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LOC112840917 Sharpr-MPRA regulatory region 4589 [ Homo sapiens (human) ]

Gene ID: 112840917, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112840917
Gene description
Sharpr-MPRA regulatory region 4589
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2018]
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Genomic context

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See LOC112840917 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 (24482700..24482994)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (24517353..24517647)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (24705569..24705863)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene intersectin 2 Neighboring gene ribosomal protein L36a pseudogene 13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11229 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11230 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15432 Neighboring gene Sharpr-MPRA regulatory region 9937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:24623030-24623530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24625230-24625736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:24625737-24626243 Neighboring gene uncharacterized LOC105374329 Neighboring gene NANOG hESC enhancer GRCh37_chr2:24679828-24680425 Neighboring gene CRISPRi-validated cis-regulatory element chr2.904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11232 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:24714093-24714251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11233 Neighboring gene nuclear receptor coactivator 1 Neighboring gene MPRA-validated peak3621 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15433 Neighboring gene RNA, 5S ribosomal pseudogene 88 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15434 Neighboring gene RNA, U6 small nuclear 936, 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_060952.1 

    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
    24482700..24482994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    24517353..24517647
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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