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

Gene ID: 79811, updated on 3-Nov-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, Nov 2024]
Expression
Ubiquitous expression in bone marrow (RPKM 26.9), thyroid (RPKM 20.0) and 25 other tissues See more
Orthologs
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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. 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
  3. 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,
  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 (92) 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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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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