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lsm7 LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated [ Danio rerio (zebrafish) ]

Gene ID: 573047, updated on 27-Mar-2024

Summary

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Official Symbol
lsm7provided by ZNC
Official Full Name
LSM7 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-8284
See related
Ensembl:ENSDARG00000058328 AllianceGenome:ZFIN:ZDB-GENE-030131-8284
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fj64g01; zgc:66405; wu:fj64g01
Summary
Predicted to contribute to RNA binding activity. Predicted to act upstream of or within mRNA splicing, via spliceosome and nuclear-transcribed mRNA catabolic process. Predicted to be located in nucleus. Predicted to be part of Lsm1-7-Pat1 complex; spliceosomal complex; and spliceosomal snRNP complex. Orthologous to human LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 22
Exon count:
4
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (10752549..10756061)
105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (10722867..10726379)

Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene major facilitator superfamily domain containing 14A 1 Neighboring gene SAS-6 centriolar assembly protein Neighboring gene transmembrane serine protease 9 Neighboring gene translocase of inner mitochondrial membrane 13 homolog (yeast)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. Systemic splicing factor deficiency causes tissue-specific defects: a zebrafish model for retinitis pigmentosa. Linder B, et al. Hum Mol Genet, 2011 Jan 15. PMID 21051334
  2. A sart1 Zebrafish Mutant Results in Developmental Defects in the Central Nervous System. Henson HE, et al. Cells, 2020 Oct 22. PMID 33105605, Free PMC Article
  3. Forward Genetic Screens in Zebrafish Identify Pre-mRNA-Processing Pathways Regulating Early T Cell Development. Iwanami N, et al. Cell Rep, 2016 Nov 22. PMID 27880902, Free PMC Article
  4. Expressed sequence tag analysis of expression profiles of zebrafish testis and ovary. Zeng S, et al. Gene, 2002 Jul 10. PMID 12234666
  5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
contributes_to RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within mRNA splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within nuclear-transcribed mRNA catabolic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of oligodendrocyte apoptotic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within response to light stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within swimming behavior IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of Lsm1-7-Pat1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
U6 snRNA-associated Sm-like protein LSm7

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_001048006.1 → NP_001041471.1  U6 snRNA-associated Sm-like protein LSm7

    See identical proteins and their annotated locations for NP_001041471.1

    Status: VALIDATED

    Source sequence(s)
    AL720230, AW305388, BC055642, BI846179
    UniProtKB/TrEMBL
    A0A8M1N9P2, A4FVI7, F1R5D6
    Related
    ENSDARP00000075631.6, ENSDART00000081188.7
    Conserved Domains (1) summary
    cd01729
    Location:9 → 97
    LSm7; Like-Sm protein 7

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_007133.7 Reference GRCz11 Primary Assembly

    Range
    10752549..10756061
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_200011.1: Suppressed sequence

    Description
    NM_200011.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
Nucleotide Protein Strain
Heading Accession and Version

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