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LOC122094881 Sharpr-MPRA regulatory region 9288 [ Homo sapiens (human) ]

Gene ID: 122094881, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122094881
Gene description
Sharpr-MPRA regulatory region 9288
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (99239693..99239987)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99088039..99088333)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (99705249..99705543)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1111 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1113 Neighboring gene sorting nexin 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:99248941-99249530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:99249531-99250120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1357 Neighboring gene phospholipid phosphatase related 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:99469275-99470249 Neighboring gene PLPPR5 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:99543443-99543978 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:99649439-99649606 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:99770787-99771986 Neighboring gene phospholipid phosphatase related 4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:99839496-99840695 Neighboring gene uncharacterized LOC107985093

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_076395.1 

    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
    99239693..99239987
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    99088039..99088333
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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