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LOC108175348 PAX7 intron homotypic clusters of transcription factor binding sites enhancer [ Homo sapiens (human) ]

Gene ID: 108175348, updated on 17-Sep-2024

Summary

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Gene symbol
LOC108175348
Gene description
PAX7 intron homotypic clusters of transcription factor binding sites enhancer
Gene type
biological region
Feature type(s)
misc_feature: conserved_region
regulatory: enhancer
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 is located in an intron of the PAX7 (paired box 7) gene. It contains multiple homotypic clusters of transcription factor binding sites (HCTs) based on the presence of multiple binding motifs for NRF1 (nuclear respiratory factor 1) and E2F4 (E2F transcription factor 4). This HCT region was validated as a functional enhancer by transgenic reporter assays in mouse embryonic midbrain. A subregion marked by the H3K4me1 histone modification was also shown to be an active enhancer by ChIP-STARR-seq in primed human embryonic stem cells. [provided by RefSeq, Nov 2022]
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Genomic context

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See LOC108175348 in Genome Data Viewer
Location:
1p36.13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (18632169..18633790)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (18452231..18453852)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (18958663..18960284)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18807375-18808246 Neighboring gene kelch domain containing 7A Neighboring gene dynein light chain LC8-type 1 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18877005-18877829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18879379-18879880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18879881-18880380 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18883865-18884372 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18884373-18884880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18898371-18898870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18901646-18902224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18902225-18902802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18925717-18926246 Neighboring gene PAX7 promoter region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18962444-18963061 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18963062-18963678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18963679-18964296 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:18967445-18967966 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:18976025-18976654 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:18978097-18978886 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:18979869-18980025 Neighboring gene Sharpr-MPRA regulatory region 1855 Neighboring gene paired box 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19018361-19018860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19064331-19064838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19064839-19065345 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19066201-19066702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19119189-19119690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19119691-19120190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19144000-19144500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19146197-19146706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19146707-19147216 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19147395-19147573 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19176158-19176291 Neighboring gene taste 1 receptor member 2 Neighboring gene Sharpr-MPRA regulatory region 7483 Neighboring gene aldehyde dehydrogenase 4 family member A1 Neighboring gene microRNA 4695

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. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Gotea V, et al. Genome Res, 2010 May. PMID 20363979, Free PMC Article
  2. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Visel A, et al. Nucleic Acids Res, 2007 Jan. PMID 17130149, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • H3K4me1 hESC enhancer GRCh37_chr1:18959681-18960216
  • NRF1 and E2F4 HCT enhancer
  • VISTA enhancer hs1702

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_050921.1 

    Range
    101..1722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    18632169..18633790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    18452231..18453852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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