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LOC125446254 Sharpr-MPRA regulatory region 15411 [ Homo sapiens (human) ]

Gene ID: 125446254, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446254
Gene description
Sharpr-MPRA regulatory region 15411
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 K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jun 2022]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (43231243..43231537)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (43712137..43712431)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43564214-43565070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43565071-43565926 Neighboring gene tubulin tyrosine ligase like 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43581791-43582295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13859 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43593145-43594077 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:43594078-43595009 Neighboring gene signal peptide, CUB domain and EGF like domain containing 1 Neighboring gene SCUBE1 antisense RNA 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43616253-43616754 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43621086-43621251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43621872-43622438 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43622439-43623004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43634226-43634726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43634727-43635227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:43643537-43644038 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:43647561-43647749 Neighboring gene uncharacterized LOC124905129 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:43659412-43660611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43664742-43665530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43665531-43666317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43673726-43674226 Neighboring gene SCUBE1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:43678267-43678767

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_081187.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    43231243..43231537
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    43712137..43712431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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