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LOC122056805 Sharpr-MPRA regulatory region 4586 [ Homo sapiens (human) ]

Gene ID: 122056805, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122056805
Gene description
Sharpr-MPRA regulatory region 4586
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122056805 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (26128658..26128952)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (25966090..25966386)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (26455149..26455443)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4919 Neighboring gene tripartite motif containing 63 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:26405707-26405883 Neighboring gene VISTA enhancer hs2271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 473 Neighboring gene PDLIM1 interacting kinase 1 like Neighboring gene Sharpr-MPRA regulatory region 12487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26480925-26481654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26481655-26482384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26482385-26483114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:26483115-26483844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:26490758-26491327 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:26494780-26494935 Neighboring gene family with sequence similarity 110 member D Neighboring gene chromosome 1 open reading frame 230

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_076261.1 

    Range
    101..395
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    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
    26128658..26128952
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    25966090..25966386
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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