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

Gene ID: 26039, updated on 17-Jun-2019

Summary

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
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
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

Genomic context

See SS18L1 in Genome Data Viewer
Location:
20q13.33
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (62143720..62182514)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (60718816..60757566)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372706 Neighboring gene LSM family member 14B Neighboring gene proteasome subunit alpha 7 Neighboring gene mitochondrial ribosome associated GTPase 2 Neighboring gene histamine receptor H3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0693, MGC26711, MGC78386

Gene Ontology Provided by GOA

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

General protein information

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)

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
    5001..43791
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301778.2NP_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
    Related
    ENSP00000359885.5, ENST00000370848.8
  2. NM_198935.3NP_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
    O75177
    Related
    ENSP00000333012.3, ENST00000331758.8
    Conserved Domains (1) summary
    pfam05030
    Location:1473
    SSXT; SSXT protein (N-terminal region)

RNA

  1. NR_125980.1 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_125981.1 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, DC375156

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    62143720..62182514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005260389.3XP_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:1473
    SSXT; SSXT protein (N-terminal region)
  2. XM_005260391.1XP_005260448.1  calcium-responsive transactivator isoform X2

    See identical proteins and their annotated locations for XP_005260448.1

    UniProtKB/Swiss-Prot
    O75177
    Conserved Domains (1) summary
    pfam05030
    Location:251
    SSXT; SSXT protein (N-terminal region)
  3. XM_017027784.2XP_016883273.1  calcium-responsive transactivator isoform X3

  4. XM_011528764.2XP_011527066.1  calcium-responsive transactivator isoform X2

    See identical proteins and their annotated locations for XP_011527066.1

    UniProtKB/Swiss-Prot
    O75177
    Conserved Domains (1) summary
    pfam05030
    Location:251
    SSXT; SSXT protein (N-terminal region)
  5. XM_011528767.1XP_011527069.1  calcium-responsive transactivator isoform X4

    See identical proteins and their annotated locations for XP_011527069.1

    UniProtKB/Swiss-Prot
    O75177
    Conserved Domains (1) summary
    pfam05030
    Location:4676
    SSXT; SSXT protein (N-terminal region)

RNA

  1. XR_001754230.1 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.
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