PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Dca8459.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus
Family Trihelix
Protein Properties Length: 881aa    MW: 97722.8 Da    PI: 7.7177
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Dca8459.1genomeDCAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix69.65.9e-22789869186
   trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                rW+ +ev++Li++r e+++r++ +k +++lWee+s+ + + gf+r+p qCk+ w +l ++y++ k+ ek++     +++py++q++
  Dca8459.1 789 RWKPEEVKKLIKLRGELHDRFQVAKGRMALWEEISSSLLSDGFNRTPAQCKSLWASLVQKYEESKNDEKSN-----TNWPYYEQMN 869
                8********************************************************************95.....58*******7 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.106.7E-6774324IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.98E-7175489IPR001279Metallo-beta-lactamase
SMARTSM008493.0E-2487284IPR001279Metallo-beta-lactamase
PfamPF127061.1E-1099234IPR001279Metallo-beta-lactamase
PfamPF075218.7E-8430461IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.293782846IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.6E-6784848IPR009057Homeodomain-like
SMARTSM007170.0038786848IPR001005SANT/Myb domain
PfamPF138372.0E-18787870No hitNo description
CDDcd122034.73E-23788853No 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: 881 aa     Download sequence    Send to blast
MAAFTCISIC PCLSYRPNLV KRYISCSLRP PAVGTSASKV PRRRSGRLEG PSKSMEDSVK  60
RKMEQFYEGS TGPPLRVLPI GGLGEIGMNC MLVGNYDRYI LIDAGIMFPD FDEFGVQKII  120
PDTTFIKRWS HKIEAVIITH GHEDHIGALP WVIPALDPKT PIFASSFTME LIKKRLKEFG  180
IFVPSRLKIF RTRKRFAAGP FEIEPVRVTH SIPDCSGLVM RCADGTIFHT GDWKIDESPV  240
DGKNFDREAL EELSKEGVTL MMSDSTNILS PGRTISESVV ADSLLRQISE AKGRVITTQF  300
ASNIHRLGSV KAAADATGRK LVFVGMSLRT YLDAAWKDGK APIDPSSLVK VEDIDSYAPR  360
DLLIVTTGSQ AEPRAALNLA SYGSSHSLKL SKEDVILYSA KVIPGNETRC MKMFNRIAEL  420
GSTLIMGKNE MLHTSGHAYR EELAEVLKIV KPQHFLPVHG ELLFLKEHEL LGKSTGVHHT  480
TVIKNGEMLG VSHLRNRRVL SNGFISLGKE NLQLMYNDGD KAFGTSAELC IDERMKIASD  540
GIIVISMEIL RPGAVEGFTE NCLKGKIRIT TRCLWLDKGK LLDALHKAAH ASLSSCPVNC  600
PLSHMERTVS EMLRKVVRKY SGKRPEIIAI ATENPAAVLS DEVNERLSGK SRPRIGISAL  660
RKTVDGHYKT KKTDIVDDQD DDLVSEATTS QLDSEDGNEF DGLLTKEDDD KAASNIARSS  720
DKSQDLNDTW KSFFASTSLP KDEIDENNAA SGLLEQNVGK ITGKEVNKDE SSELPSSPSE  780
ALKSTKRNRW KPEEVKKLIK LRGELHDRFQ VAKGRMALWE EISSSLLSDG FNRTPAQCKS  840
LWASLVQKYE ESKNDEKSNT NWPYYEQMNT ILSNLGEVSD S
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-837563319560RIBONUCLEASE J
5a0t_B1e-837563319560RIBONUCLEASE J
5a0v_A1e-837563319560RIBONUCLEASE J
5a0v_B1e-837563319560RIBONUCLEASE 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_010677898.10.0PREDICTED: uncharacterized protein LOC104893494 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]