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LOC122149328 Sharpr-MPRA regulatory region 9576 [ Homo sapiens (human) ]

Gene ID: 122149328, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122149328
Gene description
Sharpr-MPRA regulatory region 9576
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 unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122149328 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (184986377..184986671)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (184343262..184343556)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (184955509..184955803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene niban apoptosis regulator 1 Neighboring gene uncharacterized LOC107985238 Neighboring gene MPRA-validated peak504 silencer Neighboring gene RNA, U7 small nuclear 13 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1640 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:184815021-184815626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2239 Neighboring gene uncharacterized LOC124904469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2240 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1641 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1642 Neighboring gene long intergenic non-protein coding RNA 1633 Neighboring gene RNA, 5S ribosomal pseudogene 72

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_076520.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    184986377..184986671
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    184343262..184343556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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