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 KFK28054.1
Organism
Arabis alpina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Arabideae; Arabis
Family Trihelix
Protein Properties Length: 896aa    MW: 99366.4 Da    PI: 8.3385
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
KFK28054.1genomeMPIPBRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix65.21.4e-20803883186
    trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                 +W+ +e+++ i++r e+++r++  k +++lWee+s++++ +g++rsp qCk+ w +l ++y+++k+ e+++     +++p+f++++
  KFK28054.1 803 KWKPEEIKKVIRMRGELHSRFQVVKGRMALWEEISSNLSNQGINRSPGQCKSLWASLIQKYEECKAEERSK-----TSWPHFEDMD 883
                 7********************************************************************95.....36*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.5E-65103354IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.38E-71104519IPR001279Metallo-beta-lactamase
SMARTSM008496.7E-26116313IPR001279Metallo-beta-lactamase
PfamPF127061.3E-10128263IPR001279Metallo-beta-lactamase
PfamPF075212.5E-7459491IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
Gene3DG3DSA:1.10.10.601.3E-5796862IPR009057Homeodomain-like
PROSITE profilePS500908.037796860IPR017877Myb-like domain
CDDcd122033.36E-22802867No hitNo description
PfamPF138376.9E-18802885No 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: 896 aa     Download sequence    Send to blast
MKPAASLQGS SMYFDVRRPV TTPSKMAAFS ALSLCPYTFT FRQSSRIRTT VSCSVTSPPA  60
TGTSSSSKAP RRRSDRREGA GKSMEDSVKR KMEQFYEGAD GPPLRVLPIG GLGEIGMNCM  120
LVGNYDRYIL IDAGVMFPDY DEPGVQKIMP DTGFIRRWRH KIEAVVITHG HEDHIGALPW  180
VIPALDPNTP IFASSFTMEL IKKRLKEHGI FVQSRLKIFN TRRRFMAGPF EIEPITVTHS  240
IPDCSGLVLR CADGNILHTG DWKIDEAPLD GKVFDREALE EISKEGITLM MSDSTNVLSP  300
GRTISEKVVA DALVRNVMAA NGRRVITTQF ASNIHRLGSI KAAADLTGRK LVFVGMSLRT  360
YLEAAWRDGK APIDPSSLVK VEDIEAYAPK DLLIVTTGSQ AEPRAALNLA SYGSSHMFKL  420
TKEDIILYSA KVIPGNESRV MKMMNRIADI GPNIIMGKNE MLHTSGHAYR GELEEVLKIV  480
KPQHFLPVHG ELLFLKEHEL LGKSTGIRHT TVIKNGEMLG VSHLRNRRVL SNGFSFLGRE  540
NLQLMYSDGD KAFGTSSELC IDERLRIASD GIIVLSMEIM RPGASEDTIK GKIRITTRCM  600
WLDKGRLLDA LHKAAHATLS SCPVNCPLSH MERTVSEILR KTVRKYSGKR PEVIAIATEN  660
PMAVRAEEVS ARLSGDPNLG SGVAALRKVV EGNNKRNRPN KAPSREDSPK EDLIDSARVL  720
AEEETSASSY TEDADDTPVL SSSEESDDFW KSFINPSSPD ETETVNKVTN AEPKTEDSES  780
SDDPSDALDT QTKSSSKRVK KNKWKPEEIK KVIRMRGELH SRFQVVKGRM ALWEEISSNL  840
SNQGINRSPG QCKSLWASLI QKYEECKAEE RSKTSWPHFE DMDNILSELG TGTQAT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A1e-8810465919560RIBONUCLEASE J
5a0t_B1e-8810465919560RIBONUCLEASE J
5a0v_A1e-8810465919560RIBONUCLEASE J
5a0v_B1e-8810465919560RIBONUCLEASE 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
PlantRegMapKFK28054.1
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_006394279.10.0uncharacterized protein LOC18013384
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A087GDV20.0A0A087GDV2_ARAAL; Uncharacterized protein
STRINGA0A087GDV20.0(Arabis alpina)
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]