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

Rsa1.0_00832.1_g00012.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

LBD

Protein Properties

Length: 1221aa MW: 136050 Da PI: 6.3594

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_00832.1_g00012.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	50.8	4.7e-16	1091	1144	47	100
DUF260 47 kalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallkee 100 ++lpe++r+d+++s+vyeA ar+rdP+yG++g i +lq+q+++l+a+la+++ e Rsa1.0_00832.1_g00012.1 1091 QELPESQRTDVVNSIVYEAGARIRDPIYGCAGAIYNLQRQVSELQAQLAKAQVE 1144 789**********************************************99865 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF08302	6.8E-8	922	1062	IPR015965	tRNA ligase, phosphodiesterase, fungi
Pfam	PF03195	8.9E-14	1091	1142	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006388	Biological Process	tRNA splicing, via endonucleolytic cleavage and ligation
GO:0016310	Biological Process	phosphorylation
GO:0003972	Molecular Function	RNA ligase (ATP) activity
GO:0004113	Molecular Function	2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
GO:0005524	Molecular Function	ATP binding
GO:0051731	Molecular Function	polynucleotide 5'-hydroxyl-kinase activity

Sequence ? help Back to Top
Protein Sequence Length: 1221 aa Download sequence Send to blast
MDASSGSSDR SVAEAVSNQI GELTLEESNA NSVPVNHGGP SSASPGEEAI PRKADLNLEN 60 FTVDESTCCR AQIRASFYPK FENEKTDQEI RTRMIEMVSK GLATLEVSLK HSGSLFMYAG 120 HVGGAYAKNS YGNIFTAVGV FVLSRMFREA WGTQALKKEA EFNDFLEENR MCVSMELVTA 180 VLGDHGQRPL DDFVVVTAVT ELGNGKPKFY STSEIIAFCR IWRLPTNHVW LFSTRKSVTS 240 FFAAFDALCE EGIATSVCRA LDEVADISVP GSKDHVKVQG EILEGLVARI VSSGSARDME 300 DVLRDHPPPP CDGANLDLGL SLREICAAHR SSEEQQIREL LKTVGPSFCP NNLDWFGDVS 360 VDCYPKNADK AVVTKFLESQ PADYSTSKLQ EMVRLIKNRR LPAAFKCYHN FHRANDVSPD 420 NLFYKLVVHV RSDSAFRRYQ KEMRVMPGLW PLYRGFFVDI NLFKSNKGRD PMTLKSLDNT 480 VKDAGENCGQ QGKDGLDDDD ANLMIKLKFL TYKLRTFLIR NSLSILFKEG PAAYKASYLE 540 QMNRWGTSVG KQKELSKTLD EWAAHIIRKC GNNQLSSSVY LSEAEPFLKQ YAERSPENQV 600 LIGSAGNRVR AEDFLAIVDG DFDEEGDLVK KEKVTPATPE PAMQEAVQKN EGLIVFFPGI 660 PGSAKSALCK ELLNAPGGLG DDRPVHTLMG DLVKGKYWPK VADEHRKKPQ SIMLADKNAP 720 NEDVWRQIEV MCRKTKVTAV PVVTDSEGTE SNPYSLDALA VFMFRVLQRV DHPGNLDKTS 780 ANAGNVLLMF YHLYEGNNRE EFEGELIERF GSLVKMPLFR SDRSPLPDPV KSILEEGIEL 840 FQLHRRRHGR LESAKGTYAA EWSKWEKQLR DTLAANSEYF NSVQVIHPLV IDGSNLIPCL 900 VPFESAVQQV REELKRIAKG EYKPPSSVKT QHGSITFAAV NLHVTQVQSR LEKLAASNPT 960 MRSFLEGKKE SIEEKLERAH VTLAHKRSHG VAAVARYGQH LNREVPVDLT ELIFNDKMAA 1020 FTAHVGSVDG ETIVCKNEWP HVTLWTAEGV TAREANTLPQ LYADGKASRM VIDPPATVSG 1080 PLERGSDMFP QELPESQRTD VVNSIVYEAG ARIRDPIYGC AGAIYNLQRQ VSELQAQLAK 1140 AQVEIVSMQL QRSNLLELIH NMDQPNQEQH NISSDSSFGN CDELLAARTK RAMILDYSKR 1200 TGTPTPSHQR CGVMLFGYDN N

Sequence ? help Back to Top

Protein Sequence Length: 1221 aa Download sequence Send to blast

MDASSGSSDR SVAEAVSNQI GELTLEESNA NSVPVNHGGP SSASPGEEAI PRKADLNLEN  60
FTVDESTCCR AQIRASFYPK FENEKTDQEI RTRMIEMVSK GLATLEVSLK HSGSLFMYAG  120
HVGGAYAKNS YGNIFTAVGV FVLSRMFREA WGTQALKKEA EFNDFLEENR MCVSMELVTA  180
VLGDHGQRPL DDFVVVTAVT ELGNGKPKFY STSEIIAFCR IWRLPTNHVW LFSTRKSVTS  240
FFAAFDALCE EGIATSVCRA LDEVADISVP GSKDHVKVQG EILEGLVARI VSSGSARDME  300
DVLRDHPPPP CDGANLDLGL SLREICAAHR SSEEQQIREL LKTVGPSFCP NNLDWFGDVS  360
VDCYPKNADK AVVTKFLESQ PADYSTSKLQ EMVRLIKNRR LPAAFKCYHN FHRANDVSPD  420
NLFYKLVVHV RSDSAFRRYQ KEMRVMPGLW PLYRGFFVDI NLFKSNKGRD PMTLKSLDNT  480
VKDAGENCGQ QGKDGLDDDD ANLMIKLKFL TYKLRTFLIR NSLSILFKEG PAAYKASYLE  540
QMNRWGTSVG KQKELSKTLD EWAAHIIRKC GNNQLSSSVY LSEAEPFLKQ YAERSPENQV  600
LIGSAGNRVR AEDFLAIVDG DFDEEGDLVK KEKVTPATPE PAMQEAVQKN EGLIVFFPGI  660
PGSAKSALCK ELLNAPGGLG DDRPVHTLMG DLVKGKYWPK VADEHRKKPQ SIMLADKNAP  720
NEDVWRQIEV MCRKTKVTAV PVVTDSEGTE SNPYSLDALA VFMFRVLQRV DHPGNLDKTS  780
ANAGNVLLMF YHLYEGNNRE EFEGELIERF GSLVKMPLFR SDRSPLPDPV KSILEEGIEL  840
FQLHRRRHGR LESAKGTYAA EWSKWEKQLR DTLAANSEYF NSVQVIHPLV IDGSNLIPCL  900
VPFESAVQQV REELKRIAKG EYKPPSSVKT QHGSITFAAV NLHVTQVQSR LEKLAASNPT  960
MRSFLEGKKE SIEEKLERAH VTLAHKRSHG VAAVARYGQH LNREVPVDLT ELIFNDKMAA  1020
FTAHVGSVDG ETIVCKNEWP HVTLWTAEGV TAREANTLPQ LYADGKASRM VIDPPATVSG  1080
PLERGSDMFP QELPESQRTD VVNSIVYEAG ARIRDPIYGC AGAIYNLQRQ VSELQAQLAK  1140
AQVEIVSMQL QRSNLLELIH NMDQPNQEQH NISSDSSFGN CDELLAARTK RAMILDYSKR  1200
TGTPTPSHQR CGVMLFGYDN N

Functional Description ? help Back to Top
Source	Description
UniProt	Essential component of stress-response pathways entailing repair of RNA breaks with 2',3'-cyclic phosphate and 5'-OH ends (PubMed:23515942). Tri-functional enzyme that repairs RNA breaks with 2',3'-cyclic-PO(4) and 5'-OH ends. The ligation activity requires three sequential enzymatic activities: opening of the 2'3'-cyclic phosphodiester bond of the 5' half-tRNA leaving a 2'-phosphomonoester (CPDase activity), phosphorylation of the 5' terminus of the 3' half-tRNA in the presence of ATP (kinase activity) and ligation of the two tRNA halves in an ATP-dependent reaction (ligase activity) (PubMed:24554441, PubMed:23515942). Deficient in transferring AMP to pRNA(OH) to form AppRNA(OH) but proficient at sealing pre-adenylylated AppRNA(OH) (PubMed:23515942). CPDase and kinase reactions are almost insensitive to RNA length, whereas the ligase activity decreases with shorter RNA size. Can also splice DNA ended by a single 3'-terminal ribonucleoside 2',3'-cyclic-PO(4) (PubMed:24554441). Binds to mRNA, mature and immature (PubMed:20844078). Exhibits tRNA ligase activity in vitro (PubMed:15653639, PubMed:24554441). Required for the splicing of precursor tRNA molecules containing introns (PubMed:16428247, PubMed:20844078). Can circularize an intron cleaved from a pre-tRNA by splicing endonuclease in vitro (PubMed:20844078). Seems not involved in unfolded protein response (UPR) in the endoplasmic reticulum (PubMed:20844078). Involved in auxin signaling and polar transport during organ morphogenesis (PubMed:25892242). {ECO:0000269\|PubMed:15653639, ECO:0000269\|PubMed:16428247, ECO:0000269\|PubMed:20844078, ECO:0000269\|PubMed:23515942, ECO:0000269\|PubMed:24554441, ECO:0000269\|PubMed:25892242}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_00832.1_g00012.1

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
Refseq	XP_018436347.1	0.0	PREDICTED: uncharacterized protein LOC108808737
Swissprot	Q0WL81	0.0	RNL_ARATH; tRNA ligase 1
TrEMBL	A0A0D3C8E2	0.0	A0A0D3C8E2_BRAOL; Uncharacterized protein
STRING	Bo5g008600.1	0.0	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G07900.1	2e-40	LOB domain-containing protein 1

Publications ? help Back to Top
Englert M,Beier H Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res., 2005. 33(1): p. 388-99 [PMID:15653639] Wang LK,Schwer B,Englert M,Beier H,Shuman S Structure-function analysis of the kinase-CPD domain of yeast tRNA ligase (Trl1) and requirements for complementation of tRNA splicing by a plant Trl1 homolog. Nucleic Acids Res., 2006. 34(2): p. 517-27 [PMID:16428247] Mori T, et al. Dual functions of yeast tRNA ligase in the unfolded protein response: unconventional cytoplasmic splicing of HAC1 pre-mRNA is not sufficient to release translational attenuation. Mol. Biol. Cell, 2010. 21(21): p. 3722-34 [PMID:20844078] Remus BS,Shuman S A kinetic framework for tRNA ligase and enforcement of a 2'-phosphate requirement for ligation highlights the design logic of an RNA repair machine. RNA, 2013. 19(5): p. 659-69 [PMID:23515942] Remus BS,Shuman S Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases. RNA, 2014. 20(4): p. 462-73 [PMID:24554441] Leitner J, et al. Meta-regulation of Arabidopsis auxin responses depends on tRNA maturation. Cell Rep, 2015. 11(4): p. 516-26 [PMID:25892242] Yang KJ,Guo L,Hou XL,Gong HQ,Liu CM ZYGOTE-ARREST 3 that encodes the tRNA ligase is essential for zygote division in Arabidopsis. J Integr Plant Biol, 2017. 59(9): p. 680-692 [PMID:28631407]