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LOC125177405 Sharpr-MPRA regulatory region 13179 [ Homo sapiens (human) ]

Gene ID: 125177405, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125177405
Gene description
Sharpr-MPRA regulatory region 13179
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177405 in Genome Data Viewer
Location:
17p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1803655..1803949)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1692383..1692678)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1706949..1707243)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1655564-1656124 Neighboring gene serpin family F member 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1665693-1666545 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1666546-1667398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11457 Neighboring gene serpin family F member 1 Neighboring gene Sharpr-MPRA regulatory region 4981 Neighboring gene SET and MYND domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1734195-1734695 Neighboring gene replication protein A1 Neighboring gene SDHC pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810454-1810962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810963-1811470 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1825407-1825589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1834946-1835511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1835512-1836076 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1846458-1846649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1849416-1849974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851145-1851648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851649-1852150 Neighboring gene reticulon 4 receptor like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1866080-1866746 Neighboring gene MPRA-validated peak2677 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr17:1879245-1879860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1885529-1886370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1886371-1887212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1889733-1890236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1890237-1890738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1894981-1895842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1895843-1896703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1903279-1903789 Neighboring gene uncharacterized LOC105371486 Neighboring gene uncharacterized LOC105371485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11461

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_080462.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    1803655..1803949
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1692383..1692678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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