Human Gene RPS3 (uc001owg.4)
  Description: Homo sapiens ribosomal protein S3 (RPS3), transcript variant 2, mRNA.
RefSeq Summary (NM_001256802): 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, where it forms part of the domain where translation is initiated. The protein belongs to the S3P family of ribosomal proteins. Studies of the mouse and rat proteins have demonstrated that the protein has an extraribosomal role as an endonuclease involved in the repair of UV-induced DNA damage. The protein appears to be located in both the cytoplasm and nucleus but not in the nucleolus. Higher levels of expression of this gene in colon adenocarcinomas and adenomatous polyps compared to adjacent normal colonic mucosa have been observed. This gene is co-transcribed with the small nucleolar RNA genes U15A and U15B, which are located in its first and fifth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012].
Transcript (Including UTRs)
   Position: hg19 chr11:75,110,535-75,114,989 Size: 4,455 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr11:75,110,592-75,113,494 Size: 2,903 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:75,110,535-75,114,989)mRNA (may differ from genome)Protein (117 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: F2Z2S8_HUMAN
DESCRIPTION: SubName: Full=40S ribosomal protein S3;
SIMILARITY: Contains 1 KH type-2 domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RPS3
Diseases sorted by gene-association score: eumycotic mycetoma (16), dermatomycosis (16), spherocytosis, type 3 (12), bubonic plague (8), hereditary spherocytosis (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C041594 4-nonylphenol
  • D016604 Aflatoxin B1
  • D004997 Ethinyl Estradiol
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C015802 2,6-dichloro-4-nitrophenol
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • C019499 2-nitrofluorene
  • C016583 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone
          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: 477.23 RPKM in Ovary
Total median expression: 7635.32 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 -19.4057-0.340 Picture PostScript Text
3' UTR -488.461495-0.327 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
  InterPro Domains: Graphical view of domain structure
IPR004087 - KH_dom
IPR015946 - KH_dom-like_a/b
IPR004044 - KH_dom_type_2
IPR009019 - KH_prok-type

Pfam Domains:
PF07650 - KH domain

SCOP Domains:
54814 - Prokaryotic type KH domain (KH-domain type II)

ModBase Predicted Comparative 3D Structure on F2Z2S8
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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome

Biological Process:
GO:0006412 translation

Cellular Component:
GO:0005840 ribosome


-  Descriptions from all associated GenBank mRNAs
  D28344 - Homo sapiens mRNA for ribosomal protein S3, 5'UTR region.
AK130960 - Homo sapiens cDNA FLJ27450 fis, clone PNC07764.
BC034149 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone MGC:32779 IMAGE:4665438), complete cds.
AK129794 - Homo sapiens cDNA FLJ26283 fis, clone DMC06792, highly similar to 40S ribosomal protein S3.
AK313051 - Homo sapiens cDNA, FLJ93526, Homo sapiens ribosomal protein S3 (RPS3), mRNA.
BC013231 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone IMAGE:3462987).
BC100284 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone MGC:117338 IMAGE:6160514), complete cds.
X55715 - Human Hums3 mRNA for 40S ribosomal protein s3.
BC071917 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone MGC:88599 IMAGE:6297012), complete cds.
BC071669 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone IMAGE:4432379), with apparent retained intron.
BC003137 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone MGC:3657 IMAGE:2906158), complete cds.
AK223048 - Homo sapiens mRNA for ribosomal protein S3 variant, clone: KAT00103.
S42658 - S3 ribosomal protein [human, colon, mRNA, 826 nt].
KJ905908 - Synthetic construct Homo sapiens clone ccsbBroadEn_15578 RPS3 gene, encodes complete protein.
AB464166 - Synthetic construct DNA, clone: pF1KB3421, Homo sapiens RPS3 gene for ribosomal protein S3, without stop codon, in Flexi system.
DQ896136 - Synthetic construct Homo sapiens clone IMAGE:100010596; FLH190668.01L; RZPDo839C1066D ribosomal protein S3 (RPS3) gene, encodes complete protein.
DQ892888 - Synthetic construct clone IMAGE:100005518; FLH190672.01X; RZPDo839C1076D ribosomal protein S3 (RPS3) gene, encodes complete protein.
KJ892051 - Synthetic construct Homo sapiens clone ccsbBroadEn_01445 RPS3 gene, encodes complete protein.
CU678394 - Synthetic construct Homo sapiens gateway clone IMAGE:100018599 5' read RPS3 mRNA.
U14990 - Human XP1PO ribosomal protein S3 (rpS3) mRNA, complete cds.
U14991 - Human XP2NE ribosomal protein S3 (rpS3) mRNA, complete cds.
U14992 - Human IMR-90 ribosomal protein S3 (rpS3) mRNA, complete cds.
BC013196 - Homo sapiens, clone IMAGE:4347401, mRNA, partial cds.
BC003577 - Homo sapiens, clone IMAGE:3544292, mRNA, partial cds.
AB062288 - Homo sapiens OK/SW-cl.26 mRNA for IMR-90 ribosomal protein S3, complete cds.
BC017103 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone IMAGE:3503171), **** WARNING: chimeric clone ****.
BC029981 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone IMAGE:4705217).
JD022222 - Sequence 3246 from Patent EP1572962.
JD026177 - Sequence 7201 from Patent EP1572962.
BC150501 - Homo sapiens ribosomal protein S3, mRNA (cDNA clone IMAGE:40134452), partial cds.
JD035425 - Sequence 16449 from Patent EP1572962.
JD031393 - Sequence 12417 from Patent EP1572962.
JD026642 - Sequence 7666 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: BC071669, F2Z2S8, F2Z2S8_HUMAN, NM_001256802, NP_001243731, uc001owg.3
UCSC ID: uc001owg.4
RefSeq Accession: NM_001256802
Protein: F2Z2S8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC071669.1
exon count: 4CDS single in 3' UTR: no RNA size: 1880
ORF size: 354CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 908.00frame shift in genome: no % Coverage: 98.67
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: 1499# 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.