Human Gene SS18L2 (uc003clk.1) Description and Page Index
  Description: Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 2 (SS18L2), mRNA.
RefSeq Summary (NM_016305): 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]. ##Evidence-Data-START## Transcript exon combination :: BX114027.1, EL954786.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1968540, SAMEA1968968 [ECO:0000348] ##Evidence-Data-END##
Transcript (Including UTRs)
   Position: hg19 chr3:42,632,298-42,636,490 Size: 4,193 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr3:42,632,390-42,636,001 Size: 3,612 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:42,632,298-42,636,490)mRNA (may differ from genome)Protein (77 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: S18L2_HUMAN
DESCRIPTION: RecName: Full=SS18-like protein 2; AltName: Full=SYT homolog 2;
SIMILARITY: Belongs to the SS18 family.

-  MalaCards Disease Associations
  MalaCards Gene Search: SS18L2
Diseases sorted by gene-association score: synovium cancer (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.39 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 648.92 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -33.2092-0.361 Picture PostScript Text
3' UTR -125.96489-0.258 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007726 - SSXT

Pfam Domains:
PF05030 - SSXT protein (N-terminal region)

ModBase Predicted Comparative 3D Structure on Q9UHA2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity


-  Descriptions from all associated GenBank mRNAs
  AF201950 - Homo sapiens kiaa-iso protein mRNA, complete cds.
BC017804 - Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 2, mRNA (cDNA clone MGC:22369 IMAGE:4658643), complete cds.
AK312225 - Homo sapiens cDNA, FLJ92514, Homo sapiens synovial sarcoma translocation gene on chromosome18-like 2 (SS18L2), mRNA.
EU176663 - Synthetic construct Homo sapiens clone IMAGE:100011659; FLH264092.01L; RZPDo839G02257D synovial sarcoma translocation gene on chromosome 18-like 2 (SS18L2) gene, encodes complete protein.
DQ891965 - Synthetic construct clone IMAGE:100004595; FLH181885.01X; RZPDo839A04138D synovial sarcoma translocation gene on chromosome 18-like 2 (SS18L2) gene, encodes complete protein.
BC020444 - Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 2, mRNA (cDNA clone IMAGE:3867654).
JD412534 - Sequence 393558 from Patent EP1572962.
JD295004 - Sequence 276028 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5L1, NM_016305, NP_057389, Q9UHA2, S18L2_HUMAN
UCSC ID: uc003clk.1
RefSeq Accession: NM_016305
Protein: Q9UHA2 (aka S18L2_HUMAN or S18M_HUMAN)
CCDS: CCDS2701.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_016305.2
exon count: 3CDS single in 3' UTR: no RNA size: 822
ORF size: 234CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 668.00frame shift in genome: no % Coverage: 99.15
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.