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    Sltm SAFB-like, transcription modulator [ Rattus norvegicus (Norway rat) ]

    Gene ID: 315792, updated on 27-Dec-2024

    Summary

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    Official Symbol
    Sltmprovided by RGD
    Official Full Name
    SAFB-like, transcription modulatorprovided by RGD
    Primary source
    RGD:1307526
    See related
    EnsemblRapid:ENSRNOG00000054446 AllianceGenome:RGD:1307526
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307526
    Summary
    Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Predicted to be located in nuclear body. Predicted to be active in nucleus. Orthologous to human SLTM (SAFB like transcription modulator). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 170.2), Spleen (RPKM 149.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sltm in Genome Data Viewer
    Location:
    8q24
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (80096555..80142668)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (71215995..71261821)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (76977698..77022847)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene ring finger protein 111 Neighboring gene small nucleolar RNA, H/ACA box 20 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC102551907 Neighboring gene MINDY lysine 48 deubiquitinase 2 Neighboring gene ADAM metallopeptidase domain 10

    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
    • 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. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    2. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109335

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in regulation of mRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    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
    		  

    General protein information

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    Preferred Names
    SAFB-like transcription modulator; SAFB-like, transcription modulator

    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_001430279.1 → NP_001417208.1  SAFB-like, transcription modulator isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A0G2K904, A0A8I6A3K4, A6KET0

    2. NM_001430280.1 → NP_001417209.1  SAFB-like, transcription modulator isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8I6A3K4

    3. NM_001430281.1 → NP_001417210.1  SAFB-like, transcription modulator isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8I6A3K4

    4. NM_001430282.1 → NP_001417211.1  SAFB-like, transcription modulator isoform 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8I6A3K4

    5. NM_001430283.1 → NP_001417212.1  SAFB-like, transcription modulator isoform 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6KET3

    6. NM_001430284.1 → NP_001417213.1  SAFB-like, transcription modulator isoform 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6KET3

    7. NM_001430285.1 → NP_001417214.1  SAFB-like, transcription modulator isoform 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A6KET3

    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_086026.1 Reference GRCr8

      Range
      80096555..80142668
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_056984525.2 → XP_056840505.1  SAFB-like transcription modulator isoform X1

      UniProtKB/TrEMBL
      A0A8I6A3K4

    2. XM_056984526.2 → XP_056840506.1  SAFB-like transcription modulator isoform X2

      Related
      ENSRNOP00000074807.1, ENSRNOT00000090268.3

    3. XM_056984527.2 → XP_056840507.1  SAFB-like transcription modulator isoform X3

      UniProtKB/TrEMBL
      A0A8I6A3K4

    4. XM_056984528.2 → XP_056840508.1  SAFB-like transcription modulator isoform X4

    5. XM_056984529.2 → XP_056840509.1  SAFB-like transcription modulator isoform X5

      UniProtKB/TrEMBL
      A6KES8

    6. XM_063266421.1 → XP_063122491.1  SAFB-like transcription modulator isoform X6

      UniProtKB/TrEMBL
      A0A8I6AB75, A6KES8
      Related
      ENSRNOP00000089853.1, ENSRNOT00000117345.2

    7. XM_056984530.2 → XP_056840510.1  SAFB-like transcription modulator isoform X7

      UniProtKB/TrEMBL
      A6KES8

    8. XM_063266422.1 → XP_063122492.1  SAFB-like transcription modulator isoform X8

      UniProtKB/TrEMBL
      A6KES8

    9. XM_063266423.1 → XP_063122493.1  SAFB-like transcription modulator isoform X10

    10. XM_056984532.2 → XP_056840512.1  SAFB-like transcription modulator isoform X10

    11. XM_056984531.2 → XP_056840511.1  SAFB-like transcription modulator isoform X9

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001017460.1: Suppressed sequence

      Description
      NM_001017460.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein Strain
    Heading Accession and Version

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