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 DCAR_026220
Organism
Daucus carota
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Apiineae; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus
Family Trihelix
Protein Properties Length: 899aa    MW: 99755.6 Da    PI: 8.4169
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
DCAR_026220genomeARS-USDAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix58.61.6e-18806886186
     trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +ev++Li++r e+++r++  k +++lWee+s+ + + g+ rsp qCk+ w +l ++y++ k+ ++++     +++ yf++++
  DCAR_026220 806 KWKPEEVKKLIQFRGELNSRFQVIKGRMALWEEISASLLACGIYRSPGQCKSLWASLTQKYEESKKDMESE-----KSWLYFEDMN 886
                  7****************************************************************999983.....56******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.4E-65103353IPR001279Metallo-beta-lactamase
SuperFamilySSF562816.26E-73104518IPR001279Metallo-beta-lactamase
SMARTSM008493.7E-25116313IPR001279Metallo-beta-lactamase
PfamPF007537.9E-10117261IPR001279Metallo-beta-lactamase
PfamPF075212.9E-8457490IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.77799863IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.606.3E-5800865IPR009057Homeodomain-like
PfamPF138379.0E-17804887No hitNo description
CDDcd122034.52E-20805870No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 899 aa     Download sequence    Send to blast
MAIAFSTMPL YPYKLWHRRP NCKKSFISCS PPSTTTSTAN AGGVMLPGHC DLHKIAVHGL  60
GTGRIGSKGP QKRSGRLEGA GKSMEDSVKR KMEHFYEGSD GPPLRVLPIG GLGEIGMNCM  120
LVGNFDRYIM IDAGIMFPDD DELGIQKIIP DTTFIKKWSH KIEAVIITHG HEDHIGALPW  180
VIPALDPRTP IFASSFTMEL IKRRLKEFGI FVPSRLKTFR TKRKFNAGPF EIEPIRVTHS  240
IPDCSGLVLR CADGTILHTG DWKIDETPLD GKVFDREGLE ELSKEGVTLM MSDSTNILSP  300
GRTFSEAVVA NSLLRHISAA KGRVITTQFA SNIHRLGSIK AAADLTGRKL VFVGMSLRTY  360
LDAAYKDGKA PIDPSTLVKI EDIDAYAPKD LLIVTTGSQA EPRAALNLAS HGSSHSLKLS  420
KEDVILYSAK VIPGNENQVM KMLNRVAEIG STIVMGKHEQ LHTSGHAYRE ELEEVIRIVK  480
PQHFLPIHGE LLFLKEHELL GRANGIQHTT VIKNGEMLGV SHLRNRRVLS NGFVSLGKEN  540
LQLMYSDGDK AFGTSTDLCV DERQRIATDG IIVVSMEIMR PQTTDGFEKA LKGKIRITTR  600
CLWLDKGKLL DALHKAAHAA LSSCPVNCPL AHMERIVSEV LRKMVRKYSS KRPDIIAIAI  660
ENPAAVLADE INEKLSGRSH VDSGLRAMRK GINELAKNKK SNRRRDEKDN DHTYPVHTRP  720
EETEEYGTEI ERLLPEEETC SNSGLSDTNS EDFDDIQKSS MVLTAVDSLE DGSNGAPTVE  780
ECREMAKKAS SEGDSPKSSK SAKRNKWKPE EVKKLIQFRG ELNSRFQVIK GRMALWEEIS  840
ASLLACGIYR SPGQCKSLWA SLTQKYEESK KDMESEKSWL YFEDMNNILL KLEATPTK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A2e-8710466119560RIBONUCLEASE J
5a0t_B2e-8710466119560RIBONUCLEASE J
5a0v_A2e-8710466119560RIBONUCLEASE J
5a0v_B2e-8710466119560RIBONUCLEASE 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_017219494.10.0PREDICTED: ribonuclease J isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A164UNR90.0A0A164UNR9_DAUCS; Uncharacterized protein
STRINGSolyc03g111260.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58742331
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]