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    SLTM SAFB like transcription modulator [ Homo sapiens (human) ]

    Gene ID: 79811, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SLTMprovided by HGNC
    Official Full Name
    SAFB like transcription modulatorprovided by HGNC
    Primary source
    HGNC:HGNC:20709
    See related
    Ensembl:ENSG00000137776 MIM:620992; AllianceGenome:HGNC:20709
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Met
    Summary
    Enables RNA binding activity. Predicted to be involved in regulation of mRNA processing and regulation of transcription by RNA polymerase II. Located in nuclear body. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 26.9), thyroid (RPKM 20.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLTM in Genome Data Viewer
    Location:
    15q22.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (58879050..58933679, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (56681092..56735731, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (59171249..59225878, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 444 pseudogene 1 Neighboring gene MPRA-validated peak2357 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9479 Neighboring gene ribosomal protein L21 pseudogene 14 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:59219581-59220080 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9482 Neighboring gene ribosome binding factor A (putative) pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9484 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:59280581-59280745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59283309-59283808 Neighboring gene ring finger protein 111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6486 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:59317258-59317441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59317581-59318082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:59318083-59318582 Neighboring gene ribosomal protein L21 pseudogene 113

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. circSLTM knockdown attenuates chondrocyte inflammation, apoptosis and ECM degradation in osteoarthritis by regulating the miR-515-5p/VAPB axis. Chen R, et al. Int Immunopharmacol, 2024 Sep 10. PMID 38981227
    2. MET exon 14 skipping mutation drives cancer progression and recurrence via activation of SMAD2 signalling. Liang Q, et al. Br J Cancer, 2024 Feb. PMID 38110666,
    3. Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen. Pedersen SF, et al. J Virol, 2022 Jul 13. PMID 35730977, Free PMC Article
    4. A DNA-PK phosphorylation site on MET regulates its signaling interface with the DNA damage response. Koch JP, et al. Oncogene, 2023 Jun. PMID 37188738, Free PMC Article
    5. Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression. Feng X, et al. Genes Genomics, 2024 May. PMID 38470543

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. circSLTM knockdown attenuates chondrocyte inflammation, apoptosis and ECM degradation in osteoarthritis by regulating the miR-515-5p/VAPB axis.
      Title: circSLTM knockdown attenuates chondrocyte inflammation, apoptosis and ECM degradation in osteoarthritis by regulating the miR-515-5p/VAPB axis.
    2. Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression.
      Title: Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression.
    3. MET exon 14 skipping mutation drives cancer progression and recurrence via activation of SMAD2 signalling.
      Title: MET exon 14 skipping mutation drives cancer progression and recurrence via activation of SMAD2 signalling.
    4. SPOP promotes CREB5 ubiquitination to inhibit MET signaling in liver cancer.
      Title: SPOP promotes CREB5 ubiquitination to inhibit MET signaling in liver cancer.
    5. Long noncoding RNA FTX promotes epithelial-mesenchymal transition of epithelial ovarian cancer through modulating miR-7515/TPD52 and activating Met/Akt/mTOR.
      Title: Long noncoding RNA FTX promotes epithelial-mesenchymal transition of epithelial ovarian cancer through modulating miR-7515/TPD52 and activating Met/Akt/mTOR.
    6. A DNA-PK phosphorylation site on MET regulates its signaling interface with the DNA damage response.
      Title: A DNA-PK phosphorylation site on MET regulates its signaling interface with the DNA damage response.
    7. 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.
    8. Lack of correlation between MET and PD-L1 expression in non-small cell lung cancer revealed by comparative study of matched biopsies and surgical resection samples.
      Title: Lack of correlation between MET and PD-L1 expression in non-small cell lung cancer revealed by comparative study of matched biopsies and surgical resection samples.
    9. Circular RNA SLTM as a miR-421-competing endogenous RNA to mediate HMGB2 expression stimulates apoptosis and inflammation in arthritic chondrocytes.
      Title: Circular RNA SLTM as a miR-421-competing endogenous RNA to mediate HMGB2 expression stimulates apoptosis and inflammation in arthritic chondrocytes.
    10. Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis.
      Title: Plexin-B3 expression stimulates MET signaling, breast cancer stem cell specification, and lung metastasis.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Variants in several genomic regions associated with asperger disorder.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10005, FLJ13213, DKFZp762G052

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    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
    modulator of estrogen-induced transcription

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001013843.3 → NP_001013865.1  SAFB-like transcription modulator isoform b

      See identical proteins and their annotated locations for NP_001013865.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform b).
      Source sequence(s)
      AC025918, BC046119, BC140851, DA215437
      Conserved Domains (6) summary
      smart00513
      Location:22 → 56
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PTZ00121
      Location:145 → 705
      PTZ00121; MAEBL; Provisional
      PLN03124
      Location:25 → 168
      PLN03124; poly [ADP-ribose] polymerase; Provisional
      PHA03307
      Location:780 → 1015
      PHA03307; transcriptional regulator ICP4; Provisional
      COG0724
      Location:271 → 478
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:367 → 440
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. NM_024755.4 → NP_079031.2  SAFB-like transcription modulator isoform a

      See identical proteins and their annotated locations for NP_079031.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest isoform (a).
      Source sequence(s)
      AC025918, BC046119, BC140851, DA215437
      Consensus CDS
      CCDS10168.2
      UniProtKB/Swiss-Prot
      A8K5V8, B2RTX3, Q2VPK7, Q52MB3, Q658J7, Q6ZNF2, Q86TK6, Q9H7C3, Q9H8U9, Q9NWH9
      Related
      ENSP00000369887.2, ENST00000380516.7
      Conserved Domains (5) summary
      smart00513
      Location:22 → 56
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      PTZ00121
      Location:34 → 723
      PTZ00121; MAEBL; Provisional
      PHA03307
      Location:798 → 1033
      PHA03307; transcriptional regulator ICP4; Provisional
      COG0724
      Location:289 → 496
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:385 → 458
      RRM_SF; RNA recognition motif (RRM) superfamily

    RNA

    1. NR_135042.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC025918, AK055195, BC046119, DA215437
      Related
      ENST00000492526.5

    2. NR_135043.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC025918, AK291423, BC046119, BC140851, DA215437
      Related
      ENST00000557924.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      58879050..58933679 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011522031.3 → XP_011520333.1  SAFB-like transcription modulator isoform X19

      See identical proteins and their annotated locations for XP_011520333.1

      Conserved Domains (4) summary
      COG0724
      Location:61 → 268
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:157 → 230
      RRM_SF; RNA recognition motif (RRM) superfamily
      cl26511
      Location:8 → 495
      Neuromodulin_N; Gap junction protein N-terminal region
      cl28033
      Location:570 → 805
      Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

    2. XM_047433051.1 → XP_047289007.1  SAFB-like transcription modulator isoform X19

    3. XM_047433046.1 → XP_047289002.1  SAFB-like transcription modulator isoform X12

    4. XM_017022578.2 → XP_016878067.2  SAFB-like transcription modulator isoform X10

    5. XM_047433045.1 → XP_047289001.1  SAFB-like transcription modulator isoform X11

    6. XM_006720686.4 → XP_006720749.4  SAFB-like transcription modulator isoform X8

    7. XM_017022576.2 → XP_016878065.1  SAFB-like transcription modulator isoform X6

    8. XM_047433043.1 → XP_047288999.1  SAFB-like transcription modulator isoform X4

    9. XM_011522028.2 → XP_011520330.2  SAFB-like transcription modulator isoform X9

    10. XM_011522027.2 → XP_011520329.2  SAFB-like transcription modulator isoform X7

    11. XM_047433044.1 → XP_047289000.1  SAFB-like transcription modulator isoform X5

    12. XM_011522023.2 → XP_011520325.2  SAFB-like transcription modulator isoform X2

    13. XM_011522024.2 → XP_011520326.2  SAFB-like transcription modulator isoform X3

    14. XM_011522022.2 → XP_011520324.2  SAFB-like transcription modulator isoform X1

    15. XM_047433049.1 → XP_047289005.1  SAFB-like transcription modulator isoform X17

    16. XM_047433048.1 → XP_047289004.1  SAFB-like transcription modulator isoform X15

    17. XM_017022579.2 → XP_016878068.1  SAFB-like transcription modulator isoform X14

      Conserved Domains (4) summary
      PHA03307
      Location:745 → 980
      PHA03307; transcriptional regulator ICP4; Provisional
      COG0724
      Location:236 → 443
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      COG5271
      Location:1 → 281
      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

    18. XM_011522029.3 → XP_011520331.1  SAFB-like transcription modulator isoform X13

      Conserved Domains (2) summary
      COG0724
      Location:243 → 450
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cl17169
      Location:339 → 412
      RRM_SF; RNA recognition motif (RRM) superfamily

    19. XM_047433052.1 → XP_047289008.1  SAFB-like transcription modulator isoform X19

    20. XM_011522030.3 → XP_011520332.2  SAFB-like transcription modulator isoform X16

    21. XM_047433050.1 → XP_047289006.1  SAFB-like transcription modulator isoform X18

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      56681092..56735731 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378814.1 → XP_054234789.1  SAFB-like transcription modulator isoform X19

    2. XM_054378812.1 → XP_054234787.1  SAFB-like transcription modulator isoform X19

    3. XM_054378806.1 → XP_054234781.1  SAFB-like transcription modulator isoform X12

    4. XM_054378804.1 → XP_054234779.1  SAFB-like transcription modulator isoform X10

    5. XM_054378805.1 → XP_054234780.1  SAFB-like transcription modulator isoform X11

    6. XM_054378802.1 → XP_054234777.1  SAFB-like transcription modulator isoform X8

    7. XM_054378800.1 → XP_054234775.1  SAFB-like transcription modulator isoform X6

    8. XM_054378798.1 → XP_054234773.1  SAFB-like transcription modulator isoform X4

    9. XM_054378803.1 → XP_054234778.1  SAFB-like transcription modulator isoform X9

    10. XM_054378801.1 → XP_054234776.1  SAFB-like transcription modulator isoform X7

    11. XM_054378799.1 → XP_054234774.1  SAFB-like transcription modulator isoform X5

    12. XM_054378796.1 → XP_054234771.1  SAFB-like transcription modulator isoform X2

    13. XM_054378797.1 → XP_054234772.1  SAFB-like transcription modulator isoform X3

    14. XM_054378795.1 → XP_054234770.1  SAFB-like transcription modulator isoform X1

    15. XM_054378811.1 → XP_054234786.1  SAFB-like transcription modulator isoform X17

    16. XM_054378808.1 → XP_054234783.1  SAFB-like transcription modulator isoform X14

    17. XM_054378809.1 → XP_054234784.1  SAFB-like transcription modulator isoform X15

    18. XM_054378807.1 → XP_054234782.1  SAFB-like transcription modulator isoform X13

    19. XM_054378813.1 → XP_054234788.1  SAFB-like transcription modulator isoform X19

    20. XM_054378810.1 → XP_054234785.1  SAFB-like transcription modulator isoform X16

    21. XM_054378815.1 → XP_054234790.1  SAFB-like transcription modulator isoform X18

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_017968.2: Suppressed sequence

      Description
      NM_017968.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NWH9.2 GenPept UniProtKB/Swiss-Prot:Q9NWH9

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