U4G5_COFCA; Auxin response factor
STRING	XP_009620963.1	0.0	(Nicotiana tomentosiformis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1302	24	65

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]