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Protein

60S ribosomal protein L13-3

Gene

RPL13D

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-ATH-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-ATH-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-ATH-72689. Formation of a pool of free 40S subunits.
R-ATH-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Names & Taxonomyi

Protein namesi
Recommended name:
60S ribosomal protein L13-3
Gene namesi
Name:RPL13D
Ordered Locus Names:At5g23900
ORF Names:MRO11.6
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G23900.

Subcellular locationi

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: TAIR
  • cytosolic ribosome Source: TAIR
  • membrane Source: TAIR
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 20620660S ribosomal protein L13-3PRO_0000240515Add
BLAST

Proteomic databases

PaxDbiQ9FF90.
PRIDEiQ9FF90.

PTM databases

iPTMnetiQ9FF90.

Expressioni

Gene expression databases

GenevisibleiQ9FF90. AT.

Interactioni

Protein-protein interaction databases

BioGridi17730. 2 interactions.
STRINGi3702.AT5G23900.1.

Structurei

3D structure databases

ProteinModelPortaliQ9FF90.
SMRiQ9FF90. Positions 1-196.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L13e family.Curated

Phylogenomic databases

eggNOGiKOG3295. Eukaryota.
COG4352. LUCA.
HOGENOMiHOG000170452.
InParanoidiQ9FF90.
KOiK02873.
OMAiIAHNHFR.
PhylomeDBiQ9FF90.

Family and domain databases

InterProiIPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
[Graphical view]
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiPF01294. Ribosomal_L13e. 1 hit.
[Graphical view]
PROSITEiPS01104. RIBOSOMAL_L13E. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9FF90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKHNNVIPSS HFRKHWQNYV KTWFNQPARK TRRRVARQKK AVKIFPRPTS
60 70 80 90 100
GPLRPVVHGQ TLKYNMKVRA GKGFTLEELK VAGIPKKLAP TIGISVDHRR
110 120 130 140 150
KNRSLEGLQS NVQRLKTYKA KLVVFPRRSR QVKAGDSTPE ELANATQVQG
160 170 180 190 200
DYMPIASVKA AMELVKLTAD LKAFKAYDKI RLERTNARHA GARAKRAAEA

EKEEKK
Length:206
Mass (Da):23,485
Last modified:March 1, 2001 - v1
Checksum:iE29C7C6C3E9C35D2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB005244 Genomic DNA. Translation: BAB10063.1.
CP002688 Genomic DNA. Translation: AED93230.1.
AF378895 mRNA. Translation: AAK55698.1.
AY052746 mRNA. Translation: AAK96460.1.
RefSeqiNP_197778.1. NM_122295.3.
UniGeneiAt.8750.

Genome annotation databases

EnsemblPlantsiAT5G23900.1; AT5G23900.1; AT5G23900.
GeneIDi832455.
GrameneiAT5G23900.1; AT5G23900.1; AT5G23900.
KEGGiath:AT5G23900.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB005244 Genomic DNA. Translation: BAB10063.1.
CP002688 Genomic DNA. Translation: AED93230.1.
AF378895 mRNA. Translation: AAK55698.1.
AY052746 mRNA. Translation: AAK96460.1.
RefSeqiNP_197778.1. NM_122295.3.
UniGeneiAt.8750.

3D structure databases

ProteinModelPortaliQ9FF90.
SMRiQ9FF90. Positions 1-196.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi17730. 2 interactions.
STRINGi3702.AT5G23900.1.

PTM databases

iPTMnetiQ9FF90.

Proteomic databases

PaxDbiQ9FF90.
PRIDEiQ9FF90.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G23900.1; AT5G23900.1; AT5G23900.
GeneIDi832455.
GrameneiAT5G23900.1; AT5G23900.1; AT5G23900.
KEGGiath:AT5G23900.

Organism-specific databases

TAIRiAT5G23900.

Phylogenomic databases

eggNOGiKOG3295. Eukaryota.
COG4352. LUCA.
HOGENOMiHOG000170452.
InParanoidiQ9FF90.
KOiK02873.
OMAiIAHNHFR.
PhylomeDBiQ9FF90.

Enzyme and pathway databases

ReactomeiR-ATH-156827. L13a-mediated translational silencing of Ceruloplasmin expression.
R-ATH-1799339. SRP-dependent cotranslational protein targeting to membrane.
R-ATH-72689. Formation of a pool of free 40S subunits.
R-ATH-72706. GTP hydrolysis and joining of the 60S ribosomal subunit.
R-ATH-975956. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
R-ATH-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).

Miscellaneous databases

PROiQ9FF90.

Gene expression databases

GenevisibleiQ9FF90. AT.

Family and domain databases

InterProiIPR001380. Ribosomal_L13e.
IPR018256. Ribosomal_L13e_CS.
[Graphical view]
PANTHERiPTHR11722. PTHR11722. 1 hit.
PfamiPF01294. Ribosomal_L13e. 1 hit.
[Graphical view]
PROSITEiPS01104. RIBOSOMAL_L13E. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones."
    Sato S., Kotani H., Nakamura Y., Kaneko T., Asamizu E., Fukami M., Miyajima N., Tabata S.
    DNA Res. 4:215-230(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  2. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  3. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  4. "The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome."
    Barakat A., Szick-Miranda K., Chang I.-F., Guyot R., Blanc G., Cooke R., Delseny M., Bailey-Serres J.
    Plant Physiol. 127:398-415(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: GENE FAMILY ORGANIZATION, NOMENCLATURE.
  5. "Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks."
    Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S.
    Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiRL133_ARATH
AccessioniPrimary (citable) accession number: Q9FF90
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: March 1, 2001
Last modified: February 17, 2016
This is version 89 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.