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Aliases for RPL13A Gene

Aliases for RPL13A Gene

  • Ribosomal Protein L13a 2 3 5
  • Tissue Specific Transplantation Antigen 1 2 3
  • Large Ribosomal Subunit Protein UL13 3 4
  • 23 KDa Highly Basic Protein 3 4
  • 60S Ribosomal Protein L13a 3
  • TSTA1 3
  • L13A 3

External Ids for RPL13A Gene

Previous HGNC Symbols for RPL13A Gene

  • TSTA1

Previous GeneCards Identifiers for RPL13A Gene

  • GC19P050649
  • GC19P050359
  • GC19P054666
  • GC19P054682
  • GC19P049991

Summaries for RPL13A Gene

Entrez Gene Summary for RPL13A Gene

  • Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L13P family of ribosomal proteins that is a component of the 60S subunit. The encoded protein also plays a role in the repression of inflammatory genes as a component of the IFN-gamma-activated inhibitor of translation (GAIT) complex. This gene is co-transcribed with the small nucleolar RNA genes U32, U33, U34, and U35, which are located in the second, fourth, fifth, and sixth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed throughout the genome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

GeneCards Summary for RPL13A Gene

RPL13A (Ribosomal Protein L13a) is a Protein Coding gene. Diseases associated with RPL13A include Retinitis Pigmentosa 22. Among its related pathways are Viral mRNA Translation and rRNA processing in the nucleus and cytosol. GO annotations related to this gene include poly(A) RNA binding and structural constituent of ribosome.

UniProtKB/Swiss-Prot for RPL13A Gene

  • Associated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA.

Gene Wiki entry for RPL13A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RPL13A Gene

Genomics for RPL13A Gene

Regulatory Elements for RPL13A Gene

Enhancers for RPL13A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19G049494 2 FANTOM5 Ensembl ENCODE dbSUPER 10.9 +11.5 11490 9.7 CREB3L1 AGO1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC RPS11 ALDH16A1 SNORD35A PIH1D1 SNORD35B RPL18 FLT3LG PRR12 CD37 POLD1
GH19G049552 1.4 Ensembl ENCODE dbSUPER 11.9 +67.8 67796 5.7 PKNOX1 CBX3 NFRKB ARID4B ZBTB40 GATA2 CBX5 FOS MIXL1 EGR2 NOSIP PRR12 FCGRT RCN3 PRRG2 MIR150 RPS11 SNORD35B SNORD35A SNORD34
GH19G049558 1.2 Ensembl ENCODE dbSUPER 11.9 +73.2 73171 4.3 BCOR TFAP4 ZMYM3 ZNF664 ZFHX2 FOXK2 EGR1 ADNP ZSCAN29 NFE2 PRR12 NOSIP RCN3 FCGRT MIR150 SNORD35B RPS11 SNORD35A SNORD34 RPL13A
GH19G049457 1.2 Ensembl ENCODE dbSUPER 11.7 -29.2 -29189 1.6 HDGF HCFC1 L3MBTL2 BHLHE40 NR2F1 DPF2 ZBTB40 ZNF592 GABPA POLR2A RPL13A SNORD35A SNORD33 SNORD34 SNORD32A SLC6A16 CD37 FLT3LG PIH1D1 ENSG00000269469
GH19G049511 1 ENCODE 12.9 +26.8 26803 5.7 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 ZNF48 TCF12 ZNF121 GLIS2 PRR12 RCN3 FCGRT SNORD32A SNORD33 SNORD34 SNORD35A RPL13A PRRG2 NOSIP
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RPL13A on UCSC Golden Path with GeneCards custom track

Promoters for RPL13A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000110904 646 2401 HDGF PKNOX1 CREB3L1 ARNT AGO1 ZFP64 WRNIP1 ARID4B SIN3A DMAP1

Genomic Location for RPL13A Gene

Chromosome:
19
Start:
49,487,554 bp from pter
End:
49,492,308 bp from pter
Size:
4,755 bases
Orientation:
Plus strand

Genomic View for RPL13A Gene

Genes around RPL13A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPL13A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPL13A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPL13A Gene

Proteins for RPL13A Gene

  • Protein details for RPL13A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P40429-RL13A_HUMAN
    Recommended name:
    60S ribosomal protein L13a
    Protein Accession:
    P40429
    Secondary Accessions:
    • A8K505

    Protein attributes for RPL13A Gene

    Size:
    203 amino acids
    Molecular mass:
    23577 Da
    Quaternary structure:
    • Component of the 60S ribosome. Component of the GAIT complex. Interacts with EIF4G1.

    Three dimensional structures from OCA and Proteopedia for RPL13A Gene

neXtProt entry for RPL13A Gene

Post-translational modifications for RPL13A Gene

  • Citrullinated by PADI4.
  • Phosphorylation at Ser-77 upon interferon-gamma treatment in monocytes involves a DAPK1-DAPK3 kinase cascade and is causing release from the ribosome, association with the GAIT complex and subsequent involvement in transcript-selective translation inhibition.
  • Ubiquitination at isoforms=25, Lys53, isoforms=134, Lys148, and isoforms=191
  • Modification sites at PhosphoSitePlus

Other Protein References for RPL13A Gene

No data available for DME Specific Peptides for RPL13A Gene

Domains & Families for RPL13A Gene

Gene Families for RPL13A Gene

Protein Domains for RPL13A Gene

Graphical View of Domain Structure for InterPro Entry

P40429

UniProtKB/Swiss-Prot:

RL13A_HUMAN :
  • Belongs to the universal ribosomal protein uL13 family.
Family:
  • Belongs to the universal ribosomal protein uL13 family.
genes like me logo Genes that share domains with RPL13A: view

Function for RPL13A Gene

Molecular function for RPL13A Gene

GENATLAS Biochemistry:
60S ribosomal protein L13-2
UniProtKB/Swiss-Prot Function:
Associated with ribosomes but is not required for canonical ribosome function and has extra-ribosomal functions. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma activation and subsequent phosphorylation dissociates from the ribosome and assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation. In the GAIT complex interacts with m7G cap-bound eIF4G at or near the eIF3-binding site and blocks the recruitment of the 43S ribosomal complex. Involved in methylation of rRNA.

Gene Ontology (GO) - Molecular Function for RPL13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0003729 mRNA binding IBA --
GO:0003735 structural constituent of ribosome IEA,NAS 12962325
genes like me logo Genes that share ontologies with RPL13A: view
genes like me logo Genes that share phenotypes with RPL13A: view

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RPL13A Gene

Localization for RPL13A Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPL13A Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RPL13A gene
Compartment Confidence
nucleus 5
cytosol 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RPL13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005730 nucleolus IDA 16791210
GO:0005737 cytoplasm IDA,IEA 16791210
GO:0005829 cytosol TAS --
GO:0005840 ribosome IEA --
genes like me logo Genes that share ontologies with RPL13A: view

Pathways & Interactions for RPL13A Gene

genes like me logo Genes that share pathways with RPL13A: view

Pathways by source for RPL13A Gene

1 Cell Signaling Technology pathway for RPL13A Gene
1 BioSystems pathway for RPL13A Gene
1 KEGG pathway for RPL13A Gene
1 GeneGo (Thomson Reuters) pathway for RPL13A Gene

SIGNOR curated interactions for RPL13A Gene

Is activated by:

Gene Ontology (GO) - Biological Process for RPL13A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay TAS --
GO:0006364 rRNA processing TAS --
GO:0006412 translation NAS,IEA 12962325
GO:0006413 translational initiation TAS --
GO:0006417 regulation of translation IEA --
genes like me logo Genes that share ontologies with RPL13A: view

Drugs & Compounds for RPL13A Gene

(3) Drugs for RPL13A Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Alpha-Hydroxy-Beta-Phenyl-Propionic Acid Experimental Pharma Target 0
Anisomycin Experimental Pharma Target JNK agonist, potent and specific 0
puromycin Experimental Pharma Target 0
genes like me logo Genes that share compounds with RPL13A: view

Transcripts for RPL13A Gene

Unigene Clusters for RPL13A Gene

Ribosomal protein L13a:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RPL13A Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b · 10c · 10d
SP1: - - - -
SP2: - - - -
SP3: - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - -
SP7: - - -
SP8: - - - -
SP9: - - - - -
SP10: - - - -
SP11: - - -
SP12: -
SP13: - -
SP14:

Relevant External Links for RPL13A Gene

GeneLoc Exon Structure for
RPL13A
ECgene alternative splicing isoforms for
RPL13A

Expression for RPL13A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RPL13A Gene

Protein differential expression in normal tissues from HIPED for RPL13A Gene

This gene is overexpressed in Nasal epithelium (13.7) and Peripheral blood mononuclear cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RPL13A Gene



Protein tissue co-expression partners for RPL13A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RPL13A Gene:

RPL13A

SOURCE GeneReport for Unigene cluster for RPL13A Gene:

Hs.523185

Evidence on tissue expression from TISSUES for RPL13A Gene

  • Lung(5)
  • Pancreas(5)
  • Skin(5)
  • Nervous system(5)
  • Eye(4.9)
  • Intestine(4.9)
  • Liver(4.9)
  • Muscle(4.9)
  • Kidney(4.6)
  • Stomach(4.6)
  • Blood(4.5)
  • Bone(4.5)
  • Heart(4)
  • Spleen(3.8)
  • Bone marrow(2.6)
  • Lymph node(2.3)
  • Thyroid gland(2.2)
  • Adrenal gland(2.1)
genes like me logo Genes that share expression patterns with RPL13A: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPL13A Gene

Orthologs for RPL13A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RPL13A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPL13A 34 35
  • 100 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RPL13A 35
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RPL13A 34 35
  • 92.12 (n)
cow
(Bos Taurus)
Mammalia RPL13A 34 35
  • 90.8 (n)
-- 35
  • 83 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Rpl13a-ps1 35
  • 89 (a)
OneToMany
Rpl13a 34 16 35
  • 88.01 (n)
rat
(Rattus norvegicus)
Mammalia Rpl13a 34
  • 87.19 (n)
oppossum
(Monodelphis domestica)
Mammalia RPL13A 35
  • 44 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RPL13A 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpl13a 34
  • 78.89 (n)
Str.6691 34
African clawed frog
(Xenopus laevis)
Amphibia rpl13a-prov 34
zebrafish
(Danio rerio)
Actinopterygii rpl13a 34 35
  • 75.88 (n)
Gstp1 34
fruit fly
(Drosophila melanogaster)
Insecta RpL13A 34 35
  • 63.65 (n)
CG1475 36
  • 58 (a)
worm
(Caenorhabditis elegans)
Secernentea rpl-16 36 34 35
  • 59.15 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F04675g 34
  • 61.68 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AER367C 34
  • 57.94 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL16A 35
  • 57 (a)
OneToMany
RPL16B 35
  • 55 (a)
OneToMany
soybean
(Glycine max)
eudicotyledons Gma.2053 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.7126 34
barley
(Hordeum vulgare)
Liliopsida Hv.12482 34
wheat
(Triticum aestivum)
Liliopsida Ta.807 34
corn
(Zea mays)
Liliopsida Zm.4020 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3458 35
  • 63 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU01221 34
  • 62.22 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rpl1601 34
  • 61.01 (n)
Species where no ortholog for RPL13A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for RPL13A Gene

ENSEMBL:
Gene Tree for RPL13A (if available)
TreeFam:
Gene Tree for RPL13A (if available)

Paralogs for RPL13A Gene

(1) SIMAP similar genes for RPL13A Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with RPL13A: view

No data available for Paralogs for RPL13A Gene

Variants for RPL13A Gene

Sequence variations from dbSNP and Humsavar for RPL13A Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1001030771 -- 49,486,790(+) AGATA(A/C)GGCCA upstream-variant-2KB, utr-variant-3-prime
rs1001127408 -- 49,489,093(+) CATGG(A/G)CTTTT intron-variant, upstream-variant-2KB
rs1001145061 -- 49,486,433(+) ATGGA(C/T)GAGAA intron-variant, downstream-variant-500B, upstream-variant-2KB, utr-variant-3-prime
rs1001344901 -- 49,485,628(+) CCGCC(C/T)GCCTC intron-variant, upstream-variant-2KB
rs1001661897 -- 49,489,293(+) AGTAC(-/AAG)AAGAG intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for RPL13A Gene

Variant ID Type Subtype PubMed ID
nsv1160655 CNV deletion 26073780
nsv833862 CNV loss 17160897
nsv833863 CNV loss 17160897
nsv953599 CNV deletion 24416366
nsv960858 CNV duplication 23825009
nsv9739 CNV gain+loss 18304495

Variation tolerance for RPL13A Gene

Residual Variation Intolerance Score: 49.1% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RPL13A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPL13A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPL13A Gene

Disorders for RPL13A Gene

MalaCards: The human disease database

(1) MalaCards diseases for RPL13A Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 22
  • rp22
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for RPL13A

Genetic Association Database (GAD)
RPL13A
Human Genome Epidemiology (HuGE) Navigator
RPL13A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RPL13A
genes like me logo Genes that share disorders with RPL13A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPL13A Gene

Publications for RPL13A Gene

  1. DAPK-ZIPK-L13a axis constitutes a negative-feedback module regulating inflammatory gene expression. (PMID: 18995835) Mukhopadhyay R. … Fox P.L. (Mol. Cell 2008) 3 4 22 64
  2. Human ribosomal protein L13a is dispensable for canonical ribosome function but indispensable for efficient rRNA methylation. (PMID: 17921318) Chaudhuri S. … Mazumder B. (RNA 2007) 3 4 22 64
  3. L13a blocks 48S assembly: role of a general initiation factor in mRNA-specific translational control. (PMID: 17218275) Kapasi P. … Mazumder B. (Mol. Cell 2007) 3 4 22 64
  4. Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control. (PMID: 14567916) Mazumder B. … Fox P.L. (Cell 2003) 3 4 22 64
  5. Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome. (PMID: 10580157) Higa S. … Kenmochi N. (Gene 1999) 3 4 22 64

Products for RPL13A Gene

Sources for RPL13A Gene

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