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LOC123881326 Sharpr-MPRA regulatory region 8239 [ Homo sapiens (human) ]

Gene ID: 123881326, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123881326
Gene description
Sharpr-MPRA regulatory region 8239
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123881326 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (148347713..148348007)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (149543969..149544266)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (148668849..148669143)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901423 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:148467567-148468766 Neighboring gene NANOG hESC enhancer GRCh37_chr6:148495187-148495773 Neighboring gene SAM and SH3 domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148573377-148573878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148573879-148574378 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:148585683-148586236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:148612147-148612648 Neighboring gene RNA, U6 small nuclear 1222, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:148628353-148629039 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:148652682-148653673 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148655656-148656645 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:148662621-148663200 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:148668049-148668557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148669576-148670085 Neighboring gene MPRA-validated peak6206 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148687682-148688558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148688559-148689434 Neighboring gene Sharpr-MPRA regulatory region 6687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148766834-148767334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148773672-148774208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148775249-148775748 Neighboring gene cytochrome P450 family 51 subfamily A member 1 pseudogene 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148834032-148834830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:148834831-148835628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148837963-148838463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148841275-148841814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148854137-148854638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148854639-148855138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17651 Neighboring gene SNRPE pseudogene 6

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_078231.1 

    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
    148347713..148348007
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    149543969..149544266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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