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LOC108281186 AJAP1-NPHP4 intergenic nontranscribed DNase I hypersensitive site-defined enhancer [ Homo sapiens (human) ]

Gene ID: 108281186, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281186
Gene description
AJAP1-NPHP4 intergenic nontranscribed DNase I hypersensitive site-defined enhancer
Gene type
biological region
Feature type(s)
regulatory: DNase_I_hypersensitive_site, 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 element is located in the intergenic region between the AJAP1 (adherens junctions associated protein 1) and NPHP4 (nephronophthisis 4) genes. It was defined as a nontranscribed region with regulatory potential based on the presence of a DNase I hypersensitive site (DHS), with an absence of capped transcripts by cap analysis of gene expression (CAGE) in HeLa cells. It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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Genomic context

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See LOC108281186 in Genome Data Viewer
Location:
1p36
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (5742551..5743135)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5265016..5265600)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (5802611..5803195)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORD66 Neighboring gene uncharacterized LOC124903830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5778898-5779859 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:5800808-5801308 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:5801309-5801809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5805858-5806654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5814163-5814801 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:5815304-5815502 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5826901-5827548 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:5827549-5828196 and GRCh37_chr1:5828197-5828844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5857583-5858292 Neighboring gene NANOG hESC enhancer GRCh37_chr1:5883532-5884116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5886314-5886814 Neighboring gene Sharpr-MPRA regulatory region 9093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5891751-5892261 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:5896941-5897093 Neighboring gene MPRA-validated peak24 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5910393-5910894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5910895-5911394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5913107-5913951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5917575-5918327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5918328-5919080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5939868-5940372 Neighboring gene microRNA 4689 Neighboring gene nephrocystin 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5956455-5957256 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5957257-5958056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5968773-5969298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5979954-5980454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5999651-6000151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6004026-6004526 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6009504-6009801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6027103-6027602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6031677-6032176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6051054-6051908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 134

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. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  3. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, 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

  • AJAP1-NPHP4 interval no CAGE DHS 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_051146.1 

    Range
    101..685
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    5742551..5743135
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    5265016..5265600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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