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LOC122056809 Sharpr-MPRA regulatory region 5798 [ Homo sapiens (human) ]

Gene ID: 122056809, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056809
Gene description
Sharpr-MPRA regulatory region 5798
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (26961458..26961752)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (26799513..26799807)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (27287949..27288243)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear distribution C, dynein complex regulator Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27241933-27242433 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:27245085-27245285 Neighboring gene nuclear receptor subfamily 0 group B member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 531 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:27248501-27249042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 498 Neighboring gene Sharpr-MPRA regulatory region 10310 Neighboring gene keratinocyte differentiation factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:27286397-27287079 Neighboring gene negCOR silencer S3 Neighboring gene ribosomal protein L12 pseudogene 13 Neighboring gene ribosomal protein L32 pseudogene 6

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_076265.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    26961458..26961752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    26799513..26799807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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