This web page was produced as an assignment for an undergraduate course at Davidson College.


MRPL28 Gene in Saccharomyces cerevisiae  

 

Note:  My conclusions are displayed directly below each microarray data set, and final conclusions located at the bottom of the page.

 

Databases Searched


[X] Expression at different alpha-factor concentrations  (Rosetta Inpharmatics).

 
Saccharomyces Genome Database

Expression at different alpha-factor concentrations for MRPL28/YDR462W

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Scale : (fold repression/induction)

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Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YOR389W         biological_process unknown   molecular_function unknown   not yet annotated
YLR006C   SSK1     osmosensory signaling pathway via two-component system   enzyme activator*   cellular_component unknown
YPL270W   MDL2     transport   not yet annotated   not yet annotated
YNL215W   IES2     biological_process unknown   molecular_function unknown   not yet annotated
YOR022C         biological_process unknown   molecular_function unknown   not yet annotated
YGL220W         biological_process unknown   molecular_function unknown   not yet annotated
YER172C   BRR2     lariat formation, 5'-splice site cleavage   ATP dependent RNA helicase*   snRNP U5e*
YHL021C         biological_process unknown   molecular_function unknown   not yet annotated
YLR306W   UBC12     polyubiquitylation*   ubiquitin conjugating enzyme   cellular_component unknown
YPL099C         biological_process unknown   molecular_function unknown   not yet annotated
YLR230W         biological_process unknown   molecular_function unknown   not yet annotated
YGR246C   BRF1     transcription initiation, from Pol III promoter   RNA polymerase III transcription factor   transcription factor TFIIIB
YGL107C         biological_process unknown   molecular_function unknown   not yet annotated
YGR169C   PUS6     biological_process unknown   molecular_function unknown   not yet annotated
YIR003W         biological_process unknown   molecular_function unknown   not yet annotated
YOR154W         biological_process unknown   molecular_function unknown   not yet annotated
YAL009W   SPO7     meiosis   molecular_function unknown   not yet annotated
YMR052W   FAR3     pheromone response (sensu Saccharomyces)*   molecular_function unknown   cellular_component unknown
YJR002W   MPP10     rRNA modification*   small nuclear ribonucleoprotein   small nucleolar ribonucleoprotein particle
YJL197W   UBP12     deubiquitylation   ubiquitin-specific protease   cellular_component unknown

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression at different alpha-factor concentrations for MRPL28/YDR462W

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SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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The data set from the different Alpha factor concentrations has very little information contained in it. It is impossible to deduce anything from this microarray, because the amount of change in the expression of MRPL28 is almost zero. However, the genes to which MRPL28 is compared show much variability in their expression.  This gives rise to questions about the clustering algorithm used, because the colors do not match up very well for the genes clustered together. Most of the genes are involved in some aspect of transcription, though, which makes sense. Because MRPL28 is involved in protein biosynthesis, it should cluster with other genes that involve transcription. Overall, though, it appears that the type of reproduction that the yeast undergoes (the stage in the life cycle of yeast) does not affect the expression of MRPL28.


[X] Expression in response to alpha-factor  (Rosetta Inpharmatics).

 
Saccharomyces Genome Database

Expression in response to alpha-factor for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YHR134W   WSS1     biological_process unknown   molecular_function unknown   not yet annotated
YDR188W   CCT6     protein folding*   chaperone   cytoplasm*
YLR317W   KRE34     biological_process unknown   molecular_function unknown   not yet annotated
YDR040C   ENA1     transport   not yet annotated   not yet annotated
YMR255W   GFD1     mRNA-nucleus export   molecular_function unknown   cytoplasm*
YML113W   DAT1     not yet annotated   not yet annotated   not yet annotated
YBR045C   GIP1     not yet annotated   not yet annotated   not yet annotated
YMR146C   TIF34     not yet annotated   not yet annotated   not yet annotated
YBL071C         biological_process unknown   molecular_function unknown   not yet annotated
YNL097C   PHO23     not yet annotated   not yet annotated   not yet annotated
YKL125W   RRN3     transcription, from Pol I promoter   RNA polymerase I transcription factor   RNA polymerase I transcription factor complex
YLR426W         biological_process unknown   molecular_function unknown   not yet annotated
YMR143W   RPS16A     protein biosynthesis   structural protein of ribosome   cytosolic small ribosomal (40S) subunit
YBR206W         biological_process unknown   molecular_function unknown   not yet annotated
YNR046W         biological_process unknown   molecular_function unknown   not yet annotated
YPR011C         biological_process unknown   molecular_function unknown   not yet annotated
YDR185C         biological_process unknown   molecular_function unknown   not yet annotated
YAL046C         biological_process unknown   molecular_function unknown   not yet annotated
YLR072W         biological_process unknown   molecular_function unknown   not yet annotated
YAL013W   DEP1     phospholipid metabolism   not yet annotated   not yet annotated

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression in response to alpha-factor for MRPL28/YDR462W

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Browse clustered data


SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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As is shown above, MRPL28 shows very little response to the Alpha factor. However, it is again clustered with genes with biological processes that involve transcription, which is expected. The clustering algorithm seems to be better in this array set, as the different genes in the set show the same general trend of initial stability, followed by a slight repression and then more significant induction.  However, the amount of either repression or induction shown by MRPL28 is small, and drastic conclusions based on this array must not be made, as this could be just noise.


[X] Expression in response to DNA-damaging agents  (Stanford University).

 
Saccharomyces Genome Database

Expression in response to DNA-damaging agents for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression in response to DNA-damaging agents for MRPL28/YDR462W

Visit the Website

SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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MRPL28 again shows nearly no response to the stresses put upon it in these microarrays. The amount of either fold repression or induction is slight, and few conclusions can be drawn.  The only spots out of the many in these microarrays that show real deviation from the control expression are those involving the mec1 mutant. It is shown that gamma irradiation has an effect on the MRPL28 gene in mec1 mutants, but not in the wild type strain. Therefore, it could be assumed that there is a difference in the MRPL28 gene in mec1 mutants versus wild type cells, and further research could isolate this difference.


[X] Expression during the diauxic shift  (Stanford University).

 
Saccharomyces Genome Database

Expression during the diauxic shift for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YKL002W   DID4     biological_process unknown   molecular_function unknown   not yet annotated
YKL087C   CYT2     not yet annotated   not yet annotated   not yet annotated
YNL051W   COD4     biological_process unknown   molecular_function unknown   not yet annotated
YPR166C   MRP2     protein biosynthesis   structural protein of ribosome   mitochondrial small ribosomal subunit
YMR284W   YKU70     DNA repair   not yet annotated   not yet annotated
YGL004C         biological_process unknown   molecular_function unknown   not yet annotated
YJL170C   ASG7     mating (sensu Saccharomyces)   molecular_function unknown   cellular_component unknown
YKL003C   MRP17     protein biosynthesis   structural protein of ribosome   mitochondrial small ribosomal subunit
YKL169C         biological_process unknown   molecular_function unknown   not yet annotated
YJL042W   MHP1     cell wall organization and biogenesis*   structural protein of cytoskeleton   microtubule
YHR116W         biological_process unknown   molecular_function unknown   not yet annotated
YPL013C         biological_process unknown   molecular_function unknown   cellular_component unknown
YDL193W         biological_process unknown   molecular_function unknown   endoplasmic reticulum*
YNL073W   MSK1     not yet annotated   lysine--tRNA ligase   not yet annotated
YGR219W         biological_process unknown   molecular_function unknown   not yet annotated
YBR177C   EHT1     lipid metabolism   molecular_function unknown   lipid particle
YMR157C         biological_process unknown   molecular_function unknown   not yet annotated
YMR158W         biological_process unknown   molecular_function unknown   not yet annotated
YNL122C         biological_process unknown   molecular_function unknown   not yet annotated
YLR254C         biological_process unknown   molecular_function unknown   not yet annotated

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression during the diauxic shift for MRPL28/YDR462W

Visit the Website
Browse clustered data


SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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The MRPL28 gene showed a slight initial repression of expression followed by a more drastic induction in the diauxic shift microarray.   The change from anaerobic to aerobic respiration seemed to have some influence on the expression of MRPL28. This would signal that the gene controls protein biosynthesis (already known) that varies based on the type and amount of carbon source present. This makes sense, because MRPL28 codes for a protein on the mitochondrial large ribosomal subunit, meaning that MRPL28 might change expression to alter the energy production in the cell.  However, the amounts of repression and induction are slight, and possibly insignificant noise, meaning that MRPL28 is not one of the primary genes that affect the energy production in the cell, but may have a lesser role in this pathway. 


[X] Evolution of expression during glucose limitation  (Stanford University).


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Name Process Function
MRPL28 protein biosynthesis structural protein of ribosome
YOR314W biological_process unknown molecular_function unknown
ISY1 mRNA splicing molecular_function unknown
SRP21 not yet annotated not yet annotated
MMT1 not yet annotated not yet annotated
YLR154C biological_process unknown molecular_function unknown
YNL254C biological_process unknown molecular_function unknown
PRI1 DNA replication initiation* alpha DNA polymerase
HXT3 transport not yet annotated
KAR3 meiosis* motor
TFC4 transcription initiation, from Pol III promoter RNA polymerase III transcription factor
YDR057W biological_process unknown molecular_function unknown
YBL032W biological_process unknown molecular_function unknown
YNL319W biological_process unknown molecular_function unknown
YBL060W biological_process unknown molecular_function unknown
FUN26 biological_process unknown molecular_function unknown
YKR035C biological_process unknown molecular_function unknown
SAS4 not yet annotated molecular_function unknown
YJL218W biological_process unknown molecular_function unknown
YEL018W biological_process unknown molecular_function unknown
YFR035C biological_process unknown molecular_function unknown


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MRPL28 again shows very little response, which is not surprising based on the results of the diauxic shift microarray. The limitation of glucose for the yeast does not significantly affect the level of MRPL28 expression. The fact that MRPL28 expression was not significantly affected signifies again that it is not involved in the primary control of energy production for the cell. The data support the already known fact that the protein encoded by MRPL28 is most likely a structural protein in the large ribosomal subunit of the mitochondria, static in its expression.


[X] Expression in response to environmental changes  (Stanford University).

 
Saccharomyces Genome Database

Expression in response to environmental changes for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YBR269C         biological_process unknown   molecular_function unknown   not yet annotated
YBR273C         biological_process unknown   molecular_function unknown   not yet annotated

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group
 
Expression in response to environmental changes for MRPL28/YDR462W

Visit the Website

SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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MRPL28 shows some interesting trends in this microarray. First, the heat shock spots show that MRPL28 is induced for all values except one (which did not return any data, in gray).  This could mean that the heat is denaturing the structural proteins, so more must be created.  Thus, MRPL28 is upregulated. This is consistent with the other stresses involving the heating of the cell - MRPL28 is upregulated when ambient temperature is high enough to denature structural proteins, then downregulated when that stress is removed. The 37C to 25C shock shows downregulation of MRPL28 (which would be expected with the "cooling" of the cell), and the shock of the different starting temperatures to 37C shows upregulation of the gene (again consistent with the "heating" of the cell).  Other variations in expression are consistent with the known role of MRPL28, the synthesis of proteins.


[X] Expression during the cell cycle  (Stanford University, Cold Spring Harbor).


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Name Score Peak
MRPL28 0.182
Reference Genes
CLN2 10.9 G1
HTA1 10.68 S
CLB4 3.08 G2
SWI5 6.726 M
ASH1 11.8 M/G1
Plot of MRPL28 (YDR462W)


Note: We only generated a list of genes with similar patterns of expression for genes whose "aggregate CDC scores" were in the top 1200 (Score >= 0.95).  MRPL28 did not have a score high enough for us to generate such a list.
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MRPL28 produced spots that showed no significant change throughout the cell cycle. In fact, a whole section of the microarray returned no data (shown in gray) for MRPL28. One of the only conclusions that can be reached from this array is the fact that the proteins that MRPL28 synthesizes do not vary with the stage in the cell cycle. It is also noted that MRPL28 did not cluster with any genes which showed an aggregate CDC score >.95. Therefore, little can be drawn from this array set.


[X] Expression in response to histone depletion  (The Whitehead Institute).

 
Saccharomyces Genome Database

Expression in response to histone depletion for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YMR188C         biological_process unknown   molecular_function unknown   not yet annotated
YGR138C   TPO2     biological_process unknown*   spermine transporter*   vacuolar membrane
YBR244W   GPX2     not yet annotated   glutathione peroxidase   not yet annotated
YER037W   PHM8     biological_process unknown   molecular_function unknown   cellular_component unknown
YFL026W   STE2     pheromone response (sensu Saccharomyces)   mating-type alpha-factor pheromone receptor   integral plasma membrane protein
YHL026C         biological_process unknown   molecular_function unknown   not yet annotated
YGR189C   CRH1     biological_process unknown   molecular_function unknown   cell wall
YDL173W         biological_process unknown   molecular_function unknown   not yet annotated
YKR018C         biological_process unknown   molecular_function unknown   not yet annotated
YDL048C   STP4     tRNA splicing   molecular_function unknown   not yet annotated
YGR007W   MUQ1     not yet annotated   cholinephosphate cytidylyltransferase   not yet annotated
YKL119C   VPH2     vacuolar acidification*   molecular_function unknown   endoplasmic reticulum membrane
YPR104C   FHL1     rRNA processing*   transcription factor   nucleus
YGR195W   SKI6     35S primary transcript processing*   3'-5' exoribonuclease   nuclear exosome (RNase complex)*
YGR031W         biological_process unknown   molecular_function unknown   not yet annotated
YFL039C   ACT1     establishment of cell polarity (sensu Saccharomyces)*   structural protein of cytoskeleton   actin cortical patch (sensu Saccharomyces)*
YHR136C   SPL2     cell cycle   protein kinase inhibitor   not yet annotated
YBR016W         biological_process unknown   molecular_function unknown   not yet annotated
YGL097W   SRM1     not yet annotated   not yet annotated   not yet annotated
YKL211C   TRP3     not yet annotated   indole-3-glycerol-phosphate synthase   not yet annotated

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression in response to histone depletion for MRPL28/YDR462W

Visit the Website
Browse clustered data


SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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MRPL28 shows little data again for the histone depletion microarray. One would expect genes to show some change in expression if involved in any transcription with this array, because changes in the histone concentrations would affect the yeast's ability to continue cellular pathways involving DNA replication or DNA-RNA transcription.  However, the translation of RNA into proteins seems unaffected by histone depletion, and MRPL28 did not show any significant change in expression.


[X] Expression during sporulation  (UCSF, Stanford University).

 
Saccharomyces Genome Database

Expression during sporulation for MRPL28/YDR462W

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Scale : (fold repression/induction)

Click on a color strip to see data for that gene.

Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene

Orf Gene Process Function Component
YDR462W   MRPL28     protein biosynthesis   structural protein of ribosome   mitochondrial large ribosomal subunit
YPL096W   PNG1     degradation of misfolded or incompletely synthesized proteins*   peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase   nucleus*
YPL213W   LEA1     mRNA splicing   not yet annotated   not yet annotated
YHR091C   MSR1     not yet annotated   arginine--tRNA ligase   not yet annotated
YMR027W   HRT2     not yet annotated   molecular_function unknown   not yet annotated
YOL086C   ADH1     not yet annotated   acylglycerone-phosphate reductase   not yet annotated
YOL019W   TOS7     biological_process unknown   molecular_function unknown   not yet annotated
YDR353W   TRR1     not yet annotated   not yet annotated   not yet annotated
YJR103W   URA8     not yet annotated   CTP synthase   not yet annotated
YCR030C         biological_process unknown   molecular_function unknown   not yet annotated
YCL051W   LRE1     not yet annotated   molecular_function unknown   not yet annotated
YGR124W   ASN2     not yet annotated   asparagine synthase (glutamine-hydrolyzing)   not yet annotated
YLR121C   YPS3     protein metabolism and modification   aspartic-type endopeptidase   plasma membrane
YHL021C         biological_process unknown   molecular_function unknown   not yet annotated
YJR125C   ENT3     actin filament organization*   cytoskeletal adaptor   actin cortical patch (sensu Saccharomyces)
YPR131C   NAT3     not yet annotated   not yet annotated   not yet annotated
YLR420W   URA4     not yet annotated   dihydroorotase   not yet annotated
YLR298C   YHC1     mRNA splicing   not yet annotated   not yet annotated
YPL168W         biological_process unknown   molecular_function unknown   not yet annotated
YNL168C         biological_process unknown   molecular_function unknown   not yet annotated
YHL019C   APM2     endocytosis   not yet annotated   not yet annotated

* : indicates that more than one annotation exists for the gene.
See the Summary of the Gene Ontology annotations for this gene group

Expression during sporulation for MRPL28/YDR462W

Visit the Website
Browse clustered data


SGDtm pages Database Copyright © 1997-2001 The Board of Trustees of Leland Stanford Junior University. Permission to use the information contained in this database was given by the researchers/institutes who contributed or published the information. Users of the database are solely responsible for compliance with any copyright restrictions, including those applying to the author abstracts. Documents from this server are provided "AS-IS" without any warranty, expressed or implied.
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MRPL28 shows a repression for nearly every time point (excluding 0.5 hours) in the sporulation microarray. Initially, the repression is small, then becomes more pronounced, and levels out after time=5.0 hours. Overall, the repression is less pronounced than in many other genes, which show a fold repression of >2.8. The peak for MRPL28 repression is slightly >0.5 at time=5.0 hours. MRPL28 clusters with many genes of more significant repression, but many of them have functions having to do with protein synthesis. This is consistent with the arrays above and for expected results.  It seems that the cell is downregulating the protein synthesis of MRPL28 during sporulation to allocate more energy to the vital sporulation process.



CONCLUSIONS

Though the data that was received through these microarrays was limited, it agrees with previous knowledge of MRPL28. MRPL28 is consistent in the fact that it shows little response to nearly all environmental stresses and cell cycle stage changes. Therefore it can be assumed that MRPL28 synthesizes proteins that are not vital to the cell cycle.  The cell even downregulates MRPL28 during one specific process (sporulation), possibly to allow the cell to "concentrate" on more important pathways.  However, when the cell is introduced to heat shock, MRPL28 is upregulated, most likely to replace proteins lost to denaturation.  All of this data supports the belief that MRPL28 is in fact a structural protein in the large ribosomal subunit in the mitochondria.


 

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Peter Lowry
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