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    Sltm SAFB-like, transcription modulator [ Mus musculus (house mouse) ]

    Gene ID: 66660, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Sltmprovided by MGI
    Official Full Name
    SAFB-like, transcription modulatorprovided by MGI
    Primary source
    MGI:MGI:1913910
    See related
    Ensembl:ENSMUSG00000032212 AllianceGenome:MGI:1913910
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Met; 5730455C01Rik; 5730555F13Rik; 9130215G10Rik
    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. Is expressed in several structures, including central nervous system; early conceptus; oocyte; and sensory organ. Orthologous to human SLTM (SAFB like transcription modulator). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in CNS E11.5 (RPKM 28.4), CNS E14 (RPKM 16.4) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sltm in Genome Data Viewer
    Location:
    9 D; 9 39.53 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (70449717..70499519)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (70542177..70592237)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_24557 Neighboring gene predicted gene, 23730 Neighboring gene predicted gene, 22229 Neighboring gene MINDY lysine 48 deubiquitinase 2 Neighboring gene STARR-positive B cell enhancer ABC_E11748 Neighboring gene predicted gene 10642 Neighboring gene predicted gene, 31872

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Impact of SMAD2 and MET Expression on Lymph Node Metastasis of HER2-positive Gastric Cancer Cells.
      Title: Impact of SMAD2 and MET Expression on Lymph Node Metastasis of HER2-positive Gastric Cancer Cells.
    2. SLTM regulates GLI factor binding to chromatin and contributes to the transcriptional outcomes of SHH signaling via a novel molecular mechanism.
      Title: A proteomic approach identifies SAFB-like transcription modulator (SLTM) as a bidirectional regulator of GLI family zinc finger transcription factors.
    3. Inhibition of gene expression by STLM appears to result from generalized down-regulation of mRNA synthesis and initiation of apoptosis following SLTM overexpression.
      Title: A novel member of the SAF (scaffold attachment factor)-box protein family inhibits gene expression and induces apoptosis.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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 apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    SAFB-like transcription modulator
    Names
    SAF-like transcription modulator
    modulator of estrogen induced transcription

    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_001357911.1 → NP_001344840.1  SAFB-like transcription modulator isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC158995
      Conserved Domains (5) summary
      smart00513
      Location:22 → 56
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      COG0724
      Location:250 → 416
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:309 → 382
      RRM_SF; RNA recognition motif (RRM) superfamily
      cl26511
      Location:140 → 550
      Neuromodulin_N; Gap junction protein N-terminal region
      cl27333
      Location:25 → 176
      PARP_reg; Poly(ADP-ribose) polymerase, regulatory domain

    2. NM_025690.4 → NP_079966.2  SAFB-like transcription modulator isoform a

      See identical proteins and their annotated locations for NP_079966.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC158995
      Consensus CDS
      CCDS23322.1
      UniProtKB/Swiss-Prot
      Q3UYE5, Q8BP76, Q8BR40, Q8CH25, Q8VCF4, Q9CS57
      UniProtKB/TrEMBL
      B9EI57
      Related
      ENSMUSP00000049112.8, ENSMUST00000049263.9
      Conserved Domains (3) summary
      smart00513
      Location:22 → 56
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      COG0724
      Location:326 → 492
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:385 → 458
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. NM_026337.2 → NP_080613.1  SAFB-like transcription modulator isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC158995
      Consensus CDS
      CCDS90615.1
      UniProtKB/Swiss-Prot
      Q8CH25
      Related
      ENSMUSP00000149059.2, ENSMUST00000216816.2
      Conserved Domains (3) summary
      smart00513
      Location:22 → 56
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      COG0724
      Location:308 → 474
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:367 → 440
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. NR_152142.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC158995
      Related
      ENSMUST00000217593.2

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000075.7 Reference GRCm39 C57BL/6J

      Range
      70449717..70499519
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006511349.5 → XP_006511412.1  SAFB-like transcription modulator isoform X1

      Conserved Domains (4) summary
      smart00513
      Location:110 → 144
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PLN03124
      Location:113 → 278
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:348 → 514
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:407 → 480
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. XM_036155181.1 → XP_036011074.1  SAFB-like transcription modulator isoform X3

      Conserved Domains (5) summary
      smart00513
      Location:110 → 144
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PTZ00121
      Location:223 → 630
      PTZ00121; MAEBL; Provisional
      PLN03124
      Location:113 → 260
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:330 → 496
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12678
      Location:389 → 462
      RRM_SLTM; RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

    3. XM_006511350.5 → XP_006511413.1  SAFB-like transcription modulator isoform X2

      Conserved Domains (4) summary
      smart00513
      Location:110 → 144
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PLN03124
      Location:113 → 262
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:332 → 498
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:391 → 464
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. XM_006511351.5 → XP_006511414.1  SAFB-like transcription modulator isoform X4

      Conserved Domains (5) summary
      smart00513
      Location:110 → 144
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PTZ00121
      Location:207 → 614
      PTZ00121; MAEBL; Provisional
      PLN03124
      Location:113 → 193
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      COG0724
      Location:314 → 480
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:373 → 446
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. XM_030244499.2 → XP_030100359.1  SAFB-like transcription modulator isoform X7

      Conserved Domains (1) summary
      cl17169
      Location:1 → 27
      RRM_SF; RNA recognition motif (RRM) superfamily

    6. XM_030244496.1 → XP_030100356.1  SAFB-like transcription modulator isoform X6

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    7. XM_036155182.1 → XP_036011075.1  SAFB-like transcription modulator isoform X7

      Conserved Domains (1) summary
      cl17169
      Location:1 → 27
      RRM_SF; RNA recognition motif (RRM) superfamily

    8. XM_006511355.3 → XP_006511418.1  SAFB-like transcription modulator isoform X6

      See identical proteins and their annotated locations for XP_006511418.1

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    9. XM_011242786.2 → XP_011241088.1  SAFB-like transcription modulator isoform X6

      See identical proteins and their annotated locations for XP_011241088.1

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    10. XM_006511354.2 → XP_006511417.1  SAFB-like transcription modulator isoform X6

      See identical proteins and their annotated locations for XP_006511417.1

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    11. XM_036155183.1 → XP_036011076.1  SAFB-like transcription modulator isoform X7

      Conserved Domains (1) summary
      cl17169
      Location:1 → 27
      RRM_SF; RNA recognition motif (RRM) superfamily

    12. XM_030244501.2 → XP_030100361.1  SAFB-like transcription modulator isoform X7

      Conserved Domains (1) summary
      cl17169
      Location:1 → 27
      RRM_SF; RNA recognition motif (RRM) superfamily

    13. XM_030244497.2 → XP_030100357.1  SAFB-like transcription modulator isoform X6

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    14. XM_030244498.1 → XP_030100358.1  SAFB-like transcription modulator isoform X6

      Conserved Domains (3) summary
      PTZ00121
      Location:8 → 398
      PTZ00121; MAEBL; Provisional
      COG0724
      Location:98 → 264
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily

    15. XM_030244500.2 → XP_030100360.1  SAFB-like transcription modulator isoform X7

      Conserved Domains (1) summary
      cl17169
      Location:1 → 27
      RRM_SF; RNA recognition motif (RRM) superfamily

    16. XM_006511352.5 → XP_006511415.1  SAFB-like transcription modulator isoform X5

      Conserved Domains (3) summary
      COG0724
      Location:273 → 439
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      COG5271
      Location:9 → 280
      MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:332 → 405
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. XR_001778967.3 RNA Sequence

    2. XR_004935515.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8CH25.1 GenPept UniProtKB/Swiss-Prot:Q8CH25

    Gene LinkOut

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