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LOC124849307 Sharpr-MPRA regulatory region 3331 [ Homo sapiens (human) ]

Gene ID: 124849307, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849307
Gene description
Sharpr-MPRA regulatory region 3331
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 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 9:DNaseU). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (30569892..30570186)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (29792289..29792583)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene high mobility group box 1 Neighboring gene microfibril associated protein 1 pseudogene 1 Neighboring gene PTPN2 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7536 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7539 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7542 Neighboring gene ubiquitin specific peptidase like 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:31233439-31234198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5236 Neighboring gene tRNA-Asn (anticodon GTT) 2-4

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

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_079956.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    30569892..30570186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    29792289..29792583
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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