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 AT5G63420.1
Common Nameemb2746
Organism
Arabidopsis thaliana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family Trihelix
Protein Properties Length: 911aa    MW: 100554 Da    PI: 8.3897
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT5G63420.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.16.2e-20820900186
     trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                  +W+ +e+++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y++ k+ e+++     +++p+f++++
  AT5G63420.1 820 KWKPEEIKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEESKADERSK-----TSWPHFEDMN 900
                  7********************************************************************95.....36******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.0E-66109359IPR001279Metallo-beta-lactamase
SuperFamilySSF562813.74E-72110524IPR001279Metallo-beta-lactamase
SMARTSM008492.6E-25122319IPR001279Metallo-beta-lactamase
PfamPF127064.6E-10134269IPR001279Metallo-beta-lactamase
PfamPF075215.5E-7464496IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.84813877IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.604.4E-5815879IPR009057Homeodomain-like
PfamPF138375.3E-17819901No hitNo description
CDDcd122032.96E-22819884No 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
GO:0003824Molecular Functioncatalytic activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009005anatomyroot
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009010anatomyseed
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0009052anatomyflower pedicel
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025281anatomypollen
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 911 aa     Download sequence    Send to blast
MMKPASLQGF SSHASSSIYS DVRRPATTPS KMAAFSALSL CPYTFTFRQS SRIKSTVSCS  60
VTSAPASGTS SSSKTPRRRS GRLEGVGKSM EDSVKRKMEQ FYEGTDGPPL RILPIGGLGE  120
IGMNCMLVGN YDRYILIDAG IMFPDYDEPG IQKIMPDTGF IRRWKHKIEA VVITHGHEDH  180
IGALPWVIPA LDPNTPIFAS SFTMELIKKR LKEHGIFVQS RLKTFSTRRR FMAGPFEIEP  240
ITVTHSIPDC SGLFLRCADG NILHTGDWKI DEAPLDGKVF DREALEELSK EGVTLMMSDS  300
TNVLSPGRTI SEKVVADALV RNVMAAKGRV ITTQFASNIH RLGSIKAAAD ITGRKLVFVG  360
MSLRTYLEAA WRDGKAPIDP SSLIKVEDIE AYAPKDLLIV TTGSQAEPRA ALNLASYGSS  420
HAFKLTKEDI ILYSAKVIPG NESRVMKMMN RIADIGPNII MGKNEMLHTS GHAYRGELEE  480
VLKIVKPQHF LPIHGELLFL KEHELLGKST GIRHTTVIKN GEMLGVSHLR NRRVLSNGFS  540
SLGRENLQLM YSDGDKAFGT SSELCIDERL RISSDGIIVL SMEIMRPGVS ENTLKGKIRI  600
TTRCMWLDKG RLLDALHKAA HAALSSCPVT CPLSHMERTV SEVLRKIVRK YSGKRPEVIA  660
IATENPMAVR ADEVSARLSG DPSVGSGVAA LRKVVEGNDK RSRAKKAPSQ EASPKEVDRT  720
LEDDIIDSAR LLAEEETAAS TYTEEVDTPV GSSSEESDDF WKSFINPSSS PSPSETENMN  780
KVADTEPKAE GKENSRDDDE LADASDSETK SSPKRVRKNK WKPEEIKKVI RMRGELHSRF  840
QVVKGRMALW EEISSNLSAE GINRSPGQCK SLWASLIQKY EESKADERSK TSWPHFEDMN  900
NILSELGTPA S
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A6e-8711066419560RIBONUCLEASE J
5a0t_B6e-8711066419560RIBONUCLEASE J
5a0v_A6e-8711066419560RIBONUCLEASE J
5a0v_B6e-8711066419560RIBONUCLEASE J
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.289990.0flower| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO283936160.0
Genevisible247386_at0.0
Expression AtlasAT5G63420-
AtGenExpressAT5G63420-
ATTED-IIAT5G63420-
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}.
Function -- GeneRIF ? help Back to Top
  1. a major role of chloroplast RNase J is RNA surveillance to prevent overaccumulation of antisense RNA, which would otherwise exert deleterious effects on chloroplast gene expression. [RNase J]
    [PMID: 22033332]
  2. Ribonuclease J (RNase J) may play a vital role in embryo morphogenesis and apical-basal pattern formation by regulating chloroplast development.
    [PMID: 25871650]
  3. The robust endonucleolytic activity of AtRNase J suggests its involvement in the processing and degradation of RNA in the chloroplast.
    [PMID: 30511330]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT5G63420.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT5G63420
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
RefseqNP_201147.20.0RNA-metabolising metallo-beta-lactamase family protein
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A178UH950.0A0A178UH95_ARATH; Emb2746
STRINGAT5G63420.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
Representative plantOGRP30821521
Publications ? help Back to Top
  1. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  2. Kleffmann T, et al.
    The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions.
    Curr. Biol., 2004. 14(5): p. 354-62
    [PMID:15028209]
  3. Tzafrir I, et al.
    Identification of genes required for embryo development in Arabidopsis.
    Plant Physiol., 2004. 135(3): p. 1206-20
    [PMID:15266054]
  4. Thimmapuram J,Duan H,Liu L,Schuler MA
    Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome.
    RNA, 2005. 11(2): p. 128-38
    [PMID:15659355]
  5. Hammond JP, et al.
    A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes.
    New Phytol., 2006. 170(2): p. 239-60
    [PMID:16608451]
  6. Zybailov B, et al.
    Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.
    PLoS ONE, 2008. 3(4): p. e1994
    [PMID:18431481]
  7. Jones AM, et al.
    Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.
    J Proteomics, 2009. 72(3): p. 439-51
    [PMID:19245862]
  8. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
    [PMID:19376835]
  9. 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]
  10. Sharwood RE,Halpert M,Luro S,Schuster G,Stern DB
    Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA.
    RNA, 2011. 17(12): p. 2165-76
    [PMID:22033332]
  11. Stoppel R,Meurer J
    The cutting crew - ribonucleases are key players in the control of plastid gene expression.
    J. Exp. Bot., 2012. 63(4): p. 1663-73
    [PMID:22140236]
  12. Ingelsson B,Vener AV
    Phosphoproteomics of Arabidopsis chloroplasts reveals involvement of the STN7 kinase in phosphorylation of nucleoid protein pTAC16.
    FEBS Lett., 2012. 586(9): p. 1265-71
    [PMID:22616989]
  13. Chen H,Zou W,Zhao J
    Ribonuclease J is required for chloroplast and embryo development in Arabidopsis.
    J. Exp. Bot., 2015. 66(7): p. 2079-91
    [PMID:25871650]
  14. 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]