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LOC113788254 Sharpr-MPRA regulatory region 2006 [ Homo sapiens (human) ]

Gene ID: 113788254, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113788254
Gene description
Sharpr-MPRA regulatory region 2006
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 DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113788254 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 (123396589..123396883)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (124527697..124527991)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (124408829..124409123)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATPase family AAA domain containing 2 Neighboring gene microRNA 548aa-1 Neighboring gene microRNA 548d-1 Neighboring gene deoxyuridine triphosphatase pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:124405259-124405759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27874 Neighboring gene inosine monophosphate dehydrogenase 1 pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:124422560-124423060 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:124423061-124423561 Neighboring gene MPRA-validated peak7156 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19499 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:124429186-124429780 Neighboring gene N-terminal glutamine amidase 1 Neighboring gene uncharacterized LOC124902105

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_062547.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    123396589..123396883
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    124527697..124527991
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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