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 Thhalv10003624m
Common NameEUTSA_v10003624mg
Organism
Eutrema salsugineum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Eutremeae; Eutrema
Family Trihelix
Protein Properties Length: 917aa    MW: 101185 Da    PI: 8.7788
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Thhalv10003624mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix63.45.1e-20824904186
         trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                      +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     +++++f++++
  Thhalv10003624m 824 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHFEDMN 904
                      7********************************************************************95.....35******97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.104.2E-65115362IPR001279Metallo-beta-lactamase
SuperFamilySSF562811.07E-69116527IPR001279Metallo-beta-lactamase
SMARTSM008492.8E-22128322IPR001279Metallo-beta-lactamase
PfamPF127064.3E-11139275IPR001279Metallo-beta-lactamase
PfamPF075216.2E-7467499IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.072817881IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.7E-5818883IPR009057Homeodomain-like
PfamPF138374.7E-17822905No hitNo description
CDDcd122033.81E-22823888No 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: 917 aa     Download sequence    Send to blast
MKPAASLRGF SYPSSSHASS IYFDVRRPVT STSTPSKMAA FSALSLCPYP FTFRKSSRVR  60
STVSCSVTSP PASGTSSSSK TPRRRSGRLE GAGKSMEDSV KRKMEQFYEG TDGPPLRVLP  120
IGGLGEIGMN CMLVGNYDRY ILIDAGVMFP DFDEPGVQKI MPDTGFIRRW KHKIEAVVIT  180
HGHEDHIGAL PWVIPALDSN TPIFASSFTM ELIKKRLKEH GIFVQSRLKT FNTRRRFMAG  240
PFEIEPITVT HSIPDCSGLV LRCADGNILH TGDWKIDEAP LDGKVFDREA LEELSKEGMM  300
SDSTNVLSPG RTTSEKVVAD ALVRNVMAAK GRVITTQFAS NIHRLGSIKA AADLTGRKLV  360
FVGMSLRTYL EAAWKDGKAP IDPSSLVKVE DIEAYAPKDL LIVTTGSQAE PRAALNLASY  420
GSSHAFKLTK EDIILYSAKV IPGNESRVMK MMNRIADIGP NIVMGKNEML HTSGHAYRGE  480
LEEVLKIVKP QHFLPIHGEL LFLKEHELLG KSTGIRHTTV IKNGEMLGVS HLRNRRVLSN  540
GFSSLGRENL QLMYSDGDKA FGTSSELCID ERLRIASDGI IVLSMEIMRP GDSENTLKGK  600
IRITTRCMWL DKGRLLDALH KAAHAALSSC PVNCPLSHME RTVSEVLRKI VRKYSGKRPE  660
VIAIATENPL AVRADEVSAR LSGDPNLGSG VAALRKVVEG NNKRNRPKKA PSQDDSIKEV  720
DRTLKDDLIN SARLLAEEET TASSYTEDAD DVPVRSSSEE SDDFWKSFID PSSPPSPGET  780
ENVKKVAGAE PKADDSESSR DEDDPSDNTD SQTKSSAKRV RRNKWKPEEV KKVIRMRGEL  840
HSRFQVVKGR MALWEEISSN LSAEGINRSP GQCKSLWASL IQKYEECKAD ERSKTSWSHF  900
EDMNNILSEL DTPAPK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A3e-8411666719560RIBONUCLEASE J
5a0t_B3e-8411666719560RIBONUCLEASE J
5a0v_A3e-8411666719560RIBONUCLEASE J
5a0v_B3e-8411666719560RIBONUCLEASE 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
PlantRegMapThhalv10003624m
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_006394279.10.0uncharacterized protein LOC18013384
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLV4K1180.0V4K118_EUTSA; Uncharacterized protein
STRINGXP_006394279.10.0(Eutrema salsugineum)
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]