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 Rsa1.0_01492.1_g00008.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family Trihelix
Protein Properties Length: 906aa    MW: 100122 Da    PI: 8.6203
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_01492.1_g00008.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.21.2e-19814894186
                 trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                              +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     ++++++++++
  Rsa1.0_01492.1_g00008.1 814 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 894
                              7********************************************************************95.....35999**997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.106.4E-68108358IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.46E-72109523IPR001279Metallo-beta-lactamase
SMARTSM008495.2E-25121318IPR001279Metallo-beta-lactamase
PfamPF127069.6E-11133268IPR001279Metallo-beta-lactamase
PfamPF075215.0E-7463495IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.602.3E-5807873IPR009057Homeodomain-like
PROSITE profilePS500908.107807871IPR017877Myb-like domain
PfamPF138377.0E-17812895No hitNo description
CDDcd122034.12E-22813878No 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: 906 aa     Download sequence    Send to blast
MKPAASLQGY PSSSIYFDAR RPVPTSPSKM AAFSALSLSP YTFTFRQSSR ARPTVSCSVT  60
SPPASSGTSS SSKTPRRRSG RLEGAGKSME DSVKRKMEQF YEGTDGPPLR VLPIGGLGEI  120
GMNCMLVGNY DRYILIDAGI MFPDYDDPGV QKIMPDTGFI RRWKHKIEAV VITHGHEDHI  180
GALPWVIPAL DSNTPIFASS FTMELIKKRL KEHGIFVQSR LKTFNTRRRF MAGPFEVEPI  240
TVTHSIPDCS GLVLRCADGN ILHTGDWKID EAPLDGKVFD REALEELSKE GVTLMMSDST  300
NVLSPGRTTS EKVVADALVR NVMAAKGRVI TTQFASNIHR LGSIKAAADL TGRKLVFVGM  360
SLRTYLEAAW KDGKAPIDPS SLVKVEDIEA YSPKDLLIVT TGSQAEPRAA LNLASYGSSH  420
AFKLTKEDII LYSAKVIPGN ESRVMKMMNR LADIGPKIVM GKNEMLHTSG HAYRGELEEV  480
LKIVKPQHFL PIHGELLFLK EHELLGKSTG IRHTTVIKNG EMLGVSHLRN RRVLSNGFSS  540
LGRENLQLMY SDGDKAFGTA SELCIDERLR ISSDGIIVLS MEIMRPGVSE NTLKGKIRIT  600
TRCMWLDKGR LLDALHKAAH AALSSCPVNC PLSHMERTVS EVLRKIVRKY SGKRPEVIAI  660
AMENPMAVRA DEVSARMSGD PNLGSGVAAL RKVVEGNNKR NRTKKAPSQE EAGEIIDSSV  720
GLLGEEETAS SSSYTEGAED VPVRSSSEES DDFWNSFINP SSPSSPGETK KVDRLTDAET  780
KTEDSESRRE EEEEEGDTSD SQTKSTTKRV RRNKWKPEEV KKVIRMRGEL HSRFQVVKGR  840
MALWEEISSN LSAEGINRSP GQCKSLWASL IQKYEECKAD ERSKTSWSHY EDMNNILSEL  900
DTPAPK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A2e-8610966319560RIBONUCLEASE J
5a0t_B2e-8610966319560RIBONUCLEASE J
5a0v_A2e-8610966319560RIBONUCLEASE J
5a0v_B2e-8610966319560RIBONUCLEASE 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
PlantRegMapRsa1.0_01492.1_g00008.1
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_018432808.10.0PREDICTED: uncharacterized protein LOC108805295
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0D3BFF60.0A0A0D3BFF6_BRAOL; Uncharacterized protein
STRINGBo3g103450.10.0(Brassica oleracea)
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]