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LOC122710286 Sharpr-MPRA regulatory region 1386 [ Homo sapiens (human) ]

Gene ID: 122710286, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122710286
Gene description
Sharpr-MPRA regulatory region 1386
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Sep 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (1283137..1283431)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (1286364..1286658)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (1286909..1287203)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:954785-955304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:955305-955822 Neighboring gene SNTG2 antisense RNA 1 Neighboring gene syntrophin gamma 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1073673-1074189 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1086561-1087062 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:1104105-1105304 Neighboring gene uncharacterized LOC124905965 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:1260844-1260999 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:1265169-1266368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1309663-1310386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1310387-1311109 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:1312058-1312678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1312679-1313298 Neighboring gene uncharacterized LOC105373359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1370519-1371072 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:1391744-1392312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1407339-1407839 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:1421072-1422271 Neighboring gene thyroid peroxidase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1451513-1452123 Neighboring gene uncharacterized LOC124905966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1492359-1492916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:1492917-1493474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1499759-1500394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:1519727-1520228 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:1544276-1545475

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_076856.1 

    Range
    101..395
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    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    1283137..1283431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    1286364..1286658
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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