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LOC125078028 Sharpr-MPRA regulatory region 15213 [ Homo sapiens (human) ]

Gene ID: 125078028, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078028
Gene description
Sharpr-MPRA regulatory region 15213
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 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (93008444..93008738)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (87240434..87240728)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93403665-93404166 Neighboring gene chromogranin A Neighboring gene uncharacterized LOC124903366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93418215-93418715 Neighboring gene inositol-tetrakisphosphate 1-kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93428049-93428613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93439689-93440278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93440279-93440866 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93440867-93441454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93459858-93460540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93465116-93465630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93472927-93473838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93475437-93475938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93477163-93477664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93477665-93478164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93480925-93481426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93481427-93481926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93482386-93482886 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93484819-93485602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93485603-93486386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93500760-93501455 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93506655-93507584 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93511809-93512368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93515290-93515917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93516545-93517172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93522559-93523246 Neighboring gene ITPK1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93543288-93543801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93544610-93545178 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93550988-93551611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93554107-93554728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:93558517-93559024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93564664-93565656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:93604409-93604908 Neighboring gene cytochrome b5 type A pseudogene 3

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

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_080164.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    93008444..93008738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187601.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    123006..123300
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    87240434..87240728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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