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LOC122152339 Sharpr-MPRA regulatory region 15021 [ Homo sapiens (human) ]

Gene ID: 122152339, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122152339
Gene description
Sharpr-MPRA regulatory region 15021
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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Aug 2021]
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Genomic context

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See LOC122152339 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (233242923..233243217)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (232629272..232629566)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (233378669..233378963)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2733 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:233059320-233060519 Neighboring gene uncharacterized LOC107985361 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233086091-233086632 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233086633-233087172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233088301-233088800 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:233113500-233114699 Neighboring gene nucleoside-triphosphatase, cancer-related Neighboring gene pecanex 2 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:233215157-233215658 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:233215659-233216158 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:233250348-233251547 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:233264306-233264818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:233264819-233265329 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:233314891-233316090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233370205-233370728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233370729-233371250 Neighboring gene MPRA-validated peak771 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:233393606-233394805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2740 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233421783-233422284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:233422285-233422784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1960 Neighboring gene ribosomal protein S7 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:233463573-233463724 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1962 Neighboring gene mitogen-activated protein kinase kinase kinase 21 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:233507364-233507864

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_076605.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    233242923..233243217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    232629272..232629566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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