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LOC112997572 Sharpr-MPRA regulatory region 5199 [ Homo sapiens (human) ]

Gene ID: 112997572, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112997572
Gene description
Sharpr-MPRA regulatory region 5199
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Aug 2018]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (157694381..157694675)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (158213407..158213701)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (157121389..157121683)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene SRY-box transcription factor 30 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:157098206-157098763 Neighboring gene chromosome 5 open reading frame 52 Neighboring gene uncharacterized LOC105377676 Neighboring gene SOX30 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23531 Neighboring gene tRNA-histidine guanylyltransferase 1 like

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_061569.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    157694381..157694675
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    158213407..158213701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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