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LOC121838562 Sharpr-MPRA regulatory region 5561 [ Homo sapiens (human) ]

Gene ID: 121838562, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121838562
Gene description
Sharpr-MPRA regulatory region 5561
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121838562 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (101939831..101940125)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (101900936..101901230)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (102333609..102333903)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr12:102270762-102271544 and GRCh37_chr12:102271545-102272326 Neighboring gene DNA damage regulated autophagy modulator 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22782 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:102317122-102318321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6872 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6874 Neighboring gene ribosomal protein L9 pseudogene 24 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6876 Neighboring gene uncharacterized LOC107984548 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22809 Neighboring gene neudesin neurotrophic factor pseudogene 2 Neighboring gene WASH complex subunit 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6878

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_075925.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    101939831..101940125
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    101900936..101901230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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