Mouse Gene Rpl6 (ENSMUST00000031617.12) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus ribosomal protein L6 (Rpl6), mRNA. (from RefSeq NM_011290)
Gencode Transcript: ENSMUST00000031617.12
Gencode Gene: ENSMUSG00000029614.13
Transcript (Including UTRs)
   Position: mm10 chr5:121,204,481-121,209,241 Size: 4,761 Total Exon Count: 7 Strand: +
Coding Region
   Position: mm10 chr5:121,205,406-121,208,934 Size: 3,529 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:121,204,481-121,209,241)mRNA (may differ from genome)Protein (296 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: Q3UCH0_MOUSE
DESCRIPTION: RecName: Full=60S ribosomal protein L6;
SIMILARITY: Belongs to the ribosomal protein L6e 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


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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.7072-0.176 Picture PostScript Text
3' UTR -80.50307-0.262 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
IPR005568 - Ribosomal_L6_N
IPR000915 - Ribosomal_L6E
IPR014722 - Transl_SH3-like_sub

Pfam Domains:
PF01159 - Ribosomal protein L6e
PF03868 - Ribosomal protein L6, N-terminal domain

SCOP Domains:
50104 - Translation proteins SH3-like domain

ModBase Predicted Comparative 3D Structure on Q3UCH0
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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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details    Gene Details
Gene Sorter    Gene Sorter
GenBankRGDEnsemblEnsemblWormBaseSGD
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

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

Biological Process:
GO:0002181 cytoplasmic translation
GO:0006412 translation

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0042788 polysomal ribosome


-  Descriptions from all associated GenBank mRNAs
  AK153208 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830127H10 product:ribosomal protein L6, full insert sequence.
AK150540 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830011I22 product:ribosomal protein L6, full insert sequence.
AK151344 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830028F14 product:ribosomal protein L6, full insert sequence.
AK151759 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830036L08 product:ribosomal protein L6, full insert sequence.
AK167439 - Mus musculus 11 days pregnant adult female placenta cDNA, RIKEN full-length enriched library, clone:I530014E17 product:ribosomal protein L6, full insert sequence.
AK151022 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830020H24 product:ribosomal protein L6, full insert sequence.
AK153507 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830168L01 product:ribosomal protein L6, full insert sequence.
AK135175 - Mus musculus 12 days embryo female ovary cDNA, RIKEN full-length enriched library, clone:6620403F12 product:ribosomal protein L6, full insert sequence.
AK148479 - Mus musculus adult pancreas islet cells cDNA, RIKEN full-length enriched library, clone:C820008J02 product:ribosomal protein L6, full insert sequence.
AK002248 - Mus musculus adult male kidney cDNA, RIKEN full-length enriched library, clone:0610006I04 product:ribosomal protein L6, full insert sequence.
AK002648 - Mus musculus adult male kidney cDNA, RIKEN full-length enriched library, clone:0610019D07 product:ribosomal protein L6, full insert sequence.
AK088472 - Mus musculus 2 days neonate thymus thymic cells cDNA, RIKEN full-length enriched library, clone:E430018H24 product:ribosomal protein L6, full insert sequence.
BC106121 - Mus musculus ribosomal protein L6, mRNA (cDNA clone MGC:117949 IMAGE:3979296), complete cds.
AK010918 - Mus musculus 13 days embryo liver cDNA, RIKEN full-length enriched library, clone:2510006J16 product:ribosomal protein L6, full insert sequence.
BC062880 - Mus musculus ribosomal protein L6, mRNA (cDNA clone MGC:86071 IMAGE:5692572), complete cds.
X81987 - M.musculus mRNA for TAX responsive element binding protein 107.
DQ550952 - Mus musculus piRNA piR-19064, complete sequence.
AK219533 - Mus musculus cDNA, clone:Y2G0148M09, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031617, based on BLAT search.
AK198216 - Mus musculus cDNA, clone:Y1G0127H08, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031617, based on BLAT search.
AB349459 - Mus musculus non-coding RNA, oocyte_piRNA275, complete sequence.
AK208536 - Mus musculus cDNA, clone:Y2G0111N15, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000031617, based on BLAT search.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu03010 - Ribosome

-  Other Names for This Gene
  Alternate Gene Symbols: mCG_16023, NM_011290, Q3UCH0, Q3UCH0_MOUSE, uc008ziq.1, uc008ziq.2, uc008ziq.3, uc008ziq.4
UCSC ID: uc008ziq.4
RefSeq Accession: NM_011290
Protein: Q3UCH0 CCDS: CCDS19632.1

-  Gene Model Information
  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.