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LOC123477710 Sharpr-MPRA regulatory region 8789 [ Homo sapiens (human) ]

Gene ID: 123477710, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123477710
Gene description
Sharpr-MPRA regulatory region 8789
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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Location:
4p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (16942206..16942500)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (16923807..16924101)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (16943829..16944123)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene LIM domain binding 2 Neighboring gene uncharacterized LOC124900604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16610841-16611361 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:16694053-16695252 Neighboring gene Sharpr-MPRA regulatory region 15531 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16777326-16777893 Neighboring gene NANOG hESC enhancer GRCh37_chr4:16819631-16820182 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:16822893-16823118 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:16870067-16870626 Neighboring gene uncharacterized LOC107986188 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16909825-16910366 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16910367-16910908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15309 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16920031-16920848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:16943010-16943510 Neighboring gene NANOG hESC enhancer GRCh37_chr4:16979388-16979889 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:16996053-16996798 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16996799-16997544 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16998595-16999416 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:16999417-17000236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:17002080-17002991 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:17004513-17005034 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:17005035-17005556 Neighboring gene NANOG hESC enhancer GRCh37_chr4:17008075-17008615 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:17028696-17029895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:17032946-17033488 Neighboring gene uncharacterized LOC105374507 Neighboring gene MT-ND5 pseudogene 4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_077514.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    16942206..16942500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    16923807..16924101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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