Human Gene LSM8 (ENST00000249299.7_4) from GENCODE V47lift37
  Description: LSM8 homolog, U6 small nuclear RNA associated (from RefSeq NM_016200.5)
Gencode Transcript: ENST00000249299.7_4
Gencode Gene: ENSG00000128534.8_8
Transcript (Including UTRs)
   Position: hg19 chr7:117,824,218-117,844,089 Size: 19,872 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr7:117,824,278-117,832,056 Size: 7,779 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:117,824,218-117,844,089)mRNA (may differ from genome)Protein (96 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NAA38_HUMAN
DESCRIPTION: RecName: Full=N-alpha-acetyltransferase 38, NatC auxiliary subunit; AltName: Full=U6 snRNA-associated Sm-like protein LSm8;
FUNCTION: Binds specifically to the 3'-terminal U-tract of U6 snRNA.
SUBUNIT: LSm subunits form a heteromer with a doughnut shape.
INTERACTION: Q9Y333:LSM2; NbExp=5; IntAct=EBI-347779, EBI-347416; P62310:LSM3; NbExp=5; IntAct=EBI-347779, EBI-348239; Q9Y4Z0:LSM4; NbExp=4; IntAct=EBI-347779, EBI-372521;
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Belongs to the snRNP Sm proteins 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


-  MalaCards Disease Associations
  MalaCards Gene Search: LSM8
Diseases sorted by gene-association score: retinitis pigmentosa (0)

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.78 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 185.35 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.6060-0.343 Picture PostScript Text
3' UTR -2822.9012033-0.235 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
IPR010920 - LSM_dom
IPR001163 - Ribonucl_LSM
IPR006649 - Ribonucl_LSM_euk/arc

Pfam Domains:
PF01423 - LSM domain

SCOP Domains:
50182 - Sm-like ribonucleoproteins

ModBase Predicted Comparative 3D Structure on O95777
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 orthologNo orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0017070 U6 snRNA binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005688 U6 snRNP
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071011 precatalytic spliceosome


-  Descriptions from all associated GenBank mRNAs
  LF207041 - JP 2014500723-A/14544: Polycomb-Associated Non-Coding RNAs.
MA442618 - JP 2018138019-A/14544: Polycomb-Associated Non-Coding RNAs.
BC042464 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone IMAGE:5163799), with apparent retained intron.
AK311936 - Homo sapiens cDNA, FLJ92203, Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S.cerevisiae) (LSM8), mRNA.
AF182294 - Homo sapiens U6 snRNA-associated Sm-like protein LSm8 mRNA, complete cds.
BC045532 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone IMAGE:5268365), with apparent retained intron.
BC053644 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone IMAGE:5212975), with apparent retained intron.
BC022440 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:24761 IMAGE:4283482), complete cds.
BC002742 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:3345 IMAGE:3626875), complete cds.
BC064376 - Homo sapiens LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone IMAGE:5723621), with apparent retained intron.
AK090561 - Homo sapiens cDNA FLJ33242 fis, clone ASTRO2004051.
LF360455 - JP 2014500723-A/167958: Polycomb-Associated Non-Coding RNAs.
LF360459 - JP 2014500723-A/167962: Polycomb-Associated Non-Coding RNAs.
JD301864 - Sequence 282888 from Patent EP1572962.
JD504781 - Sequence 485805 from Patent EP1572962.
JD305704 - Sequence 286728 from Patent EP1572962.
LF360460 - JP 2014500723-A/167963: Polycomb-Associated Non-Coding RNAs.
JD351100 - Sequence 332124 from Patent EP1572962.
JD519263 - Sequence 500287 from Patent EP1572962.
JD490532 - Sequence 471556 from Patent EP1572962.
JD551095 - Sequence 532119 from Patent EP1572962.
MA596032 - JP 2018138019-A/167958: Polycomb-Associated Non-Coding RNAs.
MA596036 - JP 2018138019-A/167962: Polycomb-Associated Non-Coding RNAs.
MA596037 - JP 2018138019-A/167963: Polycomb-Associated Non-Coding RNAs.
LF360461 - JP 2014500723-A/167964: Polycomb-Associated Non-Coding RNAs.
JD220911 - Sequence 201935 from Patent EP1572962.
JD374530 - Sequence 355554 from Patent EP1572962.
JD489108 - Sequence 470132 from Patent EP1572962.
JD489109 - Sequence 470133 from Patent EP1572962.
MA596038 - JP 2018138019-A/167964: Polycomb-Associated Non-Coding RNAs.

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

Protein O95777 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000249299.1, ENST00000249299.2, ENST00000249299.3, ENST00000249299.4, ENST00000249299.5, ENST00000249299.6, LSM8_HUMAN, NM_016200, O95777, uc317ezg.1, uc317ezg.2
UCSC ID: ENST00000249299.7_4
RefSeq Accession: NM_016200.5
Protein: O95777 (aka NAA38_HUMAN)

-  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.