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LOC121048716 Sharpr-MPRA regulatory region 3462 [ Homo sapiens (human) ]

Gene ID: 121048716, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121048716
Gene description
Sharpr-MPRA regulatory region 3462
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2021]
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Genomic context

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See LOC121048716 in Genome Data Viewer
Location:
3q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (142929167..142929461)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (145676410..145676704)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (142648009..142648303)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene procollagen C-endopeptidase enhancer 2 Neighboring gene ribosomal protein L8 pseudogene 3 Neighboring gene uncharacterized LOC124909443 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14791 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:142635932-142636110 Neighboring gene hepatic lncRNA metabolic regulator 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:142677150-142678349 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:142681545-142681730 Neighboring gene progestin and adipoQ receptor family member 9 Neighboring gene PAQR9 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:142717850-142718850 Neighboring gene uncharacterized LOC100289361 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:142719850-142720849

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_074086.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    142929167..142929461
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    145676410..145676704
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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