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LOC114004380 Sharpr-MPRA regulatory region 13251 [ Homo sapiens (human) ]

Gene ID: 114004380, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004380
Gene description
Sharpr-MPRA regulatory region 13251
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 10:DNaseD). [provided by RefSeq, Jan 2019]
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Genomic context

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Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (54188182..54188476)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (54222074..54222356)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (54222209..54222503)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909381 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54121379-54121902 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54121903-54122425 Neighboring gene calcium binding tyrosine phosphorylation regulated pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14470 Neighboring gene calcium voltage-gated channel auxiliary subunit alpha2delta 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54237261-54237762 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54246728-54247322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54250734-54251234 Neighboring gene NANOG hESC enhancer GRCh37_chr3:54262808-54263341 Neighboring gene uncharacterized LOC124909382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54319420-54319921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54497979-54498480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54498481-54498980 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:54520692-54520885 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54551370-54551870 Neighboring gene uncharacterized LOC107986088 Neighboring gene ribosomal protein S15 pseudogene 5

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_063800.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    54188182..54188476
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    54222074..54222356
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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