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LOC122149323 Sharpr-MPRA regulatory region 7016 [ Homo sapiens (human) ]

Gene ID: 122149323, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122149323
Gene description
Sharpr-MPRA regulatory region 7016
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 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122149323 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (183230494..183230788)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (182589833..182590127)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (183199629..183199923)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 41, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:182990015-182990514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:182991252-182991807 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:182991808-182992362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1625 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:182992918-182993471 Neighboring gene MPRA-validated peak499 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1627 Neighboring gene laminin subunit gamma 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2210 Neighboring gene Sharpr-MPRA regulatory region 7713 Neighboring gene LAMC1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:183128249-183128750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2211 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:183154769-183155968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2212 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:183197656-183197861 Neighboring gene Sharpr-MPRA regulatory region 596 Neighboring gene laminin subunit gamma 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:183247773-183248584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:183248585-183249395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2213 Neighboring gene nicotinamide nucleotide adenylyltransferase 2 Neighboring gene RPS3A pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183271685-183272658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183272659-183273632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:183300194-183300759 Neighboring gene Sharpr-MPRA regulatory region 8277 Neighboring gene uncharacterized LOC105371646 Neighboring gene MPRA-validated peak501 silencer Neighboring gene SMG7 antisense RNA 1

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_076515.1 

    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
    183230494..183230788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    182589833..182590127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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