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 Cc03_g13140
Common NameGSCOC_T00030596001
Organism
Coffea canephora
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Rubiaceae; Ixoroideae; Coffeeae; Coffea
Family Trihelix
Protein Properties Length: 889aa    MW: 98351.7 Da    PI: 9.1787
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cc03_g13140genomeCGSCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix681.8e-21802882186
     trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +e+++Li++r e+++r++  k +++lWee+s+++ ++g++rsp qCk+ w +l ++y++ k+ +k+r     + +pyfd+++
  Cc03_g13140 802 KWKPEEIKKLIRMRGELHNRFQVVKGRMALWEEISSNLLSGGISRSPGQCKSLWASLVQKYEESKTDSKSR-----EMWPYFDDMN 882
                  7********************************************************************96.....68******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.2E-6588338IPR001279Metallo-beta-lactamase
SuperFamilySSF562815.99E-7189503IPR001279Metallo-beta-lactamase
SMARTSM008495.9E-25101298IPR001279Metallo-beta-lactamase
PfamPF127062.3E-10113248IPR001279Metallo-beta-lactamase
PfamPF075213.7E-7439475IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.223795859IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.605.6E-6796861IPR009057Homeodomain-like
PfamPF138377.8E-17800883No hitNo description
CDDcd122034.73E-22801866No 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
MAAISFSAVS LYPYAHKGSL SRAANPNPSR QCISCCGPSH STSTIGSRGG SREPHKRSRG  60
RAEGPRKSME DSVQRKMEQF YEGSDGPPLR VLPIGGLGEI GMNCMLVGNF DRYILIDAGV  120
MFPGYDELGV QKIIPDTTFI KKWSHKIEAV VITHGHEDHI GALPWVIPAL DARTPIFASS  180
FTMELIKKRL KEFGIFIPSR LKIFKTKMRF VAGPFEVEPI RVTHSIPDCC GLVLRCADGT  240
ILHTGDWKID ETPLDGKVFD RGALEELSKE GVTLMMSDST NVLSPGRTLS ETVVADALLR  300
RISAAKGRVI TTQFASNIHR LGSVKAAADL TGRKLVFVGM ALRTYLDAAW KDGKASIDPS  360
TLVKVEDIDA YSPKDLLIVT TGSQAEPRAA LNLASYGSSH SLKLTQEDLI LYSAKVIPGN  420
ETRVMKMLNR ISDIGSAIVM GKNEYLHSSG HAHREELDEV LKIVKPQHFL PIHGELLFLK  480
EHELLGKSTG IRHTVVIKNG EMLGVSHLRN RRVLSNGFTS LGKENLQLMY SDGDKAFGTS  540
TELCIDERLR IASDGIIVIS MEILRPQASN SLTEKTLKGK IKITTRCLWL DKGKLLDALH  600
KAAHAALSSC PVNSPLVHME RTVSEVLRKV VRKYSSKRPE VIAIALENPA GVLADDINGK  660
LSERSRVGLG ISTLRKAVDG HQRKRRPNGA QEVDDSDSHA HLRSIMQQDL EDNEMDFDKL  720
LSKDEANSVS TSSKAFSSNG AESDNFWKSF VQIPTNNVVE EGNTSLQLQK EHYENSEIDS  780
GELDSGLPKS ELKSSKSVKR NKWKPEEIKK LIRMRGELHN RFQVVKGRMA LWEEISSNLL  840
SGGISRSPGQ CKSLWASLVQ KYEESKTDSK SREMWPYFDD MNTIFVRH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3bk1_A1e-838964817562Metal dependent hydrolase
3bk2_A1e-838964817562Metal 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}.
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_027165522.10.0ribonuclease J isoform X3
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A068UQY70.0A0A068UQY7_COFCA; 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]