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LOC121725097 Sharpr-MPRA regulatory regions 4995 and 13004 [ Homo sapiens (human) ]

Gene ID: 121725097, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725097
Gene description
Sharpr-MPRA regulatory regions 4995 and 13004
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. One subregion was validated as a functional enhancer 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 Activating non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved), and the same subregion also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). Another subregion displayed repressive activity by Sharpr-MPRA in both HepG2 cells (group: HepG2 Repressive non-DNase unmatched - State 4:PromP) and K562 cells (group: K562 Repressive DNase matched - State 8:EnhW). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC121725097 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (74552762..74553336)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (74561328..74561902)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (74779889..74780463)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74756279-74757161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16075 Neighboring gene DEAQ-box RNA dependent ATPase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:74763605-74764106 Neighboring gene AUP1 lipid droplet regulating VLDL assembly factor Neighboring gene HtrA serine peptidase 2 Neighboring gene lysyl oxidase like 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:74781947-74782464 Neighboring gene docking protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16079 Neighboring gene meiosis 1 associated protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16081 Neighboring gene TOR1B pseudogene 1 Neighboring gene TVP23B pseudogene 2

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)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 13004
  • Sharpr-MPRA regulatory region 4995

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_075566.2 

    Range
    101..675
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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
    74552762..74553336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    74561328..74561902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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