Mouse Gene Nub1 (ENSMUST00000068825.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus negative regulator of ubiquitin-like proteins 1 (Nub1), transcript variant 2, mRNA. (from RefSeq NM_016736)
Gencode Transcript: ENSMUST00000068825.7
Gencode Gene: ENSMUSG00000028954.11
Transcript (Including UTRs)
   Position: mm10 chr5:24,685,824-24,710,378 Size: 24,555 Total Exon Count: 15 Strand: +
Coding Region
   Position: mm10 chr5:24,689,394-24,709,167 Size: 19,774 Coding Exon Count: 14 

Page IndexSequence and LinksPrimersCTDRNA StructureProtein Structure
Other SpeciesmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:24,685,824-24,710,378)mRNA (may differ from genome)Protein (614 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKBWikipedia

-  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 -84.80213-0.398 Picture PostScript Text
3' UTR -395.501211-0.327 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
IPR011990 - TPR-like_helical
IPR009060 - UBA-like
IPR000449 - UBA/transl_elong_EF1B_N
IPR015940 - UBA/transl_elong_EF1B_N_euk

Pfam Domains:
PF00627 - UBA/TS-N domain

SCOP Domains:
48452 - TPR-like
46689 - Homeodomain-like
46929 - DNA helicase RuvA subunit, C-terminal domain
46934 - UBA-like
158372 - AF1782-like
54236 - Ubiquitin-like

ModBase Predicted Comparative 3D Structure on Q3UYM1
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Descriptions from all associated GenBank mRNAs
  U27462 - Mus musculus BS4 peptide mRNA, complete cds.
AK086301 - Mus musculus 15 days embryo head cDNA, RIKEN full-length enriched library, clone:D930019L13 product:NY-REN-18 antigen, full insert sequence.
AK134581 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330419K09 product:NEDD8 ultimate buster-1 (BS4 protein), full insert sequence.
AK153400 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830154L24 product:NEDD8 ultimate buster-1 (BS4 protein), full insert sequence.
AK018166 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330412F12 product:NY-REN-18 antigen, full insert sequence.
BC005640 - Mus musculus negative regulator of ubiquitin-like proteins 1, mRNA (cDNA clone IMAGE:3708853), partial cds.
BC018178 - Mus musculus negative regulator of ubiquitin-like proteins 1, mRNA (cDNA clone IMAGE:4036112), partial cds.
BC037451 - Mus musculus negative regulator of ubiquitin-like proteins 1, mRNA (cDNA clone MGC:46863 IMAGE:4018648), complete cds.
AF534114 - Mus musculus NEDD8 ultimate buster-1 (Nub1) mRNA, complete cds.
AK208385 - Mus musculus cDNA, clone:Y2G0110P22, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK184479 - Mus musculus cDNA, clone:Y0G0130E08, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK182203 - Mus musculus cDNA, clone:Y0G0121D03, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK202689 - Mus musculus cDNA, clone:Y1G0142G13, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000030796, based on BLAT search.
AK215665 - Mus musculus cDNA, clone:Y2G0135M09, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000030796, based on BLAT search.
AK218493 - Mus musculus cDNA, clone:Y2G0145F23, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000030796, based on BLAT search.
AK194716 - Mus musculus cDNA, clone:Y1G0116D16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK197478 - Mus musculus cDNA, clone:Y1G0125D19, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK196508 - Mus musculus cDNA, clone:Y1G0122B01, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.
AK195621 - Mus musculus cDNA, clone:Y1G0119B09, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000068825, based on BLAT search.

-  Other Names for This Gene
  Alternate Gene Symbols: 6330412F12Rik, mCG_16508, NM_016736, Q3UYM1, Q3UYM1_MOUSE, uc008wsf.1, uc008wsf.2, uc008wsf.3
UCSC ID: uc008wsf.3
RefSeq Accession: NM_016736
Protein: Q3UYM1 CCDS: CCDS39030.1, CCDS80230.1

-  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.