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LOC124153133 Sharpr-MPRA regulatory region 11135 [ Homo sapiens (human) ]

Gene ID: 124153133, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124153133
Gene description
Sharpr-MPRA regulatory region 11135
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124153133 in Genome Data Viewer
Location:
8p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (28666912..28667206)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (28945106..28945400)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (28524429..28524723)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs1329 Neighboring gene microRNA 4288 Neighboring gene frizzled class receptor 3 Neighboring gene RNA, 5S ribosomal pseudogene 259 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28415895-28416077 Neighboring gene NANOG hESC enhancer GRCh37_chr8:28419252-28419778 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28479657-28480093 Neighboring gene exostosin like glycosyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19064 Neighboring gene EXTL3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28583611-28584110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28609290-28610234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28610235-28611177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19065 Neighboring gene uncharacterized LOC124902104 Neighboring gene integrator complex subunit 9

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_078521.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    28666912..28667206
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    28945106..28945400
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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