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_016404
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: 889aa    MW: 98999.1 Da    PI: 7.8426
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
DCAR_016404genomeARS-USDAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.35.5e-20799879186
     trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +e+++Li++r+e+++r++  k +++lWee+s+++ + g+ rs+ qCk+ w +l ++y+++k+ ek+r     +t++yf++++
  DCAR_016404 799 KWKPEEIKKLIKFRKELNSRFQVVKGRMALWEEISAALLADGIVRSAGQCKSLWASLTQKYEECKNDEKSR-----KTWSYFEDVN 879
                  7********************************************************************96.....78****9976 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.107.8E-6676326IPR001279Metallo-beta-lactamase
SuperFamilySSF562815.24E-7177491IPR001279Metallo-beta-lactamase
SMARTSM008491.3E-2489286IPR001279Metallo-beta-lactamase
PfamPF127069.4E-11101236IPR001279Metallo-beta-lactamase
PfamPF075216.4E-8430464IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.677792856IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.2E-4796858IPR009057Homeodomain-like
PfamPF138375.7E-16797880No hitNo description
CDDcd122031.14E-20798863No 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: 889 aa     Download sequence    Send to blast
MAAFSAISLY PYKIWHTPTF RKSPISCALP SGNVTGTRGS RSPRNRSGRR EGAGKSMEDS  60
VKRKMEQFYE GSDGPPLRVL PIGGLGEIGM NCMLVGNFDR YILIDAGIMF PDYDDLGVQK  120
IIPDTTFIKK WRHKIEAVII THGHEDHIGA LPWVIPALDS RTPIFASSFT MELIKRRLKE  180
FGIFVSSRLK TFKTKRRFNA GPFEIEPIRV THSIPDCCGL VLRCADGTIL HTGDWKIDES  240
PLDGKVFDRE GLEELSKEGV TLMMSDSTNV LSPGRTFSET VVADSLLRHI SAATGRVITT  300
QFASNIHRLG SVKAAADLTG RKLVFVGMSL RTYLEAAWRD GNAPIDPSTL VKVEDIDAYA  360
PKDLLIVTTG SQAEPRAALN LASYGSSHSL KLSKEDLILY SAKVIPGNET RVMKMMNRIA  420
EIGSTLVMGK NEQLHTSGHA HREELEEVLR IVKPQHFLPI HGELLFLKEH ELLGKANGIH  480
HTTVIKNGEM LGVSHLRNRK VLSNGFISLG KENLQLMYSD GDKAFGTSAE LRVDERLRIA  540
TDGVIVVSME IIRPQPNDSD EKTLKGKIRI TTRCLWLDKG KLLDALHKAA HAALSSCPLN  600
CPLAHMERIV SEVLRKLVRK YSSKRPDVIV IAIENPTGVL SDELNGKKPG KSQIDFRIPK  660
LKIGVHEHAE KRRASKNKEE SDKGRPVETS AQESKDGDVD NDEIDELLSE EDLTSTSEED  720
LTSTSEEDLT STSSLAKKNS ESDDFWKSFV VPVNEHEQDS EGVATPEQKA EAKIASSKND  780
PFDLPKSELK SSTPSKRNKW KPEEIKKLIK FRKELNSRFQ VVKGRMALWE EISAALLADG  840
IVRSAGQCKS LWASLTQKYE ECKNDEKSRK TWSYFEDVND ILVEFQNN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-827763419560RIBONUCLEASE J
5a0t_B1e-827763419560RIBONUCLEASE J
5a0v_A1e-827763419560RIBONUCLEASE J
5a0v_B1e-827763419560RIBONUCLEASE 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_017252987.10.0PREDICTED: ribonuclease J-like isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A161YIS60.0A0A161YIS6_DAUCS; Uncharacterized protein
STRINGXP_002511207.10.0(Ricinus communis)
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]