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LOC124500663 Sharpr-MPRA regulatory region 288 [ Homo sapiens (human) ]

Gene ID: 124500663, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124500663
Gene description
Sharpr-MPRA regulatory region 288
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124500663 in Genome Data Viewer
Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65066757..65067051)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65060037..65060331)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64834229..64834523)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ARL2-SNX15 readthrough (NMD candidate) Neighboring gene Sharpr-MPRA regulatory region 4003 Neighboring gene sorting nexin 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4938 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3506 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64811302-64811848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64814570-64815448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64815449-64816327 Neighboring gene SAC3 domain containing 1 Neighboring gene N-acetylated alpha-linked acidic dipeptidase like 1 Neighboring gene cell division cycle associated 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:64846103-64846604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64852413-64852997 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64857368-64857540 Neighboring gene zinc finger protein like 1 Neighboring gene transmembrane protein 262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64863491-64864285 Neighboring gene Sharpr-MPRA regulatory region 6888 Neighboring gene VPS51 subunit of GARP complex Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64877599-64878526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64878527-64879452

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 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_079321.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65066757..65067051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65060037..65060331
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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