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LOC122757931 Sharpr-MPRA regulatory region 15185 [ Homo sapiens (human) ]

Gene ID: 122757931, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757931
Gene description
Sharpr-MPRA regulatory region 15185
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Sep 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (45394290..45394584)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45399519..45399813)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45621429..45621723)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1121 Neighboring gene uncharacterized LOC105374576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45446124-45447052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45447053-45447979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45483718-45484291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45484292-45484864 Neighboring gene uncharacterized LOC105374577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45570374-45571192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45571193-45572010 Neighboring gene S1 RNA binding domain 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45693107-45693617 Neighboring gene Sharpr-MPRA regulatory region 7031 Neighboring gene RNA, 7SL, cytoplasmic 414, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15687 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45867535-45867711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11438 Neighboring gene uncharacterized LOC102724965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11440 Neighboring gene Sharpr-MPRA regulatory region 4153

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_076923.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    45394290..45394584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    45399519..45399813
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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