Details for: SS18L1

Gene ID: 26039

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: SS18L1

Ensembl ID: ENSG00000184402

Description: SS18L1 subunit of BAF chromatin remodeling complex

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • progenitor cell CL0011026
    CSI 12.97
    rCSI 27.59%
    PRS 87.84
  • stem cell CL0000034
    CSI 7.63
    rCSI 7.35%
    PRS 90.79
  • innate lymphoid cell CL0001065
    CSI 7.43
    rCSI 15.35%
    PRS 87.96
  • melanocyte CL0000148
    CSI 5.02
    rCSI 3.72%
    PRS 91.25
  • cerebellar granule cell CL0001031
    CSI 3.79
    rCSI 5.57%
    PRS 89.72
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 3.75
    rCSI 4.67%
    PRS 81.68
  • brush cell of tracheobronchial tree CL0002075
    CSI 3.56
    rCSI 10.56%
    PRS 97.23
  • midzonal region hepatocyte CL0019028
    CSI 3.5
    rCSI 8.22%
    PRS 90.72
  • choroid plexus epithelial cell CL0000706
    CSI 3.44
    rCSI 5.64%
    PRS 88.3
  • alveolar macrophage CL0000583
    CSI 3.19
    rCSI 5.25%
    PRS 95.01
  • centrilobular region hepatocyte CL0019029
    CSI 3.14
    rCSI 8.18%
    PRS 89.8
  • cerebral cortex endothelial cell CL1001602
    CSI 3.06
    rCSI 5.29%
    PRS 89.73
  • cerebral cortex GABAergic interneuron CL0010011
    CSI 3.03
    rCSI 8.95%
    PRS 93.09
  • Kupffer cell CL0000091
    CSI 2.88
    rCSI 6.59%
    PRS 94.5
  • interneuron CL0000099
    CSI 2.77
    rCSI 5.56%
    PRS 89.06
  • periportal region hepatocyte CL0019026
    CSI 2.75
    rCSI 10.7%
    PRS 90.45
  • inhibitory interneuron CL0000498
    CSI 2.72
    rCSI 6.29%
    PRS 86.61
  • kidney loop of Henle thin ascending limb epithelial cell CL1001107
    CSI 2.69
    rCSI 6.96%
    PRS 91.87
  • neural crest cell CL0011012
    CSI 2.6
    rCSI 2.05%
    PRS 88.36
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 2.48
    rCSI 2.87%
    PRS 87.25
  • regular ventricular cardiac myocyte CL0002131
    CSI 2.4
    rCSI 14.98%
    PRS 88.45
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.38
    rCSI 3.07%
    PRS 84.75
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 2.32
    rCSI 4.09%
    PRS 83.22
  • retinal bipolar neuron CL0000748
    CSI 2.31
    rCSI 4.33%
    PRS 87.1
  • hepatocyte CL0000182
    CSI 2.27
    rCSI 4.06%
    PRS 92.03
  • kidney interstitial alternatively activated macrophage CL1000695
    CSI 2.18
    rCSI 5.67%
    PRS 94.99
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 2.16
    rCSI 2.77%
    PRS 90.3
  • VIP GABAergic cortical interneuron CL4023016
    CSI 2.1
    rCSI 2.5%
    PRS 83.83
  • peripheral nervous system neuron CL2000032
    CSI 2.04
    rCSI 2.79%
    PRS 88.28
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.03
    rCSI 4.55%
    PRS 84.07
  • chondrocyte CL0000138
    CSI 2.01
    rCSI 3.2%
    PRS 90.07
  • epithelial cell of proximal tubule CL0002306
    CSI 2
    rCSI 4.9%
    PRS 88.61
  • extravillous trophoblast CL0008036
    CSI 1.96
    rCSI 2.43%
    PRS 92.29
  • central nervous system neuron CL2000029
    CSI 1.42
    rCSI 10.44%
    PRS 87.52
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.4
    rCSI 2.25%
    PRS 84.76
  • retinal ganglion cell CL0000740
    CSI 1.31
    rCSI 2.9%
    PRS 85.38
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 1.24
    rCSI 4.45%
    PRS 81.94
  • kidney connecting tubule epithelial cell CL1000768
    CSI 1.21
    rCSI 3.07%
    PRS 89.5
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.19
    rCSI 2%
    PRS 83.87
  • amacrine cell CL0000561
    CSI 1.19
    rCSI 3.44%
    PRS 86.92
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.13
    rCSI 2.74%
    PRS 81.65
  • parietal epithelial cell CL1000452
    CSI 1.01
    rCSI 2.7%
    PRS 89.92
  • direct pathway medium spiny neuron CL4023026
    CSI 0.98
    rCSI 23.38%
    PRS 81.6
  • cerebellar neuron CL1001611
    CSI 0.97
    rCSI 8.55%
    PRS 83.46
  • indirect pathway medium spiny neuron CL4023029
    CSI 0.83
    rCSI 20.13%
    PRS 81.57
  • dopaminergic neuron CL0000700
    CSI 0.8
    rCSI 4.53%
    PRS 85.03
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.76
    rCSI 2.39%
    PRS 84.78
  • near-projecting glutamatergic cortical neuron CL4023012
    CSI 0.7
    rCSI 2.66%
    PRS 83.94
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 0.69
    rCSI 2.15%
    PRS 86.61
  • corticothalamic-projecting glutamatergic cortical neuron CL4023013
    CSI 0.39
    rCSI 2.29%
    PRS 84.11

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [SS18L1](/details-gene/26039), also known as Calcium-Responsive Transactivator (CREST), is a protein-coding gene that functions as a subunit of the BAF (SWI/SNF) chromatin remodeling complex. This complex plays a crucial role in regulating gene expression by altering chromatin structure. The functional annotations for [SS18L1](/details-gene/26039) highlight its involvement in fundamental processes such as [chromatin organization](/details-ontology/GO:0006325) and the [positive regulation of dna-templated transcription](/details-ontology/GO:0045893). **Overall**, expression data reveals its highest significance in undifferentiated cell types, including [progenitor cell](/details-cell/CL0011026) and [stem cell](/details-cell/CL0000034), as well as in specific differentiated lineages such as [innate lymphoid cell](/details-cell/CL0001065) and [melanocyte](/details-cell/CL0000148), suggesting a key role in both maintaining pluripotency and directing cell-specific developmental programs. ## Cellular Roles and Expression Landscape The expression profile of [SS18L1](/details-gene/26039) indicates its importance across a diverse range of cell types, with a pronounced significance in cells characterized by high plasticity and specialized transcriptional programs. **Overall**, its highest CSI scores are observed in [progenitor cell](/details-cell/CL0011026) (CSI: 12.97) and [stem cell](/details-cell/CL0000034) (CSI: 7.63), which is consistent with the role of BAF complexes in regulating cell fate decisions and maintaining the undifferentiated state. The gene also shows significant expression in the immune system, particularly in [innate lymphoid cell](/details-cell/CL0001065), as well as in tissue-resident macrophages like [alveolar macrophage](/details-cell/CL0000583) and [Kupffer cell](/details-cell/CL0000091), suggesting a function in immune cell development or activation. A distinct role in the nervous system is suggested by its high significance in multiple neuronal subtypes, including [cerebellar granule cell](/details-cell/CL0001031), [pvalb GABAergic cortical interneuron](/details-cell/CL4023018), and other [interneuron](/details-cell/CL0000099) populations. This expression pattern aligns with its annotated function in [dendrite development](/details-ontology/GO:0016358). Furthermore, the notable expression in [melanocyte](/details-cell/CL0000148) is strongly supported by its deep involvement in pathways regulating pigmentation, underscoring its role in establishing and maintaining this specialized cell lineage. ## Pathways and Molecular Function As a core component of the BAF complex, the molecular functions of [SS18L1](/details-gene/26039) are centered on transcriptional regulation. It is annotated with [transcription coactivator activity](/details-ontology/GO:0003713) and participates broadly in [Gene expression (transcription)](/details-pathway/R-HSA-74160) and [Epigenetic regulation of gene expression](/details-pathway/R-HSA-212165). Functionally, [SS18L1](/details-gene/26039) is found within the [nBAF complex](/details-ontology/GO:0071565) located in the [nucleus](/details-ontology/GO:0005634), where it contributes to [chromatin organization](/details-ontology/GO:0006325). Its cell-specific roles are illuminated by more specialized pathways. The high expression in [melanocyte](/details-cell/CL0000148) is directly explained by its involvement in the [Mitf-m-regulated melanocyte development](/details-pathway/R-HSA-9730414) and [Regulation of mitf-m-dependent genes involved in pigmentation](/details-pathway/R-HSA-9824585) pathways. This indicates that [SS18L1](/details-gene/26039) is a key co-factor for the master regulator MITF in controlling the melanocytic gene expression program. Similarly, its role in neurodevelopment is supported by its link to [dendrite development](/details-ontology/GO:0016358) and the broader [Developmental biology](/details-pathway/R-HSA-1266738) pathway, which is consistent with its expression in neuronal and progenitor cell populations. ## Research Directions The role of [SS18L1](/details-gene/26039) as a chromatin remodeler at the intersection of development, immunity, and specialized cell function presents several avenues for future research. Since BAF complexes are frequently mutated or dysregulated in human cancers, the specific functions of [SS18L1](/details-gene/26039) in disease contexts warrant investigation. **Testable Hypotheses:** 1. **Role in Melanoma:** Given its strong functional link to MITF-M pathways and high expression in [melanocyte](/details-cell/CL0000148), dysregulation of [SS18L1](/details-gene/26039) may contribute to melanoma by altering chromatin accessibility at MITF target genes, thereby promoting a proliferative and invasive phenotype. 2. **Function in Neurodevelopment:** Based on its expression in various [interneuron](/details-cell/CL0000099) subtypes and its role in [dendrite development](/details-ontology/GO:0016358), loss-of-function mutations in [SS18L1](/details-gene/26039) could impair neuronal circuit formation, potentially contributing to neurodevelopmental disorders characterized by synaptic dysfunction. 3. **Regulation of Stem Cell Fate:** Its prominent expression in [stem cell](/details-cell/CL0000034) and [progenitor cell](/details-cell/CL0011026) suggests that [SS18L1](/details-gene/26039) is a critical factor in maintaining pluripotency or guiding lineage commitment by modulating the chromatin landscape at key developmental loci. **Proposed Experiment:** To test the hypothesis regarding its role in melanoma (Hypothesis 1), one could utilize CRISPR-Cas9 to knock out [SS18L1](/details-gene/26039) in a panel of human melanoma cell lines. The functional consequences would be assessed via proliferation assays, Matrigel invasion assays, and analysis of pigmentation. Mechanistically, tandem RNA-seq and ATAC-seq would reveal changes in the transcriptome and chromatin accessibility landscapes following [SS18L1](/details-gene/26039) loss. Furthermore, co-immunoprecipitation followed by mass spectrometry could confirm its interaction with MITF and other key transcription factors in the melanoma cellular context. **Therapeutic Potential:** As an integral component of a chromatin remodeling complex, [SS18L1](/details-gene/26039) presents a challenging but potentially valuable therapeutic target. Its widespread expression in progenitor and stem cells suggests that systemic inhibition could lead to significant toxicity. However, its specific co-option in certain malignancies, such as melanoma where it may be essential for oncogenic MITF activity, could provide a therapeutic window. A strategy involving inhibition, perhaps through targeted protein degradation (PROTACs), could be explored to selectively disrupt its function in cancer cells, thereby suppressing oncogenic transcriptional programs.

Genular Protein ID: 2511626783

Symbol: CREST_HUMAN

Name: Calcium-responsive transactivator

UniProtKB Accession Codes:

O75177 A6NNE3 A8K620 B3KWR8 E1P5H7 Q5JXJ3 Q6MZV9 Q6NTH3 Q6XYD9 Q8NE69 Q9BR55 Q9H4K6

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 11 Ensembl 2 ExpressionAtlas 1 GO 11 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 2 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 5 Pumba 1 RNAct 1 Reactome 2 RefSeq 5 SIGNOR 1 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 9734811

Title: Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro.

PubMed ID: 9734811

DOI: 10.1093/dnares/5.3.169

PubMed ID: 11230166

Title: Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs.

PubMed ID: 11230166

DOI: 10.1101/gr.gr1547r

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 11780052

Title: The DNA sequence and comparative analysis of human chromosome 20.

PubMed ID: 11780052

DOI: 10.1038/414865a

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 18331714

Title: sSgo1, a major splice variant of Sgo1, functions in centriole cohesion where it is regulated by Plk1.

PubMed ID: 18331714

DOI: 10.1016/j.devcel.2007.12.007

Sequence Information:

  • Length: 396
  • Mass: 42990
  • Checksum: B76B7D61C7DF5592
  • Sequence:
    • MSVAFASARP RGKGEVTQQT IQKMLDENHH LIQCILEYQS KGKTAECTQY QQILHRNLVY 
LATIADSNQN MQSLLPAPPT QNMNLGPGAL TQSGSSQGLH SQGSLSDAIS TGLPPSSLLQ 
GQIGNGPSHV SMQQTAPNTL PTTSMSISGP GYSHAGPASQ GVPMQGQGTI GNYVSRTNIN 
MQSNPVSMMQ QQAATSHYSS AQGGSQHYQG QSSIAMMGQG SQGSSMMGQR PMAPYRPSQQ 
GSSQQYLGQE EYYGEQYSHS QGAAEPMGQQ YYPDGHGDYA YQQSSYTEQS YDRSFEESTQ 
HYYEGGNSQY SQQQAGYQQG AAQQQTYSQQ QYPSQQSYPG QQQGYGSAQG APSQYPGYQQ 
GQGQQYGSYR APQTAPSAQQ QRPYGYEQGQ YGNYQQ

Genular Protein ID: 1623203859

Symbol: B4DSR7_HUMAN

Name: N/A

UniProtKB Accession Codes:

B4DSR7

Database IDs:

ARBA 5 AlphaFoldDB 1 BioGRID-ORCS 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 2 GO 4 InterPro 2 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PeptideAtlas 1 Pfam 2 RefSeq 1 SAM 1

Sequence Information:

  • Length: 416
  • Mass: 45291
  • Checksum: 79D8B103A767CB92
  • Sequence:
    • MSVAFASARP RGKGEVTQQT IQKMLDENHH LIQCILEYQS KGKTAECTQY QQILHRNLVY 
LATIADSNQN MQSLLPAPPT QNMNLGPGAL TQSGSSQGLH SQGSLSDAIS TGLPPSSLLQ 
GQIGNGPSHV SMQQTAPNTL PTTSMSISGP GYSHAGPASQ GVPMQGQGTI GNYVSRTNIN 
MQSNPVSMMQ QQAATSHYSS AQGGSQHYQG QSSIAMMGQG SQGSSMMGQR PMAPYRPSQQ 
GSSQQYLGQE EYYGEQYSHS QGAAEPMGQQ YYPDGHGDYA YQQSSYTEQS YDRSFEESTQ 
HYYEGGNSQY SQQQAGYQQG AAQQQTYSQQ QYPSQQSYPG QQQGYGSAQG APSQYPGYQQ 
GQGQQYGSYR APQTAPSAQQ QRPYGYEQAS FLDVSRCAHP PRLSRHNEDF SYGHEE