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 maker-scaffold01669-snap-gene-0.31-mRNA-1
Organism
Castanea mollissima
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Castanea
Family Trihelix
Protein Properties Length: 856aa    MW: 95139.1 Da    PI: 8.8154
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
maker-scaffold01669-snap-gene-0.31-mRNA-1genomeTHGPView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix60.93.1e-19762842186
                                   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikege 68 
                                                +W+ +ev++Li++r e++++++  k +++lWe++s  + + g++rsp qCk+ w +l  +y++ k+g+
  maker-scaffold01669-snap-gene-0.31-mRNA-1 762 KWKPEEVKKLIDLRGELHSKFQVVKGRMALWEQISGSLLSDGINRSPGQCKSLWTSLVLKYEESKNGK 829
                                                7****************************************************************999 PP

                                   trihelix  69 kkrtsessstcpyfdqle 86 
                                                ++     ++++p+f++++
  maker-scaffold01669-snap-gene-0.31-mRNA-1 830 ES-----TESWPFFEDMR 842
                                                98.....578******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.106.0E-5798329IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.03E-6499494IPR001279Metallo-beta-lactamase
SMARTSM008493.5E-19111289IPR001279Metallo-beta-lactamase
PfamPF007534.8E-8112181IPR001279Metallo-beta-lactamase
PfamPF075211.6E-5434466IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.084755819IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.3E-5756819IPR009057Homeodomain-like
PfamPF138375.1E-17760842No hitNo description
CDDcd122037.07E-21761826No 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: 856 aa     Download sequence    Send to blast
MKSAFRDGFA PSSALSSHQR MAAFGALSLC PYSLLCRPKY TTKRFVSCSV GSQTSSIDTR  60
RSKVPRKRSG KMDGPRKSME DSVQRKMEQF YEGSDGPPLR VLPIGGLGEI GMNCMLVGNY  120
DRYILIDAGV MFPDYDELGV QKIVPDTTFI KRWSHKIEAV VITHGHEDHI GALPWLIKKR  180
LKENGIFVPS RLRVFRTRRK FVAGPFEIEP IRVTHSIPDC CGLVLRCTDG TILHTGDWKI  240
DETPLDGKVF DREALEELSK EGVTLMMSDS TNILSPGRTI SESVVANSLL RRISEAKGRV  300
ITTQFASNIH RLGSVKAAAD LTGRKLVFVG MSLRTYLDAA WKDGKAPIDP STLVKIEDID  360
AYAPKDLLIV TTGSQAEPRA ALNLASYGGS HSLKLSKEDV ILYSAKVIPG NESRVMKMLN  420
RISEIGSSIV MGKNEGLHTS GHGYRGELEE ILQIVKPQHF LPIHGELLFL KEHELLGRST  480
GIRHSCVIKN GEMLGVSHLR NRRVLSSGFT SLGKENLQLM YSDGDKAFGT SSELCIDERQ  540
RIASDGIIVV SMEILRPQNI DGMIENSLKG KIRITTRCLW LDKGKLLDAL HKAAHAALSS  600
LPVNCPLSHM ERTVAELLRK MVRKYSSKRP EVIAIALENP AAVLSDEVNA RLSGKSHVGY  660
GISALRKVVD GHSEENRLLA EEDTIASSSS LAERPFSDSE DSDHFWKAFV TSSSPVDEVA  720
KDNNGFVPRS KHVSMVEKDS VESGKDESSK PPNSSKPVKR NKWKPEEVKK LIDLRGELHS  780
KFQVVKGRMA LWEQISGSLL SDGINRSPGQ CKSLWTSLVL KYEESKNGKE STESWPFFED  840
MRDQEWEEKQ EELAIF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-839963819560RIBONUCLEASE J
5a0t_B4e-839963819560RIBONUCLEASE J
5a0v_A4e-839963819560RIBONUCLEASE J
5a0v_B4e-839963819560RIBONUCLEASE 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_023924136.10.0uncharacterized protein LOC112035548 isoform X2
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A2I4F0F00.0A0A2I4F0F0_JUGRE; uncharacterized protein LOC108994388 isoform X1
STRINGEOY224510.0(Theobroma cacao)
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]