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

Gene ID: 66660, updated on 11-Apr-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 act upstream of or within apoptotic process. 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, Apr 2022]
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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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
  • 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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Related articles in PubMed

  1. A novel member of the SAF (scaffold attachment factor)-box protein family inhibits gene expression and induces apoptosis. Chan CW, et al. Biochem J, 2007 Nov 1. PMID 17630952, Free PMC Article
  2. A proteomic approach identifies SAFB-like transcription modulator (SLTM) as a bidirectional regulator of GLI family zinc finger transcription factors. Zhang Z, et al. J Biol Chem, 2019 Apr 5. PMID 30782847, Free PMC Article
  3. The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. Hémono M, et al. BMC Biol, 2022 Jan 10. PMID 35012549, Free PMC Article
  4. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. McKee AE, et al. BMC Dev Biol, 2005 Jul 20. PMID 16033648, Free PMC Article
  5. Tagging genes with cassette-exchange sites. Cobellis G, et al. Nucleic Acids Res, 2005 Mar 1. PMID 15741177, Free PMC Article

See all (29) citations in PubMed

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 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
acts_upstream_of_or_within 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 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

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