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LOC121967045 Sharpr-MPRA regulatory region 10763 [ Homo sapiens (human) ]

Gene ID: 121967045, updated on 12-Sep-2024

Summary

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Gene symbol
LOC121967045
Gene description
Sharpr-MPRA regulatory region 10763
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121967045 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1680310..1680604)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (1114750..1115044)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1611749..1612043)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene cyclin dependent kinase 11B Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1590308-1591030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 30 Neighboring gene solute carrier family 35 member E2B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1601211-1601711 Neighboring gene ribosomal protein S7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 31 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:1618619-1618776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1619919-1620419 Neighboring gene Sharpr-MPRA regulatory region 15043 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 88 Neighboring gene matrix metallopeptidase 23A (pseudogene) Neighboring gene cyclin dependent kinase 11A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 32

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_076185.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    1680310..1680604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    1114750..1115044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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