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    Ssb small RNA binding exonuclease protection factor La [ Rattus norvegicus (Norway rat) ]

    Gene ID: 81783, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Ssbprovided by RGD
    Official Full Name
    small RNA binding exonuclease protection factor Laprovided by RGD
    Primary source
    RGD:620804
    See related
    EnsemblRapid:ENSRNOG00000007998 AllianceGenome:RGD:620804
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable poly(U) RNA binding activity; sequence-specific mRNA binding activity; and tRNA binding activity. Involved in tRNA processing. Predicted to be located in cytoplasm. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Orthologous to human SSB (small RNA binding exonuclease protection factor La). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Thymus (RPKM 467.3), Heart (RPKM 337.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ssb in Genome Data Viewer
    Location:
    3q21
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (75024385..75034016)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (54616616..54626203)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (56092425..56102008)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene phosphatase, orphan 2 Neighboring gene small nucleolar RNA U13 Neighboring gene kelch-like family member 23 Neighboring gene methyltransferase 5, N6-adenosine Neighboring gene ubiquitin protein ligase E3 component n-recognin 3 Neighboring gene heterogeneous nuclear ribonucleoprotein C, pseudogene 5 Neighboring gene uncharacterized LOC134486377 Neighboring gene myosin IIIB

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Isolation of rat cDNA clones coding for the autoantigen SS-B/La: detection of species-specific variations. Semsei I, et al. Gene, 1993 Apr 30. PMID 7916708
    2. [Expression of SSB gene in rats with early isehemic myocardium and its implications]. Chen TY, et al. Sichuan Da Xue Xue Bao Yi Xue Ban, 2010 May. PMID 20629309
    3. Genomic structure and amino acid sequence domains of the human La autoantigen. Chambers JC, et al. J Biol Chem, 1988 Dec 5. PMID 3192525
    4. Human La protein: a stabilizer of histone mRNA. McLaren RS, et al. Mol Cell Biol, 1997 Jun. PMID 9154801, Free PMC Article
    5. Subcellular redistribution of la/SSB autoantigen during physiologic apoptosis in the fetal mouse heart and conduction system: a clue to the pathogenesis of congenital heart block. Tran HB, et al. Arthritis Rheum, 2002 Jan. PMID 11817591

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Effect of silencing SSB1 gene on the expression of NBS1 in irradiated rat submandibular gland cells.
      Title: Effect of silencing SSB1 gene on the expression of NBS1 in irradiated rat submandibular gland cells.
    2. The expression of SSB gene was down-regulated after myocardial ischemia.
      Title: [Expression of SSB gene in rats with early isehemic myocardium and its implications].
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC93380

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables poly(U) RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific mRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables tRNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in IRES-dependent viral translational initiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear histone mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to cytoplasmic stress granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA 3'-end processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA 5'-leader removal ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA export from nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA processing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    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
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    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 homolog
    Names
    Sjogren syndrome antigen B
    la autoantigen homolog
    la ribonucleoprotein
    mRNA for autoantigen

    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_031119.2 → NP_112381.2  lupus La protein homolog

      See identical proteins and their annotated locations for NP_112381.2

      Status: PROVISIONAL

      Source sequence(s)
      BC081780
      UniProtKB/Swiss-Prot
      P38656
      UniProtKB/TrEMBL
      Q66HM7
      Related
      ENSRNOP00000011175.5, ENSRNOT00000011174.7
      Conserved Domains (3) summary
      cd08028
      Location:10 → 91
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:112 → 183
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      cd12541
      Location:230 → 306
      RRM2_La; RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      75024385..75034016
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063284632.1 → XP_063140702.1  lupus La protein homolog isoform X1

    2. XM_006234321.4 → XP_006234383.1  lupus La protein homolog isoform X2

      UniProtKB/Swiss-Prot
      P38656
      UniProtKB/TrEMBL
      F7FK94
      Conserved Domains (3) summary
      cd08028
      Location:10 → 91
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:112 → 183
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:230 → 333
      RRM_3; RNA binding motif

    3. XM_006234322.4 → XP_006234384.1  lupus La protein homolog isoform X3

      See identical proteins and their annotated locations for XP_006234384.1

      UniProtKB/TrEMBL
      A0A8I6AH92, A6HM21
      Conserved Domains (3) summary
      cd08028
      Location:10 → 91
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:112 → 183
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:230 → 333
      RRM_3; RNA binding motif

    4. XM_006234323.4 → XP_006234385.1  lupus La protein homolog isoform X4

      UniProtKB/TrEMBL
      A0A8I6AH92
      Conserved Domains (3) summary
      cd08028
      Location:10 → 91
      LARP_3; La RNA-binding domain of La-related protein 3
      cd12291
      Location:112 → 183
      RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
      pfam08777
      Location:230 → 333
      RRM_3; RNA binding motif
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P38656.1 GenPept UniProtKB/Swiss-Prot:P38656

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