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LOC114004393 Sharpr-MPRA regulatory region 9536 [ Homo sapiens (human) ]

Gene ID: 114004393, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004393
Gene description
Sharpr-MPRA regulatory region 9536
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 non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Nov 2021]
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Genomic context

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See LOC114004393 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 (36696127..36696421)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (36945951..36946245)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (36696229..36696523)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:36590466-36591251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22479 Neighboring gene ribosomal protein L39 pseudogene 22 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:36619081-36619595 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:36646148-36647347 Neighboring gene solute carrier family 1 member 3 Neighboring gene SLC1A3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22481 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15974 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15976 Neighboring gene NIPBL divergent transcript Neighboring gene keratin 18 pseudogene 31 Neighboring gene NIPBL cohesin loading factor

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_063813.1 

    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
    36696127..36696421
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    36945951..36946245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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