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    ssb small RNA binding exonuclease protection factor La [ Danio rerio (zebrafish) ]

    Gene ID: 321504, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ssbprovided by ZNC
    Official Full Name
    small RNA binding exonuclease protection factor Laprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-223
    See related
    Ensembl:ENSDARG00000029252 AllianceGenome:ZFIN:ZDB-GENE-030131-223
    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:55588; wu:fb17f11
    Summary
    Predicted to enable mRNA binding activity. Predicted to be involved in positive regulation of translation and tRNA processing. Predicted to act upstream of or within RNA processing. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Is expressed in several structures, including digestive system; immature eye; mesoderm; musculature system; and nervous system. Orthologous to human SSB (small RNA binding exonuclease protection factor La). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See ssb in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (3715497..3728632)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (3552595..3567812)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase G (cyclophilin G) Neighboring gene phosphatase, orphan 2 Neighboring gene Sp5 transcription factor b Neighboring gene glutamate-rich 2

    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. Proteomic profile and toxicity pathway analysis in zebrafish embryos exposed to bisphenol A and di-n-butyl phthalate at environmentally relevant levels. Dong X, et al. Chemosphere, 2018 Feb. PMID 29145093
    2. A novel chemical screening strategy in zebrafish identifies common pathways in embryogenesis and rhabdomyosarcoma development. Le X, et al. Development, 2013 Jun. PMID 23615277, Free PMC Article
    3. Incomplete splicing, cell division defects, and hematopoietic blockage in dhx8 mutant zebrafish. English MA, et al. Dev Dyn, 2012 May. PMID 22411201, Free PMC Article
    4. Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol, 2016 Jan. PMID 26235539
    5. Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development. Farnsworth DR, et al. Exp Eye Res, 2021 May. PMID 33705730, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasmic stress granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lupus La protein
    Names
    Sjogren syndrome antigen B (autoantigen La)

    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_199547.1 → NP_955841.1  lupus La protein

      See identical proteins and their annotated locations for NP_955841.1

      Status: PROVISIONAL

      Source sequence(s)
      BC045392
      UniProtKB/TrEMBL
      A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
      Related
      ENSDARP00000041626.5, ENSDART00000041627.5
      Conserved Domains (3) summary
      cd08028
      Location:7 → 88
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:109 → 181
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:229 → 326
      RRM_3; RNA binding motif

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007117.7 Reference GRCz11 Primary Assembly

      Range
      3715497..3728632
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005172073.5 → XP_005172130.1  lupus La protein isoform X1

      See identical proteins and their annotated locations for XP_005172130.1

      UniProtKB/TrEMBL
      A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
      Conserved Domains (3) summary
      cd08028
      Location:7 → 88
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:109 → 181
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:229 → 326
      RRM_3; RNA binding motif

    2. XM_009302102.4 → XP_009300377.1  lupus La protein isoform X1

      See identical proteins and their annotated locations for XP_009300377.1

      UniProtKB/TrEMBL
      A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
      Conserved Domains (3) summary
      cd08028
      Location:7 → 88
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:109 → 181
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:229 → 326
      RRM_3; RNA binding motif
    Nucleotide Protein Strain
    Heading Accession and Version

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