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LOC122819152 Sharpr-MPRA regulatory region 14953 [ Homo sapiens (human) ]

Gene ID: 122819152, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819152
Gene description
Sharpr-MPRA regulatory region 14953
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122819152 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (128260655..128261417)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (128696603..128697365)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (129018229..129018523)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene 34 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:128994251-128994793 Neighboring gene NANOG hESC enhancer GRCh37_chr2:128999497-129000000 Neighboring gene uncharacterized LOC124907886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129019563-129020132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129020147-129020648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129028169-129028830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129028831-129029492 Neighboring gene heparan sulfate 6-O-sulfotransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129042083-129042912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129045407-129046236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129052695-129053244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129057516-129058114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129058115-129058712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129058713-129059311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16511 Neighboring gene Sharpr-MPRA regulatory region 5144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129067670-129068650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129068651-129069632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129080477-129081409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129102864-129103364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129119009-129119548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129119549-129120087 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129120088-129120626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129124244-129124934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129125695-129126536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:129132078-129132952 Neighboring gene uncharacterized LOC105373610

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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

General gene information

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Other Names

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:129018421-129018991

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_077012.2 

    Range
    101..863
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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
    128260655..128261417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    128696603..128697365
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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