Human Gene LSM4 (ENST00000593829.6_7) from GENCODE V47lift37
  Description: LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated, transcript variant 1 (from RefSeq NM_012321.5)
Gencode Transcript: ENST00000593829.6_7
Gencode Gene: ENSG00000130520.11_17
Transcript (Including UTRs)
   Position: hg19 chr19:18,417,046-18,433,886 Size: 16,841 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr19:18,418,274-18,433,830 Size: 15,557 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene 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 (chr19:18,417,046-18,433,886)mRNA (may differ from genome)Protein (139 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: LSM4_HUMAN
DESCRIPTION: RecName: Full=U6 snRNA-associated Sm-like protein LSm4; AltName: Full=Glycine-rich protein; Short=GRP;
FUNCTION: Binds specifically to the 3'-terminal U-tract of U6 snRNA.
SUBUNIT: LSm subunits form a heteromer with a doughnut shape.
INTERACTION: Q9UK45:LSM7; NbExp=5; IntAct=EBI-372521, EBI-348372; O95777:NAA38; NbExp=4; IntAct=EBI-372521, EBI-347779;
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


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

+  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: 51.97 RPKM in Testis
Total median expression: 1012.38 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 -26.9056-0.480 Picture PostScript Text
3' UTR -467.001228-0.380 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 Q9Y4Z0
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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0017070 U6 snRNA binding
GO:0042731 PH domain binding

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0033962 cytoplasmic mRNA processing body assembly
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Cellular Component:
GO:0000932 P-body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005688 U6 snRNP
GO:0005829 cytosol
GO:0016020 membrane
GO:0032991 macromolecular complex
GO:0043005 neuron projection
GO:0097526 spliceosomal tri-snRNP complex


-  Descriptions from all associated GenBank mRNAs
  AF117235 - Homo sapiens glycine-rich protein mRNA, complete cds.
BC000387 - Homo sapiens LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:8433 IMAGE:2821171), complete cds.
AF182290 - Homo sapiens U6 snRNA-associated Sm-like protein LSm4 mRNA, complete cds.
BC003652 - Homo sapiens LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:4747 IMAGE:3536946), complete cds.
BC022198 - Homo sapiens LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:4705 IMAGE:3534432), complete cds.
AF251218 - Homo sapiens LSm4 autoantigen mRNA, complete cds.
AJ238096 - Homo sapiens mRNA for Lsm4 protein.
BC023665 - Homo sapiens LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae), mRNA (cDNA clone MGC:29665 IMAGE:5015049), complete cds.
JD165499 - Sequence 146523 from Patent EP1572962.
JD072722 - Sequence 53746 from Patent EP1572962.
JD359211 - Sequence 340235 from Patent EP1572962.
JD019378 - Sequence 402 from Patent EP1572962.
DQ593018 - Homo sapiens piRNA piR-33130, complete sequence.
JD028947 - Sequence 9971 from Patent EP1572962.
JD031174 - Sequence 12198 from Patent EP1572962.
JD020703 - Sequence 1727 from Patent EP1572962.
JD479954 - Sequence 460978 from Patent EP1572962.
JD211359 - Sequence 192383 from Patent EP1572962.
JD158557 - Sequence 139581 from Patent EP1572962.
EU832676 - Synthetic construct Homo sapiens clone HAIB:100067705; DKFZo008H1131 LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) protein (LSM4) gene, encodes complete protein.
EU832756 - Synthetic construct Homo sapiens clone HAIB:100067785; DKFZo004H1132 LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) protein (LSM4) gene, encodes complete protein.
KJ893462 - Synthetic construct Homo sapiens clone ccsbBroadEn_02856 LSM4 gene, encodes complete protein.
AB463842 - Synthetic construct DNA, clone: pF1KB8276, Homo sapiens LSM4 gene for LSM4 homolog, U6 small nuclear RNA associated, without stop codon, in Flexi system.
JD024645 - Sequence 5669 from Patent EP1572962.
JD029231 - Sequence 10255 from Patent EP1572962.
DQ590181 - Homo sapiens piRNA piR-57293, complete sequence.
JD389871 - Sequence 370895 from Patent EP1572962.

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

Protein Q9Y4Z0 (Reactome details) participates in the following event(s):

R-HSA-429978 Lsm1-7 Complex binds deadenylated mRNA
R-HSA-429845 5' to 3' exoribonuclease hydrolyzes decapped mRNA
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-72172 mRNA Splicing
R-HSA-8953854 Metabolism of RNA
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000593829.1, ENST00000593829.2, ENST00000593829.3, ENST00000593829.4, ENST00000593829.5, LSM4_HUMAN, NM_012321, Q9Y4Z0, uc326zcx.1, uc326zcx.2
UCSC ID: ENST00000593829.6_7
RefSeq Accession: NM_012321.5
Protein: Q9Y4Z0 (aka LSM4_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.