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 AA4G00072
Organism
Aethionema arabicum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Aethionemeae; Aethionema
Family Trihelix
Protein Properties Length: 921aa    MW: 102306 Da    PI: 8.3416
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AA4G00072genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix55.51.5e-17811876166
   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkike 66 
                +W+ +e+++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w++l ++y+ki +
  AA4G00072 811 KWKPEEIKKVIRMRGELHSRFQVVKGRMALWEEISSNLMAEGINRSPGQCKSLWSSLIQKYEKIFA 876
                7*************************************************************9865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.105.4E-66109359IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.39E-71110524IPR001279Metallo-beta-lactamase
SMARTSM008491.4E-25122319IPR001279Metallo-beta-lactamase
PfamPF127061.8E-10134269IPR001279Metallo-beta-lactamase
PfamPF075211.5E-7460496IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.608.2E-5804870IPR009057Homeodomain-like
PROSITE profilePS500908.153804868IPR017877Myb-like domain
PfamPF138374.7E-12809909No hitNo description
CDDcd122038.12E-22810875No 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: 921 aa     Download sequence    Send to blast
MKSASLQGFS YPSSSHSSSI HSNVHRPASS PFKMASFSAL SICPYTFTFR PISRNRSTVS  60
CSVTAPATGT SSSKTPRRRS NRLEGAGKSM EDSVKRKLEQ FYEGTDGPPL RVLPIGGLGE  120
IGMNCMLVGN YDRYILIDAG VMFPDYDEPG VQKIMPDTGF IRRWKHKIEA VVITHGHEDH  180
IGALPWVIPA LDSNTPIFAS SFTMELIKKR LKENGIFVQS RLKIFKTRSR FMAGPFEIEP  240
ITVTHSIPDC SGLVLRCADG NILHTGDWKI DESPLDGNVF DRVALEEISK EGITLMMSDS  300
TNVLSPGRTL SEKVVADALV RNIMAAKGRV ITTQFASNIH RLGSIKAAAD LTGRKLVFVG  360
MSLRTYLDAA WRDGKASIDP SSLVKIEDIE AYAPKDLLIV TTGSQAEPRA ALNLASYGTS  420
HAFKLTKEDV ILYSAKVIPG NESRVMKMMN RIADIGPNII MGRNEMLHTS GHAYRGELEE  480
VLKIVKPQHF LPVHGELLFL KEHELLGKST GIRHTTVIKN GEMLGVSHLR NRRVLSNGFS  540
LLGRENLQLM YSDGDKAFGT SSELCIDERL RIASDGIIVL SMEIMRPNSD ESRTENSIKG  600
KIRITTRCMW LDKGKLLDAL HKAAHASLSS CPVNCPLSHM ERTVSEVLRK IVRKYSGKRP  660
EVIAIATENP LAVQAEEVNA RLSGEVNVGS GVAALRKVVE GHSKRNRSKK VPKETDPTSK  720
DEIVDSARLL AEEETETSVS TYREDDKLTI NTEDSDDFWK SFITPSSPDE NKTASTVTDP  780
SEAKTEDSKD DDLSDATDAE QKSSKRVRRN KWKPEEIKKV IRMRGELHSR FQVVKGRMAL  840
WEEISSNLMA EGINRSPGQC KSLWSSLIQK YEKIFADLIL NLEPVMSLLQ ECKTEERSKT  900
NWAHFEDMNN ILSELDTPAT T
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-8411066819560RIBONUCLEASE J
5a0t_B3e-8411066819560RIBONUCLEASE J
5a0v_A3e-8411066819560RIBONUCLEASE J
5a0v_B3e-8411066819560RIBONUCLEASE 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapAA4G00072
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_010444239.10.0PREDICTED: uncharacterized protein LOC104726958
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1J3H5W30.0A0A1J3H5W3_NOCCA; Ribonuclease J
STRINGBostr.0568s0468.1.p0.0(Boechera stricta)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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]