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lsm5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [ Danio rerio (zebrafish) ]

Gene ID: 563948, updated on 4-Nov-2022

Summary

Official Symbol
lsm5provided by ZNC
Official Full Name
LSM5 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by ZNC
Primary source
ZFIN:ZDB-GENE-070822-23
See related
Ensembl:ENSDARG00000071573 AllianceGenome:ZFIN:ZDB-GENE-070822-23
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:171959
Summary
Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in nucleus. Predicted to be part of Lsm1-7-Pat1 complex; U4/U6 x U5 tri-snRNP complex; and U6 snRNP. Orthologous to human LSM5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
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Genomic context

See lsm5 in Genome Data Viewer
Location:
chromosome: 12
Exon count:
5
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (13331526..13337031, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (13293223..13298728, complement)
103 previous assembly Zv9 (GCF_000002035.4) 12 NC_007123.5 (14437570..14443075, complement)

Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene interferon regulatory factor 9 Neighboring gene ER membrane protein complex subunit 9 Neighboring gene proteasome activator subunit 2 Neighboring gene drosha ribonuclease III Neighboring gene potassium voltage-gated channel, subfamily H (eag-related), member 4b

Genomic regions, transcripts, and products

Expression

  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

General gene information

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
contributes_to RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
part_of Lsm1-7-Pat1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
U6 snRNA-associated Sm-like protein LSm5
Names
LSM5 homolog, U6 small nuclear RNA associated

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001100438.1NP_001093908.1  U6 snRNA-associated Sm-like protein LSm5

    See identical proteins and their annotated locations for NP_001093908.1

    Status: PROVISIONAL

    Source sequence(s)
    BC150414
    UniProtKB/TrEMBL
    A0A8M1NFG2, A7E2L8
    Related
    ENSDARP00000096681.3, ENSDART00000105903.5
    Conserved Domains (1) summary
    cd01732
    Location:1186
    LSm5; Like-Sm protein 5

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007123.7 Reference GRCz11 Primary Assembly

    Range
    13331526..13337031 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)