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LOC123493327 Sharpr-MPRA regulatory region 14150 [ Homo sapiens (human) ]

Gene ID: 123493327, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123493327
Gene description
Sharpr-MPRA regulatory region 14150
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC123493327 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (67015021..67015315)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (67837126..67837420)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (66310849..66311143)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16067 Neighboring gene peptidylprolyl isomerase A pseudogene 78 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22621 Neighboring gene microtubule associated serine/threonine kinase family member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22622 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:66075742-66076941 Neighboring gene NANOG hESC enhancer GRCh37_chr5:66125559-66126060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16068 Neighboring gene NANOG hESC enhancer GRCh37_chr5:66137580-66138081 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:66145039-66146238 Neighboring gene Sharpr-MPRA regulatory region 1390 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66199778-66200630 Neighboring gene Sharpr-MPRA regulatory region 14441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16069 Neighboring gene MAST4 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66354795-66355337 Neighboring gene Sharpr-MPRA regulatory region 2367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:66462629-66463134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22624 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:66501978-66503177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22625 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:66515108-66515295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22626 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:66528881-66529430 Neighboring gene CD180 molecule Neighboring gene TCL1A interacting lncRNA, retroperitoneal liposarcoma associated

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_077751.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    67015021..67015315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    67837126..67837420
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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