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LOC112163676 Sharpr-MPRA regulatory region 2339 [ Homo sapiens (human) ]

Gene ID: 112163676, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112163676
Gene description
Sharpr-MPRA regulatory region 2339
Gene type
biological region
Feature type(s)
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 sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2018]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (95604175..95604469)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (94808720..94809014)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (96256429..96256723)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903193 Neighboring gene MEMO1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7877 Neighboring gene claudin 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7879 Neighboring gene CLDN10 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:96144450-96144950 Neighboring gene Sharpr-MPRA regulatory region 5370 Neighboring gene DAZ interacting zinc finger protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:96294105-96295030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7880 Neighboring gene uncharacterized LOC124903194 Neighboring gene H3K27ac hESC enhancers GRCh37_chr13:96328483-96329330 and GRCh37_chr13:96329331-96330177 Neighboring gene DNAJC3 divergent transcript

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. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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)

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_056650.1 

    Range
    101..395
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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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    95604175..95604469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    94808720..94809014
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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