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LOC108281124 PXT1 intron CAGE-defined low expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281124, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281124
Gene description
PXT1 intron CAGE-defined low expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic element is located in an intron of the PXT1 (peroxisomal, testis specific 1) gene. It was defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in both HeLa and HepG2 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]
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Genomic context

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Location:
6p21.31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (36441321..36441868)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (36261998..36262545)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36409098..36409645)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene BCL2 interacting protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24424 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24425 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36343773-36344272 Neighboring gene ETS variant transcription factor 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36354517-36355340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17113 Neighboring gene ETV7 and PTX1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17114 Neighboring gene peroxisomal testis enriched protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24427 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24429 Neighboring gene RNA, 7SL, cytoplasmic 502, pseudogene Neighboring gene potassium channel tetramerization domain containing 20 Neighboring gene uncharacterized LOC124901558 Neighboring gene serine/threonine kinase 38

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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article

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

  • ATAC-STARR-seq lymphoblastoid silent region 17115
  • PXT1 intron low CAGE FANTOM5 enhancer

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_051067.1 

    Range
    101..648
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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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    36441321..36441868
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    36261998..36262545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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