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LOC114004409 Sharpr-MPRA regulatory region 12099 [ Homo sapiens (human) ]

Gene ID: 114004409, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004409
Gene description
Sharpr-MPRA regulatory region 12099
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), with weaker repression in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114004409 in Genome Data Viewer
Location:
8q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (101159521..101159815)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (102285255..102285549)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (102171749..102172043)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 3090 Neighboring gene RN7SK pseudogene 249 Neighboring gene uncharacterized LOC105375676 Neighboring gene NFE2L2 motif-containing MPRA enhancer 220/221 Neighboring gene Sharpr-MPRA regulatory region 12327 Neighboring gene Sharpr-MPRA regulatory region 1163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27728 Neighboring gene ZNF706 neighboring transcript 1 Neighboring gene zinc finger protein 706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19432

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_063909.1 

    Range
    101..395
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    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    101159521..101159815
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    102285255..102285549
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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