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LOC122056768 Sharpr-MPRA regulatory region 10909 [ Homo sapiens (human) ]

Gene ID: 122056768, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056768
Gene description
Sharpr-MPRA regulatory region 10909
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (14996093..14996387)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (14440041..14440335)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (15322589..15322883)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kazrin, periplakin interacting protein Neighboring gene uncharacterized LOC107985469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15220320-15221320 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:15233506-15234705 Neighboring gene uncharacterized LOC124903849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15249981-15250480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 293 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:15261293-15261469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15266300-15266801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15270527-15271122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15273767-15274267 Neighboring gene Sharpr-MPRA regulatory region 2794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15294452-15295356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15296544-15297266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15347400-15348061 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15348723-15349384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 294 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 230 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15379812-15380475 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15379147-15379811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15386302-15386802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15386803-15387303 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:15390134-15391333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 295 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15427206-15427915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15438360-15438939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15438940-15439518 Neighboring gene TMEM51 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 296 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:15480425-15481086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:15481087-15481748 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 299 Neighboring gene TMEM51 antisense RNA 2 Neighboring gene transmembrane protein 51

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_076224.1 

    Range
    101..395
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    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
    14996093..14996387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    14440041..14440335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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