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LOC124849301 Sharpr-MPRA regulatory region 3220 [ Homo sapiens (human) ]

Gene ID: 124849301, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124849301
Gene description
Sharpr-MPRA regulatory region 3220
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124849301 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (26200612..26200906)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (25414418..25414712)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 415 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:26650935-26651149 Neighboring gene NANOG hESC enhancer GRCh37_chr13:26673008-26673509 Neighboring gene ATPase phospholipid transporting 8A2 pseudogene 3 Neighboring gene PRUNE1 pseudogene 1 Neighboring gene ring finger protein 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7491 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:26795223-26796104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:26796105-26796986 Neighboring gene THAP domain containing 12 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5186 Neighboring gene cyclin dependent kinase 8 Neighboring gene NANOG hESC enhancer GRCh37_chr13:26953049-26953564

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_079876.1 

    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
    26200612..26200906
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    25414418..25414712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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