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LOC125446248 Sharpr-MPRA regulatory region 1538 [ Homo sapiens (human) ]

Gene ID: 125446248, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125446248
Gene description
Sharpr-MPRA regulatory region 1538
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 non-DNase unmatched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125446248 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (42396823..42397117)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42877826..42878120)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42761307-42762149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42763534-42764468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19161 Neighboring gene Sharpr-MPRA regulatory region 6115 Neighboring gene uncharacterized LOC124905126 Neighboring gene long intergenic non-protein coding RNA 1315 Neighboring gene NFAT activating protein with ITAM motif 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42821196-42821779 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42834221-42834722 Neighboring gene uncharacterized LOC101927344 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42836600-42837599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42840373-42841139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19167 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:42894685-42895205 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:42895291-42895792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13826 Neighboring gene uncharacterized LOC101927372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42900600-42901233 Neighboring gene serine hydrolase like (pseudogene)

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_081183.1 

    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
    42396823..42397117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    42877826..42878120
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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