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LOC122847311 Sharpr-MPRA regulatory region 15130 [ Homo sapiens (human) ]

Gene ID: 122847311, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122847311
Gene description
Sharpr-MPRA regulatory region 15130
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (170006979..170007273)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (170484456..170484750)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (170863489..170863783)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:170655164-170655664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12086 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:170681961-170682164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:170685725-170686226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:170686227-170686726 Neighboring gene small RNA binding exonuclease protection factor La Neighboring gene small nucleolar RNA, C/D box 3K Neighboring gene methyltransferase 5, N6-adenosine Neighboring gene ReSE screen-validated silencer GRCh37_chr2:170696663-170696887 Neighboring gene ubiquitin protein ligase E3 component n-recognin 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:170809766-170810965 Neighboring gene VISTA enhancer hs1867 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:170934286-170935065 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:170947905-170948472 Neighboring gene NSA2 pseudogene 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:170962392-170962892 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:170962893-170963393 Neighboring gene RNA, U6 small nuclear 1006, pseudogene

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_077046.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    170006979..170007273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    170484456..170484750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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