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 Ciclev10018763m
Common NameCICLE_v10018763mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family Trihelix
Protein Properties Length: 913aa    MW: 101013 Da    PI: 8.3332
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10018763mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix68.31.5e-21819898186
         trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                      +W  +ev++Li++r e++++++  k +++lW+e+s +++ +gf+rsp qCk++w++l ++y++ k g+++      +++pyf++++
  Ciclev10018763m 819 KWRPEEVKKLIKMRGELHSKFQIVKGRMALWKEISTHLANEGFNRSPSQCKSRWSSLLQKYEESKSGNSQ------KSWPYFEEMN 898
                      7*******************************************************************98......46*******7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.0E-67108358IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.6E-70109523IPR001279Metallo-beta-lactamase
SMARTSM008492.0E-25121321IPR001279Metallo-beta-lactamase
PfamPF127067.8E-12132268IPR001279Metallo-beta-lactamase
PfamPF075214.4E-6462495IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.607.5E-9812878IPR009057Homeodomain-like
PROSITE profilePS512949.33812880IPR017930Myb domain
SuperFamilySSF466892.12E-5814884IPR009057Homeodomain-like
SMARTSM007172.5E-5816878IPR001005SANT/Myb domain
CDDcd122032.29E-22818883No hitNo description
PfamPF138372.8E-20818900No 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: 913 aa     Download sequence    Send to blast
MQLGLLGSYS FSYSVYLASS SSSTLNKVSA NMAALSALSL SPYNFLCKPI PRIRRSISCS  60
IDTPTTLGAR ESKVPRRRTG RTEGPRKSME DSVQRKMEQF YEGSNGPPLR VLPIGGLGEI  120
GMNCMLVGNY DRYILIDAGV MFPDYDELGV QKITPDTTFI KRWSHKIEAV VITHGHEDHI  180
GALPWVIPAL DSNTPIYASS FTMELIRKRL KENGIFVPSR LKTFKTRRKF MAGPFEIEPI  240
RVTHSIPDCC GLVLRCADGT ILHTGDWKID ESPLDGKVFD REALEELSKE GVTLMMSDST  300
NVLSSGRTTS ESVVKDALMR HVSAAKGRVI TTQFASNIHR LGSVKAAADL TGRKLVFVGM  360
SLRTYLDAAW KDGKAPIDPS TLVKVEDIDA YAPKDLLIVT TGSQAEPRAA LNLASYGGSH  420
SLKLTNEDVI LYSAKVIPGN ESRVMKMLNR ISEIGSTIVM GRNEGLHTSG HGYRGELEEV  480
LKLVKPQHFL PIHGELLFLK EHELLGRSTG IRHSTVIKNG EMLGVSHLRN RRVLSNGFIS  540
LGKENLQLMY SDGDKAFGTS TELCIDERLR IASDGIIVIS MEILRPQHTD GQSGYSLKGK  600
IRITTRCLWL DKGKLLDALH NAAHAALSSC PVNCPLAHME KTVSEVLRKV VRKYSSKRPE  660
VIAVAMENPA AVLSDELNAR LSGNSHVGFG MPALRKMVDR HPKRSQLNRT QAEGDGRQQN  720
LQVDGIEVEE LPEETTTTSN SDYGERLSLD SEDSDEFGKS FVAPASPINS LVKGNNVLIP  780
QEEQQMSELE EDGTEISDDD SSESSSSQPK PSKGVRQNKW RPEEVKKLIK MRGELHSKFQ  840
IVKGRMALWK EISTHLANEG FNRSPSQCKS RWSSLLQKYE ESKSGNSQKS WPYFEEMNKI  900
FSDSDSEAMA TK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A7e-8510966719560RIBONUCLEASE J
5a0t_B7e-8510966719560RIBONUCLEASE J
5a0v_A7e-8510966719560RIBONUCLEASE J
5a0v_B7e-8510966719560RIBONUCLEASE J
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
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_006440090.10.0uncharacterized protein LOC18048021 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLV4TNS70.0V4TNS7_9ROSI; Uncharacterized protein
STRINGXP_006440090.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
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]