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LOC124310642 Sharpr-MPRA regulatory region 1305 [ Homo sapiens (human) ]

Gene ID: 124310642, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124310642
Gene description
Sharpr-MPRA regulatory region 1305
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124310642 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (125506250..125506544)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (137705902..137706196)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (128268529..128268823)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929014 Neighboring gene uncharacterized LOC112268055 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128186118-128186618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128194217-128194791 Neighboring gene RNA, U5B small nuclear 5, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128207109-128207610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128207611-128208110 Neighboring gene NANOG hESC enhancer GRCh37_chr9:128208606-128209135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128209344-128209872 Neighboring gene MAPK associated protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128242575-128243076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:128243077-128243576 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128243732-128243912 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:128246700-128246866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:128257291-128258078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29007 Neighboring gene RNA, 7SL, cytoplasmic 30, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29008 Neighboring gene uncharacterized LOC124902270

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_078923.1 

    Range
    101..395
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    125506250..125506544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    137705902..137706196
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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