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 cra_locus_8014_iso_1
Organism
Catharanthus roseus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthinae; Catharanthus
Family Trihelix
Protein Properties Length: 692aa    MW: 76843.9 Da    PI: 8.9012
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
cra_locus_8014_iso_1genomeMPGR-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix66.17.2e-21600680186
                             trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtse 74 
                                          +W+ +e++ Li++r e+++r++  k +++lWee+s+++ + g++rsp qCk+ w +l ++y++ k  ++++   
  cra_locus_8014_iso_1_len_2773_ver_3 600 KWKPEEIKNLIKMRGELHSRFQVLKGRMALWEEISSNLLSAGINRSPGQCKSLWASLVQKYEESKSDSRSK--- 670
                                          7****************************************************************999984... PP

                             trihelix  75 ssstcpyfdqle 86 
                                            +++pyf++++
  cra_locus_8014_iso_1_len_2773_ver_3 671 --ENWPYFEDMD 680
                                          ..79*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.107.5E-6983333IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.97E-5584347IPR001279Metallo-beta-lactamase
SMARTSM008494.4E-2696293IPR001279Metallo-beta-lactamase
PfamPF127062.7E-11108243IPR001279Metallo-beta-lactamase
PROSITE profilePS500908.107593657IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.606.5E-5594659IPR009057Homeodomain-like
PfamPF138373.5E-18598682No hitNo description
CDDcd122031.73E-22599664No 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: 692 aa     Download sequence    Send to blast
MAAFSFSAFS LSPYTPLGAM KSDSSKRCIS LCSATPSPSK TSTHGARGPR KRSRGRMEGA  60
GRTMDDAIQR KMEEFYEGSD GPPLRVLPIG GLGEIGMNCM LVGNYDRYIL IDAGVMFPGY  120
DELGVQKIIP DTTFIKKWSH KIEAVVITHG HEDHIGALPW VIPALDSRTP IYASSFTMEL  180
IKKRLKEFGV FIPSRLKTFK TRRRFNAGPF EVEPIRVTHS IPDCCGLVLR CADGTILHTG  240
DWKIDESPLD GKVFDREALE ELSKEGVTLM MSDSTNVLSP GRTFSESIVA ESLLRHISAA  300
KGRVIATQFA SNIHRLGSVK AAADLTGRKL VFVGMSLRTY LDAAWKDERL RIASDGIIVV  360
SMEILRPQDA DGLTEKTLKG KIRITTRCLW LDKGKLLDAL HKAAHAALSS CPVNCPLAHM  420
ERTVSEVLRK MVRKYSSKRP EVIAIATENP TGVIADEINR KLSDKSHANF GMSLRKVVDG  480
HQRTQLSGTQ EDVNSRTQLG SITEQESEEH GIDFERLVPE NDEINLNSKS NERFPPNGTE  540
SAAFWQSFVG SAPLNLSEKG ENGLLPQGQH SEESESISSE LELGMPKSKL KSSKPVKRNK  600
WKPEEIKNLI KMRGELHSRF QVLKGRMALW EEISSNLLSA GINRSPGQCK SLWASLVQKY  660
EESKSDSRSK ENWPYFEDMD KILSGLETKL PS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3bk1_A8e-558435217290Metal dependent hydrolase
3bk2_A8e-558435217290Metal dependent hydrolase
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_027165522.10.0ribonuclease J isoform X3
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A068UQY70.0A0A068UQY7_COFCA; Uncharacterized protein
STRINGXP_002511207.10.0(Ricinus communis)
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]