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    SS18L2 SS18 like 2 [ Homo sapiens (human) ]

    Gene ID: 51188, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SS18L2provided by HGNC
    Official Full Name
    SS18 like 2provided by HGNC
    Primary source
    HGNC:HGNC:15593
    See related
    Ensembl:ENSG00000008324 MIM:606473; AllianceGenome:HGNC:15593
    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
    KIAA-iso
    Summary
    Synovial sarcomas occur most frequently in the extremities around large joints. More than 90% of cases have a recurrent and specific chromosomal translocation, t(X;18)(p11.2;q11.2), in which the 5-prime end of the SS18 gene (MIM 600192) is fused in-frame to the 3-prime end of the SSX1 (MIM 312820), SSX2 (MIM 300192), or SSX4 (MIM 300326) gene. The SS18L2 gene is homologous to SS18.[supplied by OMIM, Jul 2002]
    Expression
    Ubiquitous expression in lymph node (RPKM 8.2), prostate (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SS18L2 in Genome Data Viewer
    Location:
    3p22.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42581840..42596934)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42599834..42614928)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42623332..42638426)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42542633-42543206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14244 Neighboring gene Sharpr-MPRA regulatory region 5178 Neighboring gene vasoactive intestinal peptide receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42566136-42566306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42574871-42575372 Neighboring gene VIPR1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581415-42581916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581917-42582416 Neighboring gene SEC22 homolog C, vesicle trafficking protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:42622926-42623752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14246 Neighboring gene ZBTB47 and NKTR antisense RNA 1 Neighboring gene natural killer cell triggering receptor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42672544-42673392 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42673393-42674241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42695163-42695804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14248 Neighboring gene Sharpr-MPRA regulatory region 3469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42700825-42701735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42701736-42702645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42706502-42707002 Neighboring gene uncharacterized LOC124906232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42708562-42709098 Neighboring gene zinc finger and BTB domain containing 47

    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. Mapping and characterization of the mouse and human SS18 genes, two human SS18-like genes and a mouse Ss18 pseudogene. de Bruijn DR, et al. Cytogenet Cell Genet, 2001. PMID 11435705
    2. Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. Connaughton DM, et al. Am J Hum Genet, 2020 Oct 1. PMID 32891193, Free PMC Article
    3. UBE2O and USP7 co-regulate RECQL4 ubiquitinylation and homologous recombination-mediated DNA repair. Huang Q, et al. FASEB J, 2022 Jan. PMID 34921745
    4. Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance. Pech MF, et al. Elife, 2019 Aug 27. PMID 31452512, Free PMC Article
    5. Identification and functional characterization of transcriptional activators in human cells. Alerasool N, et al. Mol Cell, 2022 Feb 3. PMID 35016035

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SS18-like protein 2
    Names
    SYT homolog 2
    synovial sarcoma translocation gene on chromosome 18-like 2

    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_001370300.1 → NP_001357229.1  SS18-like protein 2

      Status: VALIDATED

      Source sequence(s)
      AC092047, BC017804, CD640145
      Consensus CDS
      CCDS2701.1
      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2
      Related
      ENSP00000011691.4, ENST00000011691.6
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    2. NM_016305.4 → NP_057389.1  SS18-like protein 2

      See identical proteins and their annotated locations for NP_057389.1

      Status: VALIDATED

      Source sequence(s)
      AC092047, AI027415, BC017804, BX114027, EL954786
      Consensus CDS
      CCDS2701.1
      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2
      Related
      ENSP00000401115.1, ENST00000447630.5
      Conserved Domains (1) summary
      pfam05030
      Location:14 → 73
      SSXT; SSXT protein (N-terminal region)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      42581840..42596934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      42599834..42614928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346745.1 → XP_054202720.1  SS18-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2

    2. XM_054346742.1 → XP_054202717.1  SS18-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2

    3. XM_054346743.1 → XP_054202718.1  SS18-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2

    4. XM_054346744.1 → XP_054202719.1  SS18-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2

    5. XM_054346741.1 → XP_054202716.1  SS18-like protein 2 isoform X1

      UniProtKB/Swiss-Prot
      B2R5L1, Q9UHA2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UHA2.1 GenPept UniProtKB/Swiss-Prot:Q9UHA2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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