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LOC108254682 PAX5 promoter region [ Homo sapiens (human) ]

Gene ID: 108254682, updated on 14-Mar-2024

Summary

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Gene symbol
LOC108254682
Gene description
PAX5 promoter region
Gene type
biological region
Feature type(s)
regulatory: promoter, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This region represents the promoter of the paired box 5 (PAX5) gene. It also includes a negative regulator of transcription located downstream of the transcription start site. This promoter may be methylated and silenced in tumor cells. This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
Orthologs
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Genomic context

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Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37034034..37034852)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37057749..37058568)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37034031..37034849)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene paired box 5 Neighboring gene uncharacterized LOC105376032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28371 Neighboring gene Sharpr-MPRA regulatory region 11996 Neighboring gene uncharacterized LOC105376031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37028766-37029440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37037999-37038576 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:37053864-37054416 Neighboring gene ribosomal protein L32 pseudogene 21 Neighboring gene MPRA-validated peak7233 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28377 Neighboring gene endogenous Bornavirus like nucleoprotein 3, pseudogene

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. Pax5 Re-expression in H460 Cells Treated with the Combination of Demethylating Agent and Histone Deacetylase Inhibitor is Associated with the Enhancement of P53 Binding to Pax5 Promoter Region. Liang Y, et al. Curr Cancer Drug Targets, 2017. PMID 27029827
  2. Aberrant promoter methylation of the transcription factor genes PAX5 alpha and beta in human cancers. Palmisano WA, et al. Cancer Res, 2003 Aug 1. PMID 12907641
  3. A repressor element in the 5'-untranslated region of human Pax5 exon 1A. Rahman M, et al. Gene, 2001 Jan 24. PMID 11223243
  4. Cloning and analysis of the human Pax-5 gene promoter. Mahmoud MS, et al. Biochem Biophys Res Commun, 1996 Nov 1. PMID 8912652
  5. Paired box 5 methylation detection by droplet digital PCR for ultra-sensitive deep surgical margins analysis of head and neck squamous cell carcinoma. Hayashi M, et al. Cancer Prev Res (Phila), 2015 Nov. PMID 26304463, Free PMC Article

See all (12) 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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Homology

Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 19901

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_051029.1 

    Range
    101..919
    Download
    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
    37034034..37034852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37057749..37058568
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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