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LOC121967050 Sharpr-MPRA regulatory region 11692 [ Homo sapiens (human) ]

Gene ID: 121967050, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121967050
Gene description
Sharpr-MPRA regulatory region 11692
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121967050 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (2629270..2629564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2070921..2071215)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2560709..2561003)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100996583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2498904-2499776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2508969-2509605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2519024-2519656 Neighboring gene peroxiredoxin like 2B Neighboring gene membrane metalloendopeptidase like 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:2556762-2557011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:2562185-2562685 Neighboring gene MPRA-validated peak16 silencer Neighboring gene MMEL1 antisense RNA 1 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2586483-2586987 Neighboring gene Sharpr-MPRA regulatory region 15700 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2587878-2588769 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2588891-2589402 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2589915-2590426 Neighboring gene tetratricopeptide repeat domain 34 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2597430-2597930 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2597931-2598431 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2600600-2601101 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2601784-2602520 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2603256-2603991 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2607057-2607636 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:2607637-2608216 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2609432-2609933 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2610686-2611577 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2613783-2614607 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:2628928-2629429 Neighboring gene uncharacterized LOC105378602 Neighboring gene uncharacterized LOC105378601

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_076190.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    2629270..2629564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2070921..2071215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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