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LOC123620097 Sharpr-MPRA regulatory region 2026 [ Homo sapiens (human) ]

Gene ID: 123620097, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123620097
Gene description
Sharpr-MPRA regulatory region 2026
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 DNase matched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123620097 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (36029512..36029806)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35849822..35850116)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35997289..35997583)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 26 member 8 Neighboring gene uncharacterized LOC105375035 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:35960877-35961390 Neighboring gene uncharacterized LOC105375034 Neighboring gene divergent-paired related homeobox pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35991863-35992364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35992365-35992864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17104 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17105 Neighboring gene mitogen-activated protein kinase 14 Neighboring gene NUDT5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36098441-36099044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36106471-36106971 Neighboring gene mitogen-activated protein kinase 13

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_078081.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    36029512..36029806
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    35849822..35850116
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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