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Aliases for SS18 Gene

Aliases for SS18 Gene

  • SS18, NBAF Chromatin Remodeling Complex Subunit 2 3 5
  • Synovial Sarcoma Translocated To X Chromosome Protein 3 4
  • Synovial Sarcoma Translocation, Chromosome 18 2 3
  • SSXT 3 4
  • SYT 3 4
  • Synovial Sarcoma, Translocated To X Chromosome 3
  • Protein SSXT 3
  • Protein SYT 4

External Ids for SS18 Gene

Previous HGNC Symbols for SS18 Gene

  • SSXT

Previous GeneCards Identifiers for SS18 Gene

  • GC18M023570
  • GC18M023308
  • GC18M021848
  • GC18M021850
  • GC18M020454
  • GC18M023596

Summaries for SS18 Gene

GeneCards Summary for SS18 Gene

SS18 (SS18, NBAF Chromatin Remodeling Complex Subunit) is a Protein Coding gene. Diseases associated with SS18 include Sarcoma, Synovial and Sarcoma. Among its related pathways are Transcriptional misregulation in cancer and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include ligand-dependent nuclear receptor transcription coactivator activity. An important paralog of this gene is SS18L1.

UniProtKB/Swiss-Prot for SS18 Gene

  • Appears to function synergistically with RBM14 as a transcriptional coactivator. Isoform 1 and isoform 2 function in nuclear receptor coactivation. Isoform 1 and isoform 2 function in general transcriptional coactivation.

Gene Wiki entry for SS18 Gene

Additional gene information for SS18 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SS18 Gene

Genomics for SS18 Gene

GeneHancer (GH) Regulatory Elements for SS18 Gene

Promoters and enhancers for SS18 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J026088 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 673.2 +1.2 1180 3.8 HDGF PKNOX1 SMAD1 MLX ARNT SIN3A DMAP1 ZBTB7B YY1 SLC30A9 SS18 TAF4B GC18M026456
GH18J026092 Enhancer 0.3 ENCODE 650.7 -1.0 -1045 0.1 ZNF512 SS18 RPS24P18
GH18J026093 Enhancer 0.3 ENCODE 650.7 -1.0 -966 0.1 ZNF512 SS18 RPS24P18
GH18J025297 Enhancer 1.2 Ensembl ENCODE dbSUPER 20.4 +792.1 792092 2.5 HDAC1 ATF1 NFIB TCF12 ZNF366 FOS ZNF362 CAVIN1 USF2 CEBPB SS18 ENSG00000264434 ZNF521 LOC105372031
GH18J026224 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.2 -135.4 -135374 3.9 PKNOX1 CLOCK FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B TAF4B GC18M026455 SS18 KCTD1 PIR33021
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SS18 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SS18 gene promoter:

Genomic Locations for SS18 Gene

Genomic Locations for SS18 Gene
chr18:26,016,253-26,091,217
(GRCh38/hg38)
Size:
74,965 bases
Orientation:
Minus strand
chr18:23,596,217-23,671,181
(GRCh37/hg19)

Genomic View for SS18 Gene

Genes around SS18 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SS18 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SS18 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SS18 Gene

Proteins for SS18 Gene

  • Protein details for SS18 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15532-SSXT_HUMAN
    Recommended name:
    Protein SSXT
    Protein Accession:
    Q15532
    Secondary Accessions:
    • B0YJ95
    • Q16404
    • Q4VAX1
    • Q9BXC6

    Protein attributes for SS18 Gene

    Size:
    418 amino acids
    Molecular mass:
    45929 Da
    Quaternary structure:
    • Interacts with MLLT10. Isoform 1 interacts with RBM14 isoform 1. Isoform 2 interacts with RBM14 isoform 1.
    SequenceCaution:
    • Sequence=AAK21314.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA55792.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SS18 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SS18 Gene

Post-translational modifications for SS18 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SS18 Gene

Domains & Families for SS18 Gene

Gene Families for SS18 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for SS18 Gene

Blocks:
InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q15532

UniProtKB/Swiss-Prot:

SSXT_HUMAN :
  • Belongs to the SS18 family.
Family:
  • Belongs to the SS18 family.
genes like me logo Genes that share domains with SS18: view

Function for SS18 Gene

Molecular function for SS18 Gene

UniProtKB/Swiss-Prot Function:
Appears to function synergistically with RBM14 as a transcriptional coactivator. Isoform 1 and isoform 2 function in nuclear receptor coactivation. Isoform 1 and isoform 2 function in general transcriptional coactivation.

Phenotypes From GWAS Catalog for SS18 Gene

Gene Ontology (GO) - Molecular Function for SS18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003712 transcription coregulator activity IBA --
GO:0003713 transcription coactivator activity IEA --
GO:0005515 protein binding IPI 15919756
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity IDA 15919756
genes like me logo Genes that share ontologies with SS18: view
genes like me logo Genes that share phenotypes with SS18: view

Animal Models for SS18 Gene

MGI Knock Outs for SS18:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SS18

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SS18 Gene

Localization for SS18 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SS18 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SS18 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SS18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS 10072425
GO:0005881 cytoplasmic microtubule IEA --
GO:0071564 npBAF complex IEA --
genes like me logo Genes that share ontologies with SS18: view

Pathways & Interactions for SS18 Gene

genes like me logo Genes that share pathways with SS18: view

Pathways by source for SS18 Gene

1 KEGG pathway for SS18 Gene
1 Cell Signaling Technology pathway for SS18 Gene

Gene Ontology (GO) - Biological Process for SS18 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000226 microtubule cytoskeleton organization IEA --
GO:0000902 cell morphogenesis IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007010 cytoskeleton organization IEA --
genes like me logo Genes that share ontologies with SS18: view

No data available for SIGNOR curated interactions for SS18 Gene

Drugs & Compounds for SS18 Gene

(3) Drugs for SS18 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with SS18: view

Transcripts for SS18 Gene

Unigene Clusters for SS18 Gene

Synovial sarcoma translocation, chromosome 18:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SS18

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SS18 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c · 11d · 11e ^ 12a · 12b ^
SP1: - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - -
SP4: - - - - - - -
SP5: - - - - - - -
SP6: - - - - - - - - - - - - - -
SP7: - - - - - - - - - - - - -
SP8: - - - - - -
SP9: - - - - - - - - -
SP10: - - - - - - - - -
SP11: - - - -
SP12: - - - - -
SP13:
SP14:

ExUns: 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17
SP1: -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for SS18 Gene

GeneLoc Exon Structure for
SS18
ECgene alternative splicing isoforms for
SS18

Expression for SS18 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SS18 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SS18 Gene

This gene is overexpressed in Fetal gut (10.9), Testis (10.3), and Placenta (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SS18 Gene



Protein tissue co-expression partners for SS18 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SS18 Gene:

SS18

SOURCE GeneReport for Unigene cluster for SS18 Gene:

Hs.129261

mRNA Expression by UniProt/SwissProt for SS18 Gene:

Q15532-SSXT_HUMAN
Tissue specificity: Fairly ubiquitously expressed. Expressed in synovial sarcomas and in other human cell lines. The fusion genes SSXT-SSX1 and SSXT-SSX2 are expressed only in synovial sarcomas.

Evidence on tissue expression from TISSUES for SS18 Gene

  • Nervous system(4)
  • Kidney(2.3)
  • Lung(2.3)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SS18 Gene

Germ Layers:
  • mesoderm
Systems:
  • skeleton
Regions:
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
genes like me logo Genes that share expression patterns with SS18: view

No data available for mRNA differential expression in normal tissues for SS18 Gene

Orthologs for SS18 Gene

This gene was present in the common ancestor of animals.

Orthologs for SS18 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SS18 34
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SS18 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SS18 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SS18 34 33
  • 95.77 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ss18 16 34 33
  • 91.95 (n)
rat
(Rattus norvegicus)
Mammalia Ss18 33
  • 90.75 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SS18 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves SS18 34 33
  • 89.23 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SS18 34
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ss18 33
  • 78.39 (n)
Str.1351 33
African clawed frog
(Xenopus laevis)
Amphibia ss18-prov 33
zebrafish
(Danio rerio)
Actinopterygii ss18 34 33
  • 71.89 (n)
OneToOne
wufe02e04 33
fruit fly
(Drosophila melanogaster)
Insecta CG10555 34
  • 10 (a)
OneToMany
Species where no ortholog for SS18 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SS18 Gene

ENSEMBL:
Gene Tree for SS18 (if available)
TreeFam:
Gene Tree for SS18 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SS18: view image

Paralogs for SS18 Gene

Paralogs for SS18 Gene

(9) SIMAP similar genes for SS18 Gene using alignment to 19 proteins:

  • SSXT_HUMAN
  • B4DLD3_HUMAN
  • B4DR34_HUMAN
  • B4E2J6_HUMAN
  • F5GWN1_HUMAN
  • J3KRP6_HUMAN
  • J3KT22_HUMAN
  • J3KT74_HUMAN
  • J3QLJ7_HUMAN
  • J3QQM2_HUMAN
  • J3QQW2_HUMAN
  • J3QQW6_HUMAN
  • J3QQX5_HUMAN
  • J3QS72_HUMAN
  • J3QSB3_HUMAN
  • J3QSG1_HUMAN
  • Q4VAX0_HUMAN
  • Q4VAX2_HUMAN
  • Q6FGL9_HUMAN
genes like me logo Genes that share paralogs with SS18: view

Variants for SS18 Gene

Sequence variations from dbSNP and Humsavar for SS18 Gene

SNP ID Clin Chr 18 pos Variation AA Info Type
rs1000039381 -- 26,075,892(-) T/C intron_variant
rs1000101965 -- 26,031,607(-) G/A intron_variant
rs1000128838 -- 26,088,418(-) T/C intron_variant
rs1000174779 -- 26,041,679(-) G/A intron_variant
rs1000212862 -- 26,076,622(-) A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SS18 Gene

Variant ID Type Subtype PubMed ID
esv2674101 CNV deletion 23128226
esv3642014 CNV loss 21293372
esv3893078 CNV gain 25118596

Variation tolerance for SS18 Gene

Residual Variation Intolerance Score: 21.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.80; 47.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SS18 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SS18

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SS18 Gene

Disorders for SS18 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SS18 Gene - From: Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
sarcoma, synovial
  • synovial sarcoma
sarcoma
  • connective and soft tissue neoplasm
kidney hemangiopericytoma
  • hemangiopericytoma of kidney
colorado tick fever
  • tick fever, american mountain
synovium cancer
  • malignant tumor of synovium
- elite association - COSMIC cancer census association via MalaCards
Search SS18 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SSXT_HUMAN
  • Note=A chromosomal aberration involving SS18 may be a cause of synovial sarcoma. Translocation t(X;18)(p11.2;q11.2). The translocation is specifically found in more than 80% of synovial sarcoma. The fusion products SSXT-SSX1 or SSXT-SSX2 are probably responsible for transforming activity. Heterogeneity in the position of the breakpoint can occur (low frequency). {ECO:0000269 PubMed:7495284, ECO:0000269 PubMed:7539744}.

Additional Disease Information for SS18

genes like me logo Genes that share disorders with SS18: view

No data available for Genatlas for SS18 Gene

Publications for SS18 Gene

  1. Identification of novel genes, SYT and SSX, involved in the t(X;18)(p11.2;q11.2) translocation found in human synovial sarcoma. (PMID: 7951320) Clark J … Cooper CS (Nature genetics 1994) 2 3 4 22 58
  2. Common origin of the human synovial sarcoma associated SS18 and SS18L1 gene loci. (PMID: 16484776) de Bruijn DR … Geurts van Kessel A (Cytogenetic and genome research 2006) 2 3 22 58
  3. The synovial sarcoma associated protein SYT interacts with the acute leukemia associated protein AF10. (PMID: 11423977) de Bruijn DR … Geurts van Kessel A (Oncogene 2001) 3 4 22 58
  4. Cloning and characterization of spliced fusion transcript variants of synovial sarcoma: SYT/SSX4, SYT/SSX4v, and SYT/SSX2v. Possible regulatory role of the fusion gene product in wild type SYT expression. (PMID: 11368913) Brodin B … Larsson O (Gene 2001) 3 4 22 58
  5. Molecular diagnosis of synovial sarcoma and characterization of a variant SYT-SSX2 fusion transcript. (PMID: 7495284) Fligman I … Ladanyi M (The American journal of pathology 1995) 3 4 22 58

Products for SS18 Gene

Sources for SS18 Gene

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