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 Csa18g036940.2
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family Trihelix
Protein Properties Length: 858aa    MW: 95099.6 Da    PI: 8.8525
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa18g036940.2genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix65.79.8e-21731811186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +e+++ i++r e+++r++  k ++ lWee+s++++++gf+rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  Csa18g036940.2 731 KWKPEEIKKVIRMRGELHSRFQVVKGRMVLWEEISSNLSAEGFNRSPGQCKSLWASLIQKYEECKAEERSK-----TSWPHFEDMN 811
                     7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.105.5E-5497312IPR001279Metallo-beta-lactamase
SuperFamilySSF562819.52E-5598435IPR001279Metallo-beta-lactamase
SMARTSM008492.0E-22110314IPR001279Metallo-beta-lactamase
PfamPF127062.1E-10122260IPR001279Metallo-beta-lactamase
Gene3DG3DSA:1.10.10.601.7E-5723790IPR009057Homeodomain-like
PROSITE profilePS500907.863724788IPR017877Myb-like domain
PfamPF138376.7E-17730812No hitNo description
CDDcd122031.39E-22730795No 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: 858 aa     Download sequence    Send to blast
MKPASLQGFS SSLNYSDVRR PAKMAAFSAL SLCPHTFNFR PNSRIKCSVT SAPASGTSSS  60
PKTQRRRSGR PEGAGKSMED SVKRKMEQFY EGTDGPPLRV LPIGGLGEIG MNCMLVGNYD  120
RYILIDAGIM FPDYDEPGVQ KIMPDTGFIR RWKHKIEAVV ITHGHEDHIG ALPWVIPALD  180
PNTPIFASSF TMELIKKRLK EHGIFVQSRL KTFSTRRRFM AGPFEIEPIT VTHSIPDCSG  240
LFLRCADGNI LHTGDWKIDE APLDGKVFDH ALVRNVMAAK GRVITTQFAS NIHRLGSIKA  300
AADLTGRKLV FVGMSLRTYL EAAWRDGKAP IDPSSLVKVE DIEAYAPKDL LIVTTGSQAE  360
PRAALNLASY GSSHAFKLTK EDIILYSAKE EVLKIVKPQH FLPIHGELLF LKEHELLGKS  420
TGIRHTTVIK NGEMLGVSHL RNRRVLSNGF SSLGRESLQL MYSDGDKAFG TSSELCIDER  480
LRISSDGIIV LSMEIMRPGV SENTLKGKIR ITTRCMWLDK GRLLDALHKA AHAALSSCPV  540
NCPLSHMERT VSEVLRKIVR KYSGKRPEVI AIATENPMAV RADEVSARLS GDPSVGSGVA  600
ALRKVVDGNN KRSRPKKTPS QEDAPKEVDR TLEDDIIDSA RLLAEEETAA LTYTEEVDMP  660
VGSSSEESDD FWKSFVNPSS SPSPGETDNV NKVTDTEPKT EDKESSRDDN DLSDTSDSET  720
KSPSKRVRKN KWKPEEIKKV IRMRGELHSR FQVVKGRMVL WEEISSNLSA EGFNRSPGQC  780
KSLWASLIQK YEECKAEERS KTSWPHFEDM NNILSETISE KVVADALVRN VMAAKGRVIT  840
TQFASNIHRL GKYQSCC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A5e-549857519560RIBONUCLEASE J
5a0t_B5e-549857519560RIBONUCLEASE J
5a0v_A5e-549857519560RIBONUCLEASE J
5a0v_B5e-549857519560RIBONUCLEASE 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa18g036940.2
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1765470.0AK176547.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL25-06-L06.
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010484076.10.0PREDICTED: uncharacterized protein LOC104762480
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLR0G7Y90.0R0G7Y9_9BRAS; Uncharacterized protein
STRINGXP_010484076.10.0(Camelina sativa)
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]