PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sp_157870_nzwt.t1
Common NameSOVF_157870
Organism
Spinacia oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia
Family Trihelix
Protein Properties Length: 876aa    MW: 97025.1 Da    PI: 8.1418
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sp_157870_nzwt.t1genomeTBVRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix66.17.2e-21784864186
           trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                        +W+ +ev++Li +r +++er++  k +++lWee+s+ + + gf+r+p qCk+ w +l ++y++ k  ek++     +++py+++++
  Sp_157870_nzwt.t1 784 KWKPEEVKKLIMLRGDLHERFQVVKGRMALWEEISSSLVADGFNRTPGQCKSLWASLVQKYEESKSDEKSQ-----KSWPYYTKMD 864
                        7********************************************************************84.....56*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.8E-6677327IPR001279Metallo-beta-lactamase
SuperFamilySSF562813.32E-7278492IPR001279Metallo-beta-lactamase
SMARTSM008496.6E-2490287IPR001279Metallo-beta-lactamase
PfamPF127061.9E-11102238IPR001279Metallo-beta-lactamase
PfamPF075211.4E-6432464IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.538777841IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.1E-4781843IPR009057Homeodomain-like
PfamPF138371.2E-18782866No hitNo description
CDDcd122031.14E-22783848No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 876 aa     Download sequence    Send to blast
MAAFTAVSIC PCSPSYRPNH LKNRYVSCSV VPPRNLSSNA TTVPRKRHVR LEGPRKSMED  60
SVKRKMEQFF EGPTGPPLRV LPIGGLGEIG MNCMLVGNYD RYILIDAGIM FPDFDEFGVQ  120
KIIPDTTFIK RWSHKIEAVI ITHGHEDHIG ALPWVIPALD PNTPIFASSF TMELIKKRLK  180
EFGIFVPSRL KMFKTKRRFT AGPFEIEPIR VTHSIPDCCG LVMRCSDGTI FHTGDWKIDE  240
KPVDGKVFDR VALEELAKEG VTLMMSDSTN IMSPGRTISE SVVADSLLRH ISTAKGRVIT  300
TQFASNIHRL GSVKAAADAT GRKLVFVGMS LRTYLDAAWK DGKAPIDPST LVKVEDIDGY  360
APKDLLIVTT GSQAEPRAAL NLASFGSSHS LKLNKEDVIL YSAKVIPGNE SRVMKMFNRI  420
SELGSNLVMG KNEMLHTSGH AYREELEEAL KIVKPQHFLP IHGELLFLKE HELLGRSTGV  480
QHTTVIKNGE MLGVSHLRNR RVLSNGFVSL GKENLQLMYN DGDKAFGTSA ELCVDERIKI  540
ATDGIIVISM EVLRPHAAEG STENCLKGKI RITTRCLWLD KGKLLDALYK AAHAALSSCP  600
VKCPLSHIER TVSEVLRKVV RKYSGKRPEV IAVATENPVA VLSDEVNERL SGKSKTGFSL  660
SGLQKAFDGQ QQKKNSGRVQ DVEDERPVSV ASSSTSHLES EDGSEFDRLL SKVDDATSTS  720
SSNVEAGSTT ESEDSDGLLE KNGEVSSLVE ESIDRSGPVE INEEEPDETV NRSSKRSKAT  780
IRNKWKPEEV KKLIMLRGDL HERFQVVKGR MALWEEISSS LVADGFNRTP GQCKSLWASL  840
VQKYEESKSD EKSQKSWPYY TKMDKILSNL GEVVNS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-857863619560RIBONUCLEASE J
5a0t_B9e-857863619560RIBONUCLEASE J
5a0v_A9e-857863619560RIBONUCLEASE J
5a0v_B9e-857863619560RIBONUCLEASE J
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021847608.10.0uncharacterized protein LOC110787304 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0K9QP060.0A0A0K9QP06_SPIOL; Uncharacterized protein
STRINGXP_010677898.10.0(Beta vulgaris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]