Human Gene RPS20 (uc003xsm.2) Description and Page Index
  Description: Homo sapiens ribosomal protein S20 (RPS20), transcript variant 1, mRNA.
RefSeq Summary (NM_001146227): 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 ribosomal protein that is a component of the 40S subunit. The protein belongs to the S10P family of ribosomal proteins. It is located in the cytoplasm. This gene is co-transcribed with the small nucleolar RNA gene U54, which is located in its second intron. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Two transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Apr 2009].
Transcript (Including UTRs)
   Position: hg19 chr8:56,980,739-56,987,140 Size: 6,402 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr8:56,982,297-56,986,942 Size: 4,646 Coding Exon Count: 5 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:56,980,739-56,987,140)mRNA (may differ from genome)Protein (142 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIOMIMPubMedReactome
Stanford SOURCEUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RPS20
CDC HuGE Published Literature: RPS20
Positive Disease Associations: height
Related Studies:
  1. height
    Gudbjartsson ,et al. 2008, Many sequence variants affecting diversity of adult human height, Nature genetics 2008 40- 5 : 609-15. [PubMed 18391951]

-  MalaCards Disease Associations
  MalaCards Gene Search: RPS20
Diseases sorted by gene-association score: familial colorectal cancer type x* (247)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 508.48 RPKM in Ovary
Total median expression: 10314.27 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -73.90198-0.373 Picture PostScript Text
3' UTR -104.70386-0.271 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00338 - Ribosomal protein S10p/S20e

SCOP Domains:
54999 - Ribosomal protein S10

ModBase Predicted Comparative 3D Structure on P60866-2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK094652 - Homo sapiens cDNA FLJ37333 fis, clone BRAMY2020106.
AK301342 - Homo sapiens cDNA FLJ58953 complete cds, highly similar to 40S ribosomal protein S20.
BC087850 - Homo sapiens ribosomal protein S20, mRNA (cDNA clone MGC:102930 IMAGE:30386230), complete cds.
BC007507 - Homo sapiens ribosomal protein S20, mRNA (cDNA clone MGC:4151 IMAGE:3029762), complete cds.
AK130961 - Homo sapiens cDNA FLJ27451 fis, clone SYN99901, highly similar to 40S ribosomal protein S20.
L06498 - Homo sapiens ribosomal protein S20 (RPS20) mRNA, complete cds.
KJ892064 - Synthetic construct Homo sapiens clone ccsbBroadEn_01458 RPS20 gene, encodes complete protein.
AK311808 - Homo sapiens cDNA, FLJ92069, Homo sapiens ribosomal protein S20 (RPS20), mRNA.
DQ893212 - Synthetic construct clone IMAGE:100005842; FLH195290.01X; RZPDo839A10152D ribosomal protein S20 (RPS20) gene, encodes complete protein.
DQ896541 - Synthetic construct Homo sapiens clone IMAGE:100011001; FLH195286.01L; RZPDo839A10151D ribosomal protein S20 (RPS20) gene, encodes complete protein.
AB464165 - Synthetic construct DNA, clone: pF1KB3982, Homo sapiens RPS20 gene for ribosomal protein S20, without stop codon, in Flexi system.
DQ577346 - Homo sapiens piRNA piR-45458, complete sequence.
DL492700 - Novel nucleic acids.
DL491142 - Novel nucleic acids.
D28358 - Homo sapiens mRNA for ribosomal protein S20, 5'UTR region.
JD021361 - Sequence 2385 from Patent EP1572962.
JD405996 - Sequence 387020 from Patent EP1572962.
JD150729 - Sequence 131753 from Patent EP1572962.
JD033369 - Sequence 14393 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03010 - Ribosome

Reactome (by CSHL, EBI, and GO)

Protein P60866 (Reactome details) participates in the following event(s):

R-HSA-72676 eIF3 and eIF1A bind to the 40S subunit
R-HSA-72673 Release of 40S and 60S subunits from the 80S ribosome
R-HSA-72672 The 60S subunit joins the translation initiation complex
R-HSA-72619 eIF2:GTP is hydrolyzed, eIFs are released
R-HSA-72691 Formation of the 43S pre-initiation complex
R-HSA-156808 Formation of translation initiation complexes yielding circularized Ceruloplasmin mRNA in a 'closed-loop' conformation
R-HSA-157849 Formation of translation initiation complexes containing mRNA that does not circularize
R-HSA-72671 eIF5B:GTP is hydrolyzed and released
R-HSA-156907 Aminoacyl-tRNA binds to the ribosome at the A-site
R-HSA-2408529 Sec-tRNA(Sec):EEFSEC:GTP binds to 80S Ribosome
R-HSA-141691 GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
R-HSA-156915 Translocation of ribosome by 3 bases in the 3' direction
R-HSA-141671 Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
R-HSA-156912 Peptide transfer from P-site tRNA to the A-site tRNA
R-HSA-927832 UPF1 binds an mRNP with a termination codon preceding an Exon Junction Complex
R-HSA-927789 Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
R-HSA-1799332 Nascent polypeptide:mRNA:ribosome complex binds signal recognition particle (SRP)
R-HSA-156923 Hydrolysis of eEF1A:GTP
R-HSA-72621 Ribosomal scanning
R-HSA-72697 Start codon recognition
R-HSA-156823 Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
R-HSA-5333615 80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC
R-HSA-141673 GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
R-HSA-927889 SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
R-HSA-1799329 Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
R-HSA-1799330 The SRP receptor binds the SRP:nascent peptide:ribosome complex
R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-72689 Formation of a pool of free 40S subunits
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex
R-HSA-72649 Translation initiation complex formation
R-HSA-72737 Cap-dependent Translation Initiation
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-156902 Peptide chain elongation
R-HSA-2408557 Selenocysteine synthesis
R-HSA-72764 Eukaryotic Translation Termination
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-72766 Translation
R-HSA-376176 Signaling by ROBO receptors
R-HSA-192823 Viral mRNA Translation
R-HSA-72702 Ribosomal scanning and start codon recognition
R-HSA-156827 L13a-mediated translation
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
R-HSA-72613 Eukaryotic Translation Initiation
R-HSA-72312 rRNA processing
R-HSA-156842 Eukaryotic Translation Elongation
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-927802 Nonsense-Mediated Decay (NMD)
R-HSA-392499 Metabolism of proteins
R-HSA-422475 Axon guidance
R-HSA-168273 Influenza Viral RNA Transcription and Replication
R-HSA-8953854 Metabolism of RNA
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1266738 Developmental Biology
R-HSA-168255 Influenza Life Cycle
R-HSA-1430728 Metabolism
R-HSA-168254 Influenza Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001146227, NP_001139699, P60866-2
UCSC ID: uc003xsm.2
RefSeq Accession: NM_001146227
Protein: P60866-2, splice isoform of P60866 CCDS: CCDS55231.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001146227.1
exon count: 6CDS single in 3' UTR: no RNA size: 1013
ORF size: 429CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1032.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.