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SCHLAP1 SWI/SNF complex antagonist associated with prostate cancer 1 [ Homo sapiens (human) ]

Gene ID: 101669767, updated on 10-Oct-2023

Summary

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Official Symbol
SCHLAP1provided by HGNC
Official Full Name
SWI/SNF complex antagonist associated with prostate cancer 1provided by HGNC
Primary source
HGNC:HGNC:48603
See related
Ensembl:ENSG00000281131 MIM:615568; AllianceGenome:HGNC:48603
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCAT11; PCAT114; LINC00913
Expression
Low expression observed in reference dataset See more
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Genomic context

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See SCHLAP1 in Genome Data Viewer
Location:
2q31.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (180692104..180916939)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (181175628..181406564)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (181556831..181781666)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373769 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:181293207-181293431 Neighboring gene uncharacterized LOC105373770 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:181449937-181450113 Neighboring gene Sharpr-MPRA regulatory region 10987 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:181520993-181522192 Neighboring gene uncharacterized LOC105373771 Neighboring gene MPRA-validated peak3955 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:181678325-181679524 Neighboring gene ferritin heavy chain 1 pseudogene 20 Neighboring gene ribosomal protein L27a pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12155 Neighboring gene UBE2E3 divergent transcript Neighboring gene ubiquitin conjugating enzyme E2 E3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Expression and clinical significance of lncRNA-SChLAP1 in breast cancer. Cheng S, et al. J BUON, 2021 May-Jun. PMID 34268927
  2. High expression of SCHLAP1 in primary prostate cancer is an independent predictor of biochemical recurrence, despite substantial heterogeneity. Kidd SG, et al. Neoplasia, 2021 Jun. PMID 34107378, Free PMC Article
  3. SWI/SNF remains localized to chromatin in the presence of SCHLAP1. Raab JR, et al. Nat Genet, 2019 Jan. PMID 30510238, Free PMC Article
  4. A Prostate Cancer "Nimbosus": Genomic Instability and SChLAP1 Dysregulation Underpin Aggression of Intraductal and Cribriform Subpathologies. Chua MLK, et al. Eur Urol, 2017 Nov. PMID 28511883
  5. Inhibiting malignant phenotypes of the bladder cancer cells by silencing long noncoding RNA SChLAP1. Zhang J, et al. Int Urol Nephrol, 2016 May. PMID 26861061

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SChLAP1 contributes to non-small cell lung cancer cell progression and immune evasion through regulating the AUF1/PD-L1 axis.
    Title: SChLAP1 contributes to non-small cell lung cancer cell progression and immune evasion through regulating the AUF1/PD-L1 axis.
  2. High expression of SCHLAP1 in primary prostate cancer is an independent predictor of biochemical recurrence, despite substantial heterogeneity.
    Title: High expression of SCHLAP1 in primary prostate cancer is an independent predictor of biochemical recurrence, despite substantial heterogeneity.
  3. Expression and clinical significance of lncRNA-SChLAP1 in breast cancer.
    Title: Expression and clinical significance of lncRNA-SChLAP1 in breast cancer.
  4. Long noncoding RNA SChLAP1 regulates the proliferation of triple negative breast cancer cells via the miR5245p/HMGA2 axis.
    Title: Long non‑coding RNA SChLAP1 regulates the proliferation of triple negative breast cancer cells via the miR‑524‑5p/HMGA2 axis.
  5. SChLAP1 promotes prostate cancer development through interacting with EZH2 to mediate promoter methylation modification of multiple miRNAs of chromosome 5 with a DNMT3a-feedback loop.
    Title: SChLAP1 promotes prostate cancer development through interacting with EZH2 to mediate promoter methylation modification of multiple miRNAs of chromosome 5 with a DNMT3a-feedback loop.
  6. SCHLAP1 may function in a SWI/SNF-independent manner.
    Title: SWI/SNF remains localized to chromatin in the presence of SCHLAP1.
  7. Our results revealed that SChLAP1 may competitively bind miR-198 and modulate the expression of MAPK1 indirectly in prostate cancer cells.
    Title: Long Noncoding RNA SChLAP1 Accelerates the Proliferation and Metastasis of Prostate Cancer via Targeting miR-198 and Promoting the MAPK1 Pathway.
  8. Genomic instability and SChLAP1 dysregulation underpin aggression of intraductal and cribriform subpathologies.
    Title: A Prostate Cancer "Nimbosus": Genomic Instability and SChLAP1 Dysregulation Underpin Aggression of Intraductal and Cribriform Subpathologies.
  9. We examined expression of the RNA molecule SChLAP1 in a large group of prostate cancer patients with long-term follow-up and found that patients with high SChLAP1 expression had a significantly higher chance of developing lethal disease.
    Title: Overexpression of the Long Non-coding RNA SChLAP1 Independently Predicts Lethal Prostate Cancer.
  10. In summary, SChLAP1 plays a tumor promoter role in bladder cancer.
    Title: Inhibiting malignant phenotypes of the bladder cancer cells by silencing long noncoding RNA SChLAP1.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Other Names

  • SWI/SNF complex antagonist associated with prostate cancer 1 (non-protein coding)
  • Second Chromosome Locus Associated with Prostate 1
  • long intergenic non-protein coding RNA 913
  • prostate cancer associated transcript 11

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_104319.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the primary transcript.
    Source sequence(s)
    JX117418
    Related
    ENST00000629145.1

  2. NR_104320.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon, compared to variant 1.
    Source sequence(s)
    JX117419

  3. NR_104321.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two exons, compared to variant 1.
    Source sequence(s)
    JX117420

  4. NR_104322.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) includes two additional exons, compared to variant 1.
    Source sequence(s)
    JX117421

  5. NR_104323.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) includes an additional exon, compared to variant 1.
    Source sequence(s)
    JX117422

  6. NR_104324.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) includes an additional exon and lacks an exon, compared to variant 1.
    Source sequence(s)
    JX117423

  7. NR_104325.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) includes an additional exon, compared to variant 1.
    Source sequence(s)
    JX117424

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    180692104..180916939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    181175628..181406564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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