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LOC120893126 Sharpr-MPRA regulatory region 12823 [ Homo sapiens (human) ]

Gene ID: 120893126, updated on 10-Oct-2023

Summary

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Gene symbol
LOC120893126
Gene description
Sharpr-MPRA regulatory region 12823
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin), with weaker activation in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Mar 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (27940418..27940712)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (27782242..27782545)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28266929..28267223)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28206149-28206649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 578 Neighboring gene thymocyte selection associated family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 532 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28240839-28241343 Neighboring gene replication protein A2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28261145-28262046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28269804-28270304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28270305-28270805 Neighboring gene sphingomyelin phosphodiesterase acid like 3B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:28286425-28286988 Neighboring gene MPRA-validated peak136 silencer Neighboring gene XK related 8 Neighboring gene EYA transcriptional coactivator and phosphatase 3 Neighboring gene RNA, 7SL, cytoplasmic 559, pseudogene

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_073885.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    27940418..27940712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    27782242..27782545
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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