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 30147.m014528
Common NameRCOM_1506620
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family Trihelix
Protein Properties Length: 880aa    MW: 97845.2 Da    PI: 8.8654
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
30147.m014528genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.54.9e-20788868186
       trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                    +W+ +e+++Li++r ++++r++  k +++lWeevs++++  g++rsp qCk+ w +ln++y++ k  e+++   +   +p++++++
  30147.m014528 788 KWKPEEIKKLIKVRGKLHDRFQVVKGRMALWEEVSNRLMIDGINRSPGQCKSLWASLNQKYEESKSDENGQ---T--VWPHYEDMD 868
                    7*******************************************************************984...3..5*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.104.4E-6978328IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.06E-7179493IPR001279Metallo-beta-lactamase
SMARTSM008499.6E-2691288IPR001279Metallo-beta-lactamase
PfamPF127063.9E-10103238IPR001279Metallo-beta-lactamase
PfamPF075218.3E-6436465IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.863781845IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.605.4E-5781846IPR009057Homeodomain-like
PfamPF138373.6E-18786870No hitNo description
CDDcd122036.81E-20787852No 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: 880 aa     Download sequence    Send to blast
MAAFSAISLC PYSLLHRPRP STRKYPISCS IGSSSTIGSH GSKAPRKRSG RMEGAGKSME  60
DSVQRKMEQF YEGSNGPPLR IVPIGGLGEI GMNCMLVGNY DRYILIDAGV MFPDYDELGV  120
QKIIPDTTFI KRWSHKIEAV IITHGHEDHI GALPWVIPAL DSRTPIYASS FTMELIKKRL  180
KEHGIFLPSR LKVFRTRKKF IAGPFEVEPI RVTHSIPDCC GLVLRCSDGT ILHTGDWKID  240
ESPLDGKVFD REALEELSKE GVTLMMSDST NVLSPGRTIS ESVVADSLLR HISAAKGRII  300
TTQFASNIHR LGSVKAAADL TGRKLVFVGM SLRTYLDAAW KDGKAPIDPS TLVKVEDIDA  360
YAPKDLLIVT TGSQAEPRAA LNLASYGSSH SFKLNKDDII LYSAKVIPGN ESRVMKMMNR  420
ISEIGSTLVM GKNELLHTSG HGYRGELEEV LRIVKPQHFL PIHGELLFLK EHELLGKSTG  480
VRHTTVIKNG EMLGVSHLRN RKVLSNGFIS LGKENLQLMY NDGDKAFGTS TELCIDERLR  540
IATDGIIVIS MEILRPQNAE SLTANTIKGK IRITTRCLWL DKGKLLDALH KAAQAALSSC  600
PVNCPLSHME KTVSEILRKM VRKYSGKRPE VIAIAVENPA GVLSDELKTR LSGNSRVGFG  660
ISALKKVVDG YPTRNRSNKT QMESNGYMHV DNTLQQNLEV DDSEVGRLQP DENTAASISS  720
SPDRLPSNSQ DQDDFWKSFV SSNPIDTLVP QSEHIKELED DGSLSSDDES MEMQDQKSKP  780
SKRVKRNKWK PEEIKKLIKV RGKLHDRFQV VKGRMALWEE VSNRLMIDGI NRSPGQCKSL  840
WASLNQKYEE SKSDENGQTV WPHYEDMDKI LSAFGEMTTK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-877963719560RIBONUCLEASE J
5a0t_B3e-877963719560RIBONUCLEASE J
5a0v_A3e-877963719560RIBONUCLEASE J
5a0v_B3e-877963719560RIBONUCLEASE 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
PlantRegMap30147.m014528
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_002511207.20.0uncharacterized protein LOC8266322 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLB9RAI20.0B9RAI2_RICCO; Uncharacterized protein
STRINGXP_002511207.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF50993450
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]