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SS18L1 SS18L1 subunit of BAF chromatin remodeling complex [ Homo sapiens (human) ]

Gene ID: 26039, updated on 11-Apr-2024

Summary

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Official Symbol
SS18L1provided by HGNC
Official Full Name
SS18L1 subunit of BAF chromatin remodeling complexprovided by HGNC
Primary source
HGNC:HGNC:15592
See related
Ensembl:ENSG00000184402 MIM:606472; AllianceGenome:HGNC:15592
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CREST; LP2261; SMARCL2
Summary
This gene encodes a calcium-responsive transactivator which is an essential subunit of a neuron-specific chromatin-remodeling complex. The structure of this gene is similar to that of the SS18 gene. Mutations in this gene are involved in amyotrophic lateral sclerosis (ALS). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
Expression
Ubiquitous expression in skin (RPKM 3.8), brain (RPKM 3.7) and 25 other tissues See more
Orthologs
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Genomic context

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See SS18L1 in Genome Data Viewer
Location:
20q13.33
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (62143769..62182514)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (63934636..63973390)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (60718825..60757570)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372706 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:60697043-60697730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60697731-60698419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60698420-60699107 Neighboring gene LSM family member 14B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60708899-60709398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13101 Neighboring gene proteasome 20S subunit alpha 7 Neighboring gene Sharpr-MPRA regulatory region 1753 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:60735092-60736291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60736587-60737199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13102 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60757942-60758126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13103 Neighboring gene mitochondrial ribosome associated GTPase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60789379-60789879 Neighboring gene histamine receptor H3

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
  • 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. The SS18L1 gene rs2295207 polymorphisms in association with hepatocellular carcinoma. Min S, et al. Asian J Surg, 2022 Oct. PMID 35584997
  2. Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis. Kukharsky MS, et al. Mol Neurodegener, 2015 Apr 10. PMID 25888396, Free PMC Article
  3. Genetic analysis of SS18L1 in French amyotrophic lateral sclerosis. Teyssou E, et al. Neurobiol Aging, 2014 May. PMID 24360741
  4. Exome sequencing to identify de novo mutations in sporadic ALS trios. Chesi A, et al. Nat Neurosci, 2013 Jul. PMID 23708140, Free PMC Article
  5. Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes. Du A, et al. Histochem Cell Biol, 2021 Apr. PMID 33398438, Free PMC Article

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The SS18L1 gene rs2295207 polymorphisms in association with hepatocellular carcinoma.
    Title: The SS18L1 gene rs2295207 polymorphisms in association with hepatocellular carcinoma.
  2. Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes.
    Title: Protein expression pattern of calcium-responsive transactivator in early postnatal and adult testes.
  3. calcium-responsive transactivator and certain other amyotrophic lateral sclerosis-linked proteins share several features implicated in amyotrophic lateral sclerosis pathogenesis
    Title: Calcium-responsive transactivator (CREST) protein shares a set of structural and functional traits with other proteins associated with amyotrophic lateral sclerosis.
  4. Its mutation causes amyotrophic lateral sclerosis.
    Title: Genetic analysis of SS18L1 in French amyotrophic lateral sclerosis.
  5. This study demonistrated that CREST mutations inhibited activity-dependent neurite outgrowth in primary neurons, and CREST associated with the ALS protein FUS.
    Title: Exome sequencing to identify de novo mutations in sporadic ALS trios.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
  7. A synovial sarcoma of classic morphology contained a novel t(20;X) SS18L1(strong homology to SS18 on Ch20)/SSX1 fusion transcript in which nucleotide 1216 (exon 10) of SS18L1 was fused in-frame with nucleotide 422 (exon 6) of SSX1.
    Title: A novel fusion gene, SS18L1/SSX1, in synovial sarcoma.
  8. analysis of the CREST domain that inhibits dendritic growth in cultured neurons
    Title: A multifunctional domain of the calcium-responsive transactivator (CREST) that inhibits dendritic growth in cultured neurons.
  9. SS18 and SS18L1 genes map within co-linear DNA segments that may have evolved through a relatively recent genomic duplication event.
    Title: Common origin of the human synovial sarcoma associated SS18 and SS18L1 gene loci.
Submit: New GeneRIF Correction

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

Clone Names

  • KIAA0693, MGC26711, MGC78386

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coactivator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in dendrite development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendrite morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in kinetochore IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nBAF complex IEA
Inferred from Electronic Annotation
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
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
calcium-responsive transactivator
Names
SS18-like protein 1
SS18L1, nBAF chromatin remodeling complex subunit
SYT homolog 1
synovial sarcoma translocation gene on chromosome 18-like 1

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.

Genomic

  1. NG_034255.1 RefSeqGene

    Range
    5050..43795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301778.2 → NP_001288707.1  calcium-responsive transactivator isoform 2

    See identical proteins and their annotated locations for NP_001288707.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an additional exon in the 5' region and an alternate splice acceptor site, which results in translation initiation at a downstream AUG start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AB014593, AK125656, AL078633, BX640848
    UniProtKB/Swiss-Prot
    O75177

  2. NM_198935.3 → NP_945173.1  calcium-responsive transactivator isoform 1

    See identical proteins and their annotated locations for NP_945173.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AB014593, AL078633, BX640848, DC375156
    Consensus CDS
    CCDS13491.1
    UniProtKB/Swiss-Prot
    A6NNE3, A8K620, B3KWR8, E1P5H7, O75177, Q5JXJ3, Q6MZV9, Q6NTH3, Q6XYD9, Q8NE69, Q9BR55, Q9H4K6
    Related
    ENSP00000333012.3, ENST00000331758.8
    Conserved Domains (1) summary
    pfam05030
    Location:14 → 73
    SSXT; SSXT protein (N-terminal region)

RNA

  1. NR_125980.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) has an additional exon and an additional segment in the 5' region and lacks an internal segment in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the absence of the 3' internal segment renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB014593, BC068993, BX640848, DC375156

  2. NR_125981.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an internal segment in the 3' terminal region, compared to variant 1. This variant is represented as non-coding because the absence of the 3' internal segment renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB014593, BC034494, BX640848

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    62143769..62182514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047440083.1 → XP_047296039.1  calcium-responsive transactivator isoform X2

  2. XM_005260389.4 → XP_005260446.1  calcium-responsive transactivator isoform X1

    See identical proteins and their annotated locations for XP_005260446.1

    UniProtKB/TrEMBL
    B4DSR7
    Conserved Domains (1) summary
    pfam05030
    Location:14 → 73
    SSXT; SSXT protein (N-terminal region)

  3. XM_047440084.1 → XP_047296040.1  calcium-responsive transactivator isoform X2

  4. XM_017027784.3 → XP_016883273.1  calcium-responsive transactivator isoform X3

  5. XM_011528767.2 → XP_011527069.1  calcium-responsive transactivator isoform X5

    See identical proteins and their annotated locations for XP_011527069.1

    UniProtKB/Swiss-Prot
    O75177
    Conserved Domains (1) summary
    pfam05030
    Location:46 → 76
    SSXT; SSXT protein (N-terminal region)

  6. XM_047440085.1 → XP_047296041.1  calcium-responsive transactivator isoform X4

    Related
    ENSP00000359885.5, ENST00000370848.8

RNA

  1. XR_007067449.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    63934636..63973390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054323321.1 → XP_054179296.1  calcium-responsive transactivator isoform X2

  2. XM_054323320.1 → XP_054179295.1  calcium-responsive transactivator isoform X1

    UniProtKB/TrEMBL
    B4DSR7

  3. XM_054323322.1 → XP_054179297.1  calcium-responsive transactivator isoform X2

  4. XM_054323323.1 → XP_054179298.1  calcium-responsive transactivator isoform X3

  5. XM_054323325.1 → XP_054179300.1  calcium-responsive transactivator isoform X5

  6. XM_054323324.1 → XP_054179299.1  calcium-responsive transactivator isoform X4

RNA

  1. XR_008485249.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_015558.3: Suppressed sequence

    Description
    NM_015558.3: 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
O75177.2 GenPept UniProtKB/Swiss-Prot:O75177

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