Human Gene MRPL42 (uc001tcr.3) Description and Page Index
  Description: Homo sapiens mitochondrial ribosomal protein L42 (MRPL42), nuclear gene encoding mitochondrial protein, transcript variant 2, mRNA.
RefSeq Summary (NM_172177): 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 protein identified as belonging to both the 28S and the 39S subunits. Alternative splicing results in multiple transcript variants. Pseudogenes corresponding to this gene are found on chromosomes 4q, 6p, 6q, 7p, and 15q. [provided by RefSeq, May 2011]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments. ##Evidence-Data-START## Transcript exon combination :: SRR1660809.8610.1, SRR1803615.242807.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## gene product(s) localized to mito. :: reported by MitoCarta RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr12:93,861,266-93,897,548 Size: 36,283 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr12:93,863,062-93,894,997 Size: 31,936 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:93,861,266-93,897,548)mRNA (may differ from genome)Protein (142 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RM42_HUMAN
DESCRIPTION: RecName: Full=39S ribosomal protein L42, mitochondrial; Short=L42mt; Short=MRP-L42; AltName: Full=28S ribosomal protein S32, mitochondrial; Short=MRP-S32; Short=S32mt; AltName: Full=39S ribosomal protein L31, mitochondrial; Short=L31mt; Short=MRP-L31; Flags: Precursor;
SUBUNIT: Component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins. Component of the mitochondrial ribosome small subunit (28S) which comprises a 12S rRNA and about 30 distinct proteins.
SUBCELLULAR LOCATION: Mitochondrion.
CAUTION: Has been found in the mitochondrial ribosome large and small subunits. Was erronously (PubMed:11551941) assigned to be MRP-S31.
SEQUENCE CAUTION: Sequence=AAF36124.1; Type=Frameshift; Positions=Several;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): MRPL42
CDC HuGE Published Literature: MRPL42
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]

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 13.32 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 276.00 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.00162-0.265 Picture PostScript Text
3' UTR -641.762551-0.252 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
IPR019346 - Ribosomal-S32_mit

Pfam Domains:
PF10210 - Mitochondrial 28S ribosomal protein S32

ModBase Predicted Comparative 3D Structure on Q9Y6G3
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 BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

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

Biological Process:
GO:0006412 translation
GO:0070125 mitochondrial translational elongation
GO:0070126 mitochondrial translational termination

Cellular Component:
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005762 mitochondrial large ribosomal subunit
GO:0005763 mitochondrial small ribosomal subunit
GO:0005840 ribosome
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AF135160 - Homo sapiens unknown mRNA.
AF078860 - Homo sapiens PTD007 mRNA, complete cds.
AL136659 - Homo sapiens mRNA; cDNA DKFZp564I2064 (from clone DKFZp564I2064).
AK000285 - Homo sapiens cDNA FLJ20278 fis, clone HEP03158.
AF151038 - Homo sapiens HSPC204 mRNA, complete cds.
CR749344 - Homo sapiens mRNA; cDNA DKFZp779G2268 (from clone DKFZp779G2268).
BC040240 - Homo sapiens mitochondrial ribosomal protein L42, mRNA (cDNA clone MGC:4918 IMAGE:3445213), complete cds.
JD345392 - Sequence 326416 from Patent EP1572962.
JD516194 - Sequence 497218 from Patent EP1572962.
EU832289 - Synthetic construct Homo sapiens clone HAIB:100067318; DKFZo008B0427 mitochondrial ribosomal protein L42 protein (MRPL42) gene, encodes complete protein; nuclear gene for mitochondrial product.
AB529083 - Synthetic construct DNA, clone: pF1KB4156, Homo sapiens MRPL42 gene for mitochondrial ribosomal protein L42, without stop codon, in Flexi system.
KJ893658 - Synthetic construct Homo sapiens clone ccsbBroadEn_03052 MRPL42 gene, encodes complete protein.
CR533495 - Homo sapiens full open reading frame cDNA clone RZPDo834H0117D for gene MRPL42, mitochondrial ribosomal protein L42; complete cds, incl. stopcodon.
JD303013 - Sequence 284037 from Patent EP1572962.
JD538102 - Sequence 519126 from Patent EP1572962.
JD043447 - Sequence 24471 from Patent EP1572962.
JD061574 - Sequence 42598 from Patent EP1572962.
JD563527 - Sequence 544551 from Patent EP1572962.
JD300789 - Sequence 281813 from Patent EP1572962.
JD197149 - Sequence 178173 from Patent EP1572962.
JD093346 - Sequence 74370 from Patent EP1572962.
JD503211 - Sequence 484235 from Patent EP1572962.
JD091204 - Sequence 72228 from Patent EP1572962.
JD303318 - Sequence 284342 from Patent EP1572962.
JD090490 - Sequence 71514 from Patent EP1572962.
JD311170 - Sequence 292194 from Patent EP1572962.
JC506682 - Sequence 50 from Patent EP2733220.
JC737794 - Sequence 50 from Patent WO2014075939.
JD161541 - Sequence 142565 from Patent EP1572962.
JD547616 - Sequence 528640 from Patent EP1572962.
JD547617 - Sequence 528641 from Patent EP1572962.
JD227595 - Sequence 208619 from Patent EP1572962.
JD510437 - Sequence 491461 from Patent EP1572962.
JD522967 - Sequence 503991 from Patent EP1572962.
JD522968 - Sequence 503992 from Patent EP1572962.
JD405598 - Sequence 386622 from Patent EP1572962.

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

Protein Q9Y6G3 (Reactome details) participates in the following event(s):

R-HSA-5389839 39S subunit binds 28S subunit:mRNA:fMet-tRNA
R-HSA-5419273 Hydrolysis of GTP and dissociation of 28S and 39S subunits
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: HSPC204, MRPL31, MRPS32, NM_172177, NP_751917, PTD007, Q6FID1, Q96Q48, Q9P0S1, Q9Y6G3, RM42_HUMAN, RPML31
UCSC ID: uc001tcr.3
RefSeq Accession: NM_172177
Protein: Q9Y6G3 (aka RM42_HUMAN)
CCDS: CCDS9045.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_172177.3
exon count: 6CDS single in 3' UTR: no RNA size: 3142
ORF size: 429CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1007.00frame 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.