Human Gene SS18L1 (ENST00000331758.8_4) from GENCODE V47lift37
  Description: SS18L1 subunit of BAF chromatin remodeling complex, transcript variant 4 (from RefSeq NR_125981.3)
Gencode Transcript: ENST00000331758.8_4
Gencode Gene: ENSG00000184402.15_8
Transcript (Including UTRs)
   Position: hg19 chr20:60,718,825-60,757,570 Size: 38,746 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr20:60,718,877-60,754,264 Size: 35,388 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:60,718,825-60,757,570)mRNA (may differ from genome)Protein (396 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CREST_HUMAN
DESCRIPTION: RecName: Full=Calcium-responsive transactivator; AltName: Full=SS18-like protein 1; AltName: Full=SYT homolog 1;
FUNCTION: Transcriptional activator which is required for calcium- dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity).
SUBUNIT: Homodimer. Dimerization may be necessary for its function in neuronal dendritic development. Interacts (via C-terminus) with CREBBP (via N-terminus), EP300 and SMARCA4/BRG1. Interacts with the nBAF complex. Association with CREBBP facilitates transcription while the association with SMARCA4/BRG1 suppresses CREST-mediated transcription in resting neurons (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome, centromere, kinetochore (By similarity). Note=Localizes to nuclear bodies. Co-localizes with SGOL1 at kinetochore (By similarity).
TISSUE SPECIFICITY: Ubiquitous; with lowest levels in spleen.
DOMAIN: The MFD (multi-functional domain) domain is involved in transcription transactivation, nuclear body targeting and dimerization (By similarity).
SIMILARITY: Belongs to the SS18 family.
SEQUENCE CAUTION: Sequence=BAA31668.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/SS18L1ID474ch20q13.html";

-  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


-  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

+  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: 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.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -13.5052-0.260 Picture PostScript Text
3' UTR -941.203306-0.285 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)

SCOP Domains:
88633 - Positive stranded ssRNA viruses

ModBase Predicted Comparative 3D Structure on O75177
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003713 transcription coactivator activity
GO:0005515 protein binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0016358 dendrite development
GO:0045893 positive regulation of transcription, DNA-templated
GO:0050773 regulation of dendrite development
GO:0050775 positive regulation of dendrite morphogenesis

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000776 kinetochore
GO:0000777 condensed chromosome kinetochore
GO:0000780 condensed nuclear chromosome, centromeric region
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005829 cytosol
GO:0016604 nuclear body
GO:0071565 nBAF complex


-  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.
JD539614 - Sequence 520638 from Patent EP1572962.
JD223069 - Sequence 204093 from Patent EP1572962.
JD317142 - Sequence 298166 from Patent EP1572962.
JD167898 - Sequence 148922 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.
JD332623 - Sequence 313647 from Patent EP1572962.
JD296678 - Sequence 277702 from Patent EP1572962.
JD036700 - Sequence 17724 from Patent EP1572962.
JD512205 - Sequence 493229 from Patent EP1572962.
JD090733 - Sequence 71757 from Patent EP1572962.
JD042306 - Sequence 23330 from Patent EP1572962.
JD350357 - Sequence 331381 from Patent EP1572962.
JD140390 - Sequence 121414 from Patent EP1572962.
JD172437 - Sequence 153461 from Patent EP1572962.
JD092809 - Sequence 73833 from Patent EP1572962.
JD337870 - Sequence 318894 from Patent EP1572962.
JD049569 - Sequence 30593 from Patent EP1572962.
JD448802 - Sequence 429826 from Patent EP1572962.
JD323361 - Sequence 304385 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NNE3, A8K620, B3KWR8, CREST, CREST_HUMAN, E1P5H7, ENST00000331758.1, ENST00000331758.2, ENST00000331758.3, ENST00000331758.4, ENST00000331758.5, ENST00000331758.6, ENST00000331758.7, KIAA0693, NR_125981, O75177, Q5JXJ3, Q6MZV9, Q6NTH3, Q6XYD9, Q8NE69, Q9BR55, Q9H4K6, uc317thc.1, uc317thc.2
UCSC ID: ENST00000331758.8_4
RefSeq Accession: NM_198935.3
Protein: O75177 (aka CREST_HUMAN)

-  Gene Model Information
  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.