Human Gene SS18L1 (uc002ybz.1)
  Description: Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 1 (SS18L1), mRNA.
RefSeq Summary (NM_198935): 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].
Transcript (Including UTRs)
   Position: hg19 chr20:60,718,822-60,755,957 Size: 37,136 Total Exon Count: 13 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:60,718,822-60,755,957)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerGeneNetworkH-INVHGNCLynx
MalacardsPubMedWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SS18L1
CDC HuGE Published Literature: SS18L1

-  MalaCards Disease Associations
  MalaCards Gene Search: SS18L1
Diseases sorted by gene-association score: synovium cancer (8)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 32.03 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 381.12 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AK299881 - Homo sapiens cDNA FLJ58470 complete cds, highly similar to SS18-like protein 1.
AK291485 - Homo sapiens cDNA FLJ77310 complete cds, highly similar to Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 1 (SS18L1), transcript variant 2, mRNA.
AK125656 - Homo sapiens cDNA FLJ43668 fis, clone SYNOV4007360, highly similar to SS18-like protein 1.
BC034494 - Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 1, mRNA (cDNA clone MGC:26711 IMAGE:4823298), complete cds.
BX640848 - Homo sapiens mRNA; cDNA DKFZp686H23229 (from clone DKFZp686H23229).
AK308765 - Homo sapiens cDNA, FLJ98806.
BC068993 - Homo sapiens synovial sarcoma translocation gene on chromosome 18-like 1, mRNA (cDNA clone MGC:78386 IMAGE:5094932), complete cds.
AB014593 - Homo sapiens KIAA0693 mRNA for KIAA0693 protein.
EU176499 - Synthetic construct Homo sapiens clone IMAGE:100011353; FLH166986.01L; RZPDo839B04253D synovial sarcoma translocation gene on chromosome 18-like 1 (SS18L1) gene, encodes complete protein.
DQ890908 - Synthetic construct clone IMAGE:100003538; FLH166987.01X; RZPDo839F1088D synovial sarcoma translocation gene on chromosome 18-like 1 (SS18L1) gene, encodes complete protein.
AB383958 - Synthetic construct DNA, clone: pF1KSDA0693, Homo sapiens SS18L1 gene for SS18-like protein 1, complete cds, without stop codon, in Flexi system.
KJ906110 - Synthetic construct Homo sapiens clone ccsbBroadEn_15780 SS18L1 gene, encodes complete protein.
CU686691 - Synthetic construct Homo sapiens gateway clone IMAGE:100023147 5' read SS18L1 mRNA.
AY203931 - Homo sapiens LP2261 mRNA, complete cds.
JD549882 - Sequence 530906 from Patent EP1572962.
JD438765 - Sequence 419789 from Patent EP1572962.
JD564769 - Sequence 545793 from Patent EP1572962.
JD082452 - Sequence 63476 from Patent EP1572962.
JD432382 - Sequence 413406 from Patent EP1572962.
JD217822 - Sequence 198846 from Patent EP1572962.
JD144768 - Sequence 125792 from Patent EP1572962.
JD231983 - Sequence 213007 from Patent EP1572962.
JD279247 - Sequence 260271 from Patent EP1572962.
JD314121 - Sequence 295145 from Patent EP1572962.
JD142618 - Sequence 123642 from Patent EP1572962.
JD196161 - Sequence 177185 from Patent EP1572962.
JD142619 - Sequence 123643 from Patent EP1572962.
JD223427 - Sequence 204451 from Patent EP1572962.
JD140170 - Sequence 121194 from Patent EP1572962.
JD238133 - Sequence 219157 from Patent EP1572962.
JD481335 - Sequence 462359 from Patent EP1572962.
JD179678 - Sequence 160702 from Patent EP1572962.
JD420110 - Sequence 401134 from Patent EP1572962.
JD438837 - Sequence 419861 from Patent EP1572962.
JD384508 - Sequence 365532 from Patent EP1572962.
JD486780 - Sequence 467804 from Patent EP1572962.
JD226352 - Sequence 207376 from Patent EP1572962.
JD243957 - Sequence 224981 from Patent EP1572962.
JD454378 - Sequence 435402 from Patent EP1572962.
JD135811 - Sequence 116835 from Patent EP1572962.
JD047628 - Sequence 28652 from Patent EP1572962.
JD197085 - Sequence 178109 from Patent EP1572962.
JD440901 - Sequence 421925 from Patent EP1572962.
JD529117 - Sequence 510141 from Patent EP1572962.
JD169196 - Sequence 150220 from Patent EP1572962.
JD041228 - Sequence 22252 from Patent EP1572962.
JD096409 - Sequence 77433 from Patent EP1572962.
JD522771 - Sequence 503795 from Patent EP1572962.
JD139832 - Sequence 120856 from Patent EP1572962.
JD451709 - Sequence 432733 from Patent EP1572962.
JD365219 - Sequence 346243 from Patent EP1572962.
JD451854 - Sequence 432878 from Patent EP1572962.
JD127809 - Sequence 108833 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC068993
UCSC ID: uc002ybz.1
RefSeq Accession: NM_198935

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: yes RNA accession: BC068993.1
exon count: 13CDS single in 3' UTR: no RNA size: 1901
ORF size: 0CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 1914.00frame shift in genome: no % Coverage: 98.63
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.