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LOC124153151 Sharpr-MPRA regulatory region 279 [ Homo sapiens (human) ]

Gene ID: 124153151, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124153151
Gene description
Sharpr-MPRA regulatory region 279
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 K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Feb 2022]
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Genomic context

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Location:
8p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (39032210..39032504)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (39309351..39309645)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38889729..38890023)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38853156-38853678 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38853679-38854200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27275 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27277 Neighboring gene TM2 domain containing 2 Neighboring gene ADAM metallopeptidase domain 9 Neighboring gene small nucleolar RNA, C/D box 38D Neighboring gene ADAM metallopeptidase domain 32 Neighboring gene ribosomal protein L3 pseudogene 10 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:39038237-39039436 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:39084432-39085631 Neighboring gene lysine acetyltransferase 2B pseudogene

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_078539.1 

    Range
    101..395
    Download
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    39032210..39032504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    39309351..39309645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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