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LOC124418420 Sharpr-MPRA regulatory region 12872 [ Homo sapiens (human) ]

Gene ID: 124418420, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124418420
Gene description
Sharpr-MPRA regulatory region 12872
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 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (3958979..3959273)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (4024250..4024544)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (3980209..3980503)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4315 Neighboring gene Sharpr-MPRA regulatory region 4669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3093 Neighboring gene microRNA 4687 Neighboring gene stromal interaction molecule 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4317 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:3915212-3915428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4318 Neighboring gene Sharpr-MPRA regulatory region 4967 Neighboring gene peptidylprolyl isomerase A pseudogene 40 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4319 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 76 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 21

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_079165.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    3958979..3959273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    4024250..4024544
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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