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APOB-ICR APOB intestinal control region [ Homo sapiens (human) ]

Gene ID: 106633812, updated on 13-Mar-2024

Summary

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Gene symbol
APOB-ICR
Gene description
APOB intestinal control region
Gene type
biological region
Feature type(s)
protein_bind
regulatory: DNase_I_hypersensitive_site, enhancer, enhancer_blocking_element, insulator, matrix_attachment_region, 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 a portion of a larger DNase I sensitive domain in intestinal cells. It contains DNase I hypersensitive sites corresponding to intestinal enhancers and other regulators of the apolipoprotein B (APOB) gene, located greater than 50 kb downstream. Enhancer activity is associated with binding by C/EBP, forkhead, and nuclear receptor family proteins, and responds to signalling by transforming growth factor beta. An additional regulatory sequence binds transcriptional repressor CTCF and can act as an insulator and an enhancer blocker. This region also includes a putative scaffold/matrix attachment region (S/MAR). [provided by RefSeq, Oct 2015]
Orthologs
mouse all
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Genomic context

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Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (21094585..21101784)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (21127781..21134980)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (21317457..21324656)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes 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 APOB 5' regulatory 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 Sharpr-MPRA regulatory region 2464 Neighboring gene tudor domain containing 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:21436748-21437248 Neighboring gene uncharacterized LOC105374317 Neighboring gene MPRA-validated peak3614 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr2:21488316-21488485

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. The 5' boundary of the human apolipoprotein B chromatin domain in intestinal cells. Antes TJ, et al. Biochemistry, 2001 Jun 12. PMID 11389587
  2. HNF-3 beta, C/EBP beta, and HNF-4 act in synergy to enhance transcription of the human apolipoprotein B gene in intestinal cells. Antes TJ, et al. DNA Cell Biol, 2001 Feb. PMID 11244563
  3. Apolipoprotein B gene expression in a series of human apolipoprotein B transgenic mice generated with recA-assisted restriction endonuclease cleavage-modified bacterial artificial chromosomes. An intestine-specific enhancer element is located between 54 and 62 kilobases 5' to the structural gene. Nielsen LB, et al. J Biol Chem, 1998 Aug 21. PMID 9705318
  4. Human apolipoprotein B transgenic mice generated with 207- and 145-kilobase pair bacterial artificial chromosomes. Evidence that a distant 5'-element confers appropriate transgene expression in the intestine. Nielsen LB, et al. J Biol Chem, 1997 Nov 21. PMID 9368045
  5. Regulation of human apolipoprotein B gene expression at multiple levels. Wang AB, et al. Exp Cell Res, 2003 Oct 15. PMID 14516783

See all (10) 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

  • apolipoprotein B ICR

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_042891.1 

    Range
    101..7300
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    21094585..21101784
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791767.1 Reference GRCh38.p14 PATCHES

    Range
    145253..152452
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    21127781..21134980
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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