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    sltm SAFB-like, transcription modulator [ Danio rerio (zebrafish) ]

    Gene ID: 406642, updated on 27-Mar-2024

    Summary

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    Official Symbol
    sltmprovided by ZNC
    Official Full Name
    SAFB-like, transcription modulatorprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-2647
    See related
    Ensembl:ENSDARG00000052728 AllianceGenome:ZFIN:ZDB-GENE-040426-2647
    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
    zgc:65985; wu:fd12b08
    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 act upstream of or within ribosome biogenesis. Predicted to be active in nucleus. Orthologous to human SLTM (SAFB like transcription modulator). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See sltm in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (30538206..30560450, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (30267056..30289300, complement)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene lipase, hepatic a Neighboring gene ADAM metallopeptidase domain 10a Neighboring gene MINDY lysine 48 deubiquitinase 2 Neighboring gene ring finger protein 111 Neighboring gene cyclin B2

    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. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. Cañestro C, et al. PLoS Genet, 2009 May. PMID 19478994, Free PMC Article
    2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    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
    5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    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 nucleic acid 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
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    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_213333.2 → NP_998498.2  SAFB-like transcription modulator

      Status: VALIDATED

      Source sequence(s)
      AL935053
      UniProtKB/TrEMBL
      A0A8M1PF00, F1Q6F9
      Related
      ENSDARP00000115812.1, ENSDART00000142818.4
      Conserved Domains (2) summary
      smart00513
      Location:13 → 47
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd12678
      Location:322 → 395
      RRM_SLTM; RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

    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_007118.7 Reference GRCz11 Primary Assembly

      Range
      30538206..30560450 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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