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 Csa18g036940.1
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: 900aa    MW: 99566.7 Da    PI: 8.3406
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa18g036940.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix65.61e-20808888186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +e+++ i++r e+++r++  k ++ lWee+s++++++gf+rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  Csa18g036940.1 808 KWKPEEIKKVIRMRGELHSRFQVVKGRMVLWEEISSNLSAEGFNRSPGQCKSLWASLIQKYEECKAEERSK-----TSWPHFEDMN 888
                     7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.107.5E-6797347IPR001279Metallo-beta-lactamase
SuperFamilySSF562817.27E-7298512IPR001279Metallo-beta-lactamase
SMARTSM008492.6E-25110307IPR001279Metallo-beta-lactamase
PfamPF127064.0E-10122257IPR001279Metallo-beta-lactamase
PfamPF075215.5E-7452484IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.601.8E-5800867IPR009057Homeodomain-like
PROSITE profilePS500907.863801865IPR017877Myb-like domain
CDDcd122031.44E-22807872No hitNo description
PfamPF138377.2E-17807889No 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: 900 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 APLDGKVFDR EALEELSKEG VTLMMSDSTN VLSPGRTISE  300
KVVADALVRN VMAAKGRVIT TQFASNIHRL GSIKAAADLT GRKLVFVGMS LRTYLEAAWR  360
DGKAPIDPSS LVKVEDIEAY APKDLLIVTT GSQAEPRAAL NLASYGSSHA FKLTKEDIIL  420
YSAKVIPGNE SRVMKMMNRI ADIGPNIIMG KNEMLHTSGH AYRGELEEVL KIVKPQHFLP  480
IHGELLFLKE HELLGKSTGI RHTTVIKNGE MLGVSHLRNR RVLSNGFSSL GRESLQLMYS  540
DGDKAFGTSS ELCIDERLRI SSDGIIVLSM EIMRPGVSEN TLKGKIRITT RCMWLDKGRL  600
LDALHKAAHA ALSSCPVNCP LSHMERTVSE VLRKIVRKYS GKRPEVIAIA TENPMAVRAD  660
EVSARLSGDP SVGSGVAALR KVVDGNNKRS RPKKTPSQED APKEVDRTLE DDIIDSARLL  720
AEEETAALTY TEEVDMPVGS SSEESDDFWK SFVNPSSSPS PGETDNVNKV TDTEPKTEDK  780
ESSRDDNDLS DTSDSETKSP SKRVRKNKWK PEEIKKVIRM RGELHSRFQV VKGRMVLWEE  840
ISSNLSAEGF NRSPGQCKSL WASLIQKYEE CKAEERSKTS WPHFEDMNNI LSELGTPAS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-879865219560RIBONUCLEASE J
5a0t_B3e-879865219560RIBONUCLEASE J
5a0v_A3e-879865219560RIBONUCLEASE J
5a0v_B3e-879865219560RIBONUCLEASE 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
PlantRegMapCsa18g036940.1
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
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)
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]