Human Gene MRPS9 (uc002tcn.4)
  Description: Homo sapiens mitochondrial ribosomal protein S9 (MRPS9), nuclear gene encoding mitochondrial protein, mRNA.
RefSeq Summary (NM_182640): Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:105,654,483-105,716,418 Size: 61,936 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr2:105,654,551-105,716,219 Size: 61,669 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
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 (chr2:105,654,483-105,716,418)mRNA (may differ from genome)Protein (396 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RT09_HUMAN
DESCRIPTION: RecName: Full=28S ribosomal protein S9, mitochondrial; Short=MRP-S9; Short=S9mt; Flags: Precursor;
SUBUNIT: Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins (By similarity).
INTERACTION: P04618:rev (xeno); NbExp=2; IntAct=EBI-721385, EBI-6164309;
SUBCELLULAR LOCATION: Mitochondrion.
SIMILARITY: Belongs to the ribosomal protein S9P family.

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MRPS9
CDC HuGE Published Literature: MRPS9
Positive Disease Associations: Basophils , Diabetes Mellitus, Type 2 , Pancreatic Neoplasms
Related Studies:
  1. Basophils
    , , . [PubMed 0]
  2. Diabetes Mellitus, Type 2
    Jukka T Salonen et al. American journal of human genetics 2007, Type 2 diabetes whole-genome association study in four populations: the DiaGen consortium., American journal of human genetics. [PubMed 17668382]
  3. Pancreatic Neoplasms
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 30.08 RPKM in Testis
Total median expression: 825.83 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 -16.4468-0.242 Picture PostScript Text
3' UTR -41.70199-0.210 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
IPR020568 - Ribosomal_S5_D2-typ_fold
IPR014721 - Ribosomal_S5_D2-typ_fold_subgr
IPR000754 - Ribosomal_S9
IPR020574 - Ribosomal_S9_CS

Pfam Domains:
PF00380 - Ribosomal protein S9/S16

SCOP Domains:
54211 - Ribosomal protein S5 domain 2-like

ModBase Predicted Comparative 3D Structure on P82933
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 BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006412 translation
GO:0042769 DNA damage response, detection of DNA damage
GO:0070125 mitochondrial translational elongation
GO:0070126 mitochondrial translational termination

Cellular Component:
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005763 mitochondrial small ribosomal subunit
GO:0005840 ribosome


-  Descriptions from all associated GenBank mRNAs
  BC057240 - Homo sapiens mitochondrial ribosomal protein S9, mRNA (cDNA clone MGC:62135 IMAGE:6495350), complete cds.
BC036575 - Homo sapiens mitochondrial ribosomal protein S9, mRNA (cDNA clone IMAGE:4791565).
AK001451 - Homo sapiens cDNA FLJ10589 fis, clone NT2RP2004389, weakly similar to PROBABLE MITOCHONDRIAL 40S RIBOSOMAL PROTEIN S9 PRECURSOR.
AK130078 - Homo sapiens cDNA FLJ26568 fis, clone LNF05406.
KJ894597 - Synthetic construct Homo sapiens clone ccsbBroadEn_03991 MRPS9 gene, encodes complete protein.
BC047784 - Homo sapiens mitochondrial ribosomal protein S9, mRNA (cDNA clone IMAGE:6160499), partial cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P82933 (Reactome details) participates in the following event(s):

R-HSA-5368279 MTIF3 binds 28S ribosomal subunit
R-HSA-5419273 Hydrolysis of GTP and dissociation of 28S and 39S subunits
R-HSA-5389849 28S subunit:MTIF3 binds MTIF2:GTP, mRNA, and formylMet-tRNA
R-HSA-5389839 39S subunit binds 28S subunit:mRNA:fMet-tRNA
R-HSA-5389848 TUFM:GTP:aminoacyl-tRNA binds 55S ribosome:mRNA:fMet-tRNA
R-HSA-5389857 Peptide transfer from P-site to A-site (peptide bond formation)
R-HSA-5389842 TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome
R-HSA-5419261 55S ribosome with peptidyl-tRNA in A site binds GFM1:GTP
R-HSA-5419281 MRRF binds 55S ribosome:mRNA:tRNA
R-HSA-5419279 Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA)
R-HSA-5419264 MTRF1L (MTRF1a) or ICT1 binds stop codon in 55S ribosome:mRNA:peptidyl-tRNA
R-HSA-5419277 GFM2:GTP binds 55S ribosome:mRNA:tRNA:MRRF releasing mRNA and tRNA
R-HSA-5368286 Mitochondrial translation initiation
R-HSA-5419276 Mitochondrial translation termination
R-HSA-5368287 Mitochondrial translation
R-HSA-5389840 Mitochondrial translation elongation
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_182640, NP_872578, P82933, Q6PG40, RPMS9, RT09_HUMAN
UCSC ID: uc002tcn.4
RefSeq Accession: NM_182640
Protein: P82933 (aka RT09_HUMAN)
CCDS: CCDS2065.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182640.2
exon count: 11CDS single in 3' UTR: no RNA size: 1473
ORF size: 1191CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2582.00frame shift in genome: no % Coverage: 98.98
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.