Mouse Gene Lsm14a (ENSMUST00000085585.11) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus LSM14A mRNA processing body assembly factor (Lsm14a), transcript variant 1, mRNA. (from RefSeq NM_025948)
Gencode Transcript: ENSMUST00000085585.11
Gencode Gene: ENSMUSG00000066568.12
Transcript (Including UTRs)
   Position: mm10 chr7:34,344,646-34,389,687 Size: 45,042 Total Exon Count: 11 Strand: -
Coding Region
   Position: mm10 chr7:34,347,959-34,389,478 Size: 41,520 Coding Exon Count: 10 

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 (chr7:34,344,646-34,389,687)mRNA (may differ from genome)Protein (462 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: LS14A_MOUSE
DESCRIPTION: RecName: Full=Protein LSM14 homolog A; AltName: Full=Protein FAM61A; AltName: Full=RNA-associated protein 55A; Short=mRAP55A;
FUNCTION: Essential for formation of P-bodies, cytoplasmic structures that provide storage sites for non-translating mRNAs (By similarity).
SUBUNIT: Component of a ribonucleoprotein (RNP) complex (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cytoplasm, P-body (By similarity). Note=Targeted to stress granules (SGs) in response to cellular stress (By similarity).
DOMAIN: The LSM14 domain and the RGG repeats are required for accumulation in P-bodies, and the region containing the FDF motif is responsible for cytoplasmic retention (By similarity).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity).
SIMILARITY: Belongs to the LSM14 family.
SIMILARITY: Contains 1 DFDF domain.

-  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 -117.70209-0.563 Picture PostScript Text
3' UTR -344.901346-0.256 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
IPR025762 - DFDF
IPR019050 - FDF_dom
IPR025761 - FFD_box
IPR025609 - Lsm14_N
IPR010920 - LSM_dom
IPR025768 - TFG_box

Pfam Domains:
PF09532 - FDF domain
PF12701 - Scd6-like Sm domain
PF14438 - Ataxin 2 SM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

ModBase Predicted Comparative 3D Structure on Q8K2F8
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
No orthologGenome BrowserNo orthologNo orthologGenome BrowserNo ortholog
     Gene Details
     Gene Sorter
 RGDEnsembl WormBaseSGD
 Protein Sequence  Protein Sequence 
 Alignment  Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003690 double-stranded DNA binding
GO:0003725 double-stranded RNA binding
GO:0003727 single-stranded RNA binding

Biological Process:
GO:0006417 regulation of translation
GO:0007275 multicellular organism development
GO:0033962 cytoplasmic mRNA processing body assembly
GO:0039529 RIG-I signaling pathway
GO:0051607 defense response to virus
GO:0060340 positive regulation of type I interferon-mediated signaling pathway

Cellular Component:
GO:0000932 P-body
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0010494 cytoplasmic stress granule
GO:0036464 cytoplasmic ribonucleoprotein granule


-  Descriptions from all associated GenBank mRNAs
  AK013143 - Mus musculus 10, 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2810423E01 product:RAP55 PROTEIN homolog [Pleurodeles waltlii], full insert sequence.
BC031521 - Mus musculus LSM14 homolog A (SCD6, S. cerevisiae), mRNA (cDNA clone MGC:6898 IMAGE:2655161), complete cds.
AK004427 - Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched library, clone:1110070L07 product:hypothetical protein, full insert sequence.
AK003611 - Mus musculus 18-day embryo whole body cDNA, RIKEN full-length enriched library, clone:1110011H05 product:hypothetical Glycine-rich region containing protein, full insert sequence.
AK012276 - Mus musculus 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2700023B17 product:HYPOTHETICAL 50.6 KDA PROTEIN homolog [Homo sapiens], full insert sequence.
AK213528 - Mus musculus cDNA, clone:Y2G0128J20, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK184993 - Mus musculus cDNA, clone:Y0G0132D19, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK209661 - Mus musculus cDNA, clone:Y2G0115M23, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK202607 - Mus musculus cDNA, clone:Y1G0142C16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK186175 - Mus musculus cDNA, clone:Y0G0136I06, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK182421 - Mus musculus cDNA, clone:Y0G0121O11, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK205955 - Mus musculus cDNA, clone:Y2G0103F01, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
AK189673 - Mus musculus cDNA, clone:Y0G0149P16, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000002711, based on BLAT search.
LF196216 - JP 2014500723-A/3719: Polycomb-Associated Non-Coding RNAs.
LF292168 - JP 2014500723-A/99671: Polycomb-Associated Non-Coding RNAs.
LF292170 - JP 2014500723-A/99673: Polycomb-Associated Non-Coding RNAs.
MA431793 - JP 2018138019-A/3719: Polycomb-Associated Non-Coding RNAs.
MA527745 - JP 2018138019-A/99671: Polycomb-Associated Non-Coding RNAs.
MA527747 - JP 2018138019-A/99673: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: Fam61a, LS14A_MOUSE, NM_025948, Q8K2F8, Q9CTG8, Rap55a, uc009gjd.1, uc009gjd.2, uc009gjd.3
UCSC ID: uc009gjd.3
RefSeq Accession: NM_025948
Protein: Q8K2F8 (aka LS14A_MOUSE)
CCDS: CCDS21140.1

-  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.