Mouse Gene Rbms3 (ENSMUST00000164018.8) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus RNA binding motif, single stranded interacting protein (Rbms3), transcript variant 4, mRNA. (from RefSeq NM_001172121)
Gencode Transcript: ENSMUST00000164018.8
Gencode Gene: ENSMUSG00000039607.16
Transcript (Including UTRs)
   Position: mm10 chr9:116,578,025-117,629,913 Size: 1,051,889 Total Exon Count: 15 Strand: -
Coding Region
   Position: mm10 chr9:116,578,696-117,629,850 Size: 1,051,155 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:116,578,025-117,629,913)mRNA (may differ from genome)Protein (463 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsMGIPubMed
SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: RBMS3_MOUSE
DESCRIPTION: RecName: Full=RNA-binding motif, single-stranded-interacting protein 3;
FUNCTION: Binds poly(A) and poly(U) oligoribonucleotides (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.
SEQUENCE CAUTION: Sequence=BAC34878.1; Type=Erroneous initiation;

-  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 -19.2063-0.305 Picture PostScript Text
3' UTR -146.60671-0.218 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
IPR002343 - Hud_Sxl_RNA
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q8BWL5
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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 orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0008143 poly(A) binding
GO:0008266 poly(U) RNA binding
GO:0035925 mRNA 3'-UTR AU-rich region binding

Biological Process:
GO:0002357 defense response to tumor cell
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0045727 positive regulation of translation
GO:0090090 negative regulation of canonical Wnt signaling pathway

Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK046197 - Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230350F07 product:similar to RNA-BINDING PROTEIN [Homo sapiens], full insert sequence.
BC108402 - Mus musculus RNA binding motif, single stranded interacting protein, mRNA (cDNA clone MGC:118437 IMAGE:6516420), complete cds.
BC033604 - Mus musculus RNA binding motif, single stranded interacting protein, mRNA (cDNA clone IMAGE:5370114), partial cds.
AK030478 - Mus musculus adult male pituitary gland cDNA, RIKEN full-length enriched library, clone:5330417B20 product:RNA-BINDING PROTEIN homolog [Homo sapiens], full insert sequence.
BC117841 - Mus musculus RNA binding motif, single stranded interacting protein, mRNA (cDNA clone MGC:143780 IMAGE:40093225), complete cds.
AK033005 - Mus musculus 12 days embryo male wolffian duct includes surrounding region cDNA, RIKEN full-length enriched library, clone:6720490M18 product:hypothetical RNA-binding region RNP-1 (RNA recognition motif) containing protein, full insert sequence.
AK030609 - Mus musculus adult male pituitary gland cDNA, RIKEN full-length enriched library, clone:5330438F10 product:RNA-BINDING PROTEIN homolog [Homo sapiens], full insert sequence.
AK032938 - Mus musculus 12 days embryo male wolffian duct includes surrounding region cDNA, RIKEN full-length enriched library, clone:6720477E09 product:RNA-BINDING PROTEIN homolog [Homo sapiens], full insert sequence.
AK041098 - Mus musculus adult male aorta and vein cDNA, RIKEN full-length enriched library, clone:A530082O13 product:RNA-BINDING PROTEIN homolog [Homo sapiens], full insert sequence.
AK052196 - Mus musculus 13 days embryo heart cDNA, RIKEN full-length enriched library, clone:D330006C15 product:RNA-BINDING PROTEIN homolog [Homo sapiens], full insert sequence.
AK051776 - Mus musculus 12 days embryo spinal ganglion cDNA, RIKEN full-length enriched library, clone:D130078B10 product:similar to RNA-BINDING PROTEIN [Homo sapiens], full insert sequence.
AK081921 - Mus musculus 16 days embryo head cDNA, RIKEN full-length enriched library, clone:C130087I15 product:similar to MSSP-2 (FRAGMENT) [Homo sapiens], full insert sequence.
AK162457 - Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430056P15 product:similar to MSSP-2 (Fragment) [Homo sapiens], full insert sequence.
AK032862 - Mus musculus 12 days embryo male wolffian duct includes surrounding region cDNA, RIKEN full-length enriched library, clone:6720463O22 product:inferred: RNA-binding protein {Homo sapiens}, full insert sequence.
AK161824 - Mus musculus 13 days embryo male testis cDNA, RIKEN full-length enriched library, clone:6030490G06 product:unclassifiable, full insert sequence.
AK084939 - Mus musculus 13 days embryo lung cDNA, RIKEN full-length enriched library, clone:D430017D17 product:hypothetical protein, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001172121, Q2VPR0, Q8BL73, Q8BLW6, Q8BMA7, Q8BMB5, Q8BML0, Q8BMN1, Q8BWL5, RBMS3_MOUSE, uc009rza.1, uc009rza.2, uc009rza.3, uc009rza.4, uc009rza.5
UCSC ID: uc009rza.5
RefSeq Accession: NM_001172121
Protein: Q8BWL5 (aka RBMS3_MOUSE)
CCDS: CCDS57712.1

-  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.