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LOC123493296 Sharpr-MPRA regulatory region 14491 [ Homo sapiens (human) ]

Gene ID: 123493296, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123493296
Gene description
Sharpr-MPRA regulatory region 14491
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 DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493296 in Genome Data Viewer
Location:
5p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (39232007..39232301)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (39481519..39481813)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (39232109..39232403)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RPTOR independent companion of MTOR complex 2 Neighboring gene androgen induced 1 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:39073334-39073860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:39074387-39074913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22495 Neighboring gene Sharpr-MPRA regulatory region 14991 Neighboring gene FYN binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22497 Neighboring gene Sharpr-MPRA regulatory region 12253 Neighboring gene golgin A5 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:39220741-39221242 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:39242438-39242627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22498 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:39283272-39283436 Neighboring gene complement C9 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:39380837-39382036 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:39382313-39383512 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84809 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_84831 Neighboring gene DAB adaptor protein 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)

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_077720.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    39232007..39232301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    39481519..39481813
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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