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LOC123744816 Sharpr-MPRA regulatory region 13557 [ Homo sapiens (human) ]

Gene ID: 123744816, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123744816
Gene description
Sharpr-MPRA regulatory region 13557
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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (47520313..47520607)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (47361961..47362255)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (47488049..47488343)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24661 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24662 Neighboring gene CRISPRi-validated cis-regulatory element chr6.3292 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:47411751-47412484 Neighboring gene Sharpr-MPRA regulatory region 15024 Neighboring gene MPRA-validated peak5833 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17275 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:47446083-47446809 Neighboring gene CD2AP divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:47464500-47465069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:47465070-47465638 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:47468840-47469047 Neighboring gene CD2 associated protein Neighboring gene ribosomal protein S12 pseudogene 14 Neighboring gene DnaJ heat shock protein family (Hsp40) member C17 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_078116.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    47520313..47520607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    47361961..47362255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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