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LOC117600004 CTSL promoter region [ Homo sapiens (human) ]

Gene ID: 117600004, updated on 10-Oct-2023

Summary

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Gene symbol
LOC117600004
Gene description
CTSL promoter region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: enhancer, promoter, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region represents the 5' regulatory region of the CTSL (cathepsin L) gene, which encodes a lysosomal protease that assists in host cell entry of human respiratory syndrome coronaviruses, including SARS-CoV and MERS-CoV, and possibly SARS-CoV-2 (COVID-19 virus). This region functions as a promoter that drives CTSL expression, and it also encompasses an alternative promoter in the first intron of the gene. Several positively- and negatively-acting cis-regulatory elements have been identified within this region, which includes known binding sites for the Sp1, Sp2, Sp3, NF-Y, FOXO1, C/EBPalpha and PPARgamma transcription factors. This promoter can be induced by both vascular endothelial growth factor (VEGF) and peroxisome proliferator-activated receptor (PPAR) gamma, and TGF-beta, Smad3, Egr-1 and CREB can also mediate promoter activity. A polymorphism within this region, the rs3118869 SNP that disrupts a predicted xenobiotic response element (XRE), is associated with hypertension and can functionally affect promoter activity. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. [provided by RefSeq, Dec 2022]
Annotation information
Note: This locus has been reviewed for its involvement in coronavirus biology, and is involved in host gene regulation.
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (87724325..87727604)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (99877938..99881224)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (90339240..90342519)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene death associated protein kinase 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:90145230-90146212 Neighboring gene ribosomal protein S29 pseudogene 18 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108388 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108397 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:90178705-90179204 Neighboring gene DAPK1 intronic transcript 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:90186048-90186548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:90207629-90208129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90215267-90215860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:90234560-90235060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:90249751-90250336 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:90308876-90309094 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:90314444-90315643 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:90317453-90318652 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:90328302-90329501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28523 Neighboring gene CTSL 3' regulatory element Neighboring gene uncharacterized LOC124902198 Neighboring gene cathepsin L Neighboring gene EIF3J pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Cathepsin L-mediated resistance of paclitaxel and cisplatin is mediated by distinct regulatory mechanisms. Zhao Y, et al. J Exp Clin Cancer Res, 2019 Aug 1. PMID 31370861, Free PMC Article
  2. Alteration of histone H3K4 methylation in glomerular podocytes associated with proteinuria in patients with membranous nephropathy. Fujino T, et al. BMC Nephrol, 2016 Nov 17. PMID 27855638, Free PMC Article
  3. Down regulation of a matrix degrading cysteine protease cathepsin L, by acetaldehyde: role of C/EBPα. Mir RA, et al. PLoS One, 2011. PMID 21687683, Free PMC Article
  4. Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-aza-2'-deoxycytidine treatment and oligonucleotide microarray. Yamashita S, et al. Cancer Sci, 2006 Jan. PMID 16367923
  5. Expression of cathepsin L in human tumor cells is under the control of distinct regulatory mechanisms. Jean D, et al. Oncogene, 2006 Mar 9. PMID 16261157

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

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 Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:90340825-90341346
  • cathepsin L promoter

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.

Genomic

  1. NG_068498.1 

    Range
    101..3380
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    GenBank, FASTA, Sequence Viewer (Graphics)

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    87724325..87727604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    99877938..99881224
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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