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LOC122817727 Sharpr-MPRA regulatory region 10261 [ Homo sapiens (human) ]

Gene ID: 122817727, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122817727
Gene description
Sharpr-MPRA regulatory region 10261
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122817727 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (111986432..111986726)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (112413383..112413677)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (112744009..112744303)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MER proto-oncogene, tyrosine kinase Neighboring gene RTRAF pseudogene 1 Neighboring gene SLC30A6 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 3720 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16389 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:112818151-112818365 Neighboring gene transmembrane protein 87B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:112897779-112898492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:112914115-112914944 Neighboring gene NANOG hESC enhancer GRCh37_chr2:112925881-112926394 Neighboring gene fibulin 7 Neighboring gene zinc finger CCCH-type containing 8

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_076999.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    111986432..111986726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    112413383..112413677
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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