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LOC106560211 APOB 5' regulatory region [ Homo sapiens (human) ]

Gene ID: 106560211, updated on 10-Oct-2023

Summary

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Gene symbol
LOC106560211
Gene description
APOB 5' regulatory region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, insulator, matrix_attachment_region, micrococcal_nuclease_hypersensitive_site, promoter, response_element, silencer, 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 region represents a portion of an approximately 50 kb DNase I sensitive domain encompassing the apolipoprotein B (APOB) gene. It includes the canonical promoter as well as multiple upstream and intronic enhancers and silencers. Activity of these regulatory elements is associated with binding of C/EBP, nuclear receptor subfamily 2, forkhead, and hepatocyte nuclear factor family proteins. An enhancer in the second intron drives expression of APOB in the liver. These elements coincide with multiple hypersensitive sites for DNase I and micrococcal nuclease. This region also includes two putative matrix attachment regions (S/MARs). The 5' distal S/MAR was found to be important for locus-independent transgene expression in cell culture, but did not function as an insulator in mouse or fly transgenic organisms. A subregion was also shown to be an enhancer by the ChIP-STARR-seq massively parallel reporter assay in primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors. [provided by RefSeq, Dec 2022]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (21041088..21049341)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (21074308..21082558)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (21263960..21272213)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr2:20893576-20893760 Neighboring gene lipid droplet associated hydrolase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:21021737-21022562 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15408 Neighboring gene long intergenic non-protein coding RNA 2850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:21211745-21212246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:21212247-21212746 Neighboring gene APOB 3' scaffold/matrix attachment region Neighboring gene apolipoprotein B Neighboring gene Sharpr-MPRA regulatory region 5245 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:21290821-21291609 Neighboring gene uncharacterized LOC124905593 Neighboring gene uncharacterized LOC124908055 Neighboring gene APOB intestinal control region Neighboring gene tudor domain containing 15

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 open chromatin structure in a liver-specific enhancer that confers high level expression to human apolipoprotein b transgenes in mice. Levy-Wilson B, et al. Mol Cell Biol Res Commun, 2000 Oct. PMID 11409913
  2. Association of hepatic nuclear factor-4 in the apolipoprotein B promoter: a preliminary report. Nóvak EM, et al. Braz J Med Biol Res, 1998 Nov. PMID 9921275
  3. Construction of two near-kilobase resolution restriction maps of the 5' regulatory region of the human apolipoprotein B gene by quantitative DNA fiber mapping (QDFM). Duell T, et al. Cytogenet Cell Genet, 1997. PMID 9533015
  4. Identification of trans-acting factors that interact with cis-acting elements present in the first nontranslated exon of the human apolipoprotein B gene. Chuang SS, et al. Biochem Biophys Res Commun, 1996 Mar 27. PMID 8607803
  5. Members of the caudal family of homeodomain proteins repress transcription from the human apolipoprotein B promoter in intestinal cells. Lee SY, et al. J Biol Chem, 1996 Jan 12. PMID 8557677

See all (43) 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

  • APOB liver expression regulatory region
  • OCT4-NANOG hESC enhancer GRCh37_chr2:21270021-21270557

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_042873.1 

    Range
    101..8354
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    21041088..21049341
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791767.1 Reference GRCh38.p14 PATCHES

    Range
    91756..100009
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    21074308..21082558
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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