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LOC122149359 Sharpr-MPRA regulatory region 10950 [ Homo sapiens (human) ]

Gene ID: 122149359, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122149359
Gene description
Sharpr-MPRA regulatory region 10950
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:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (206680264..206680558)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (205944444..205944738)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (206853609..206853903)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Ras association domain family member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:206761431-206761931 Neighboring gene eukaryotic translation initiation factor 2D Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:206775241-206776440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1760 Neighboring gene DYRK3 antisense RNA 1 Neighboring gene dual specificity tyrosine phosphorylation regulated kinase 3 Neighboring gene uncharacterized LOC124904496 Neighboring gene uncharacterized LOC124904495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1762 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1763 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1764 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:206860855-206861416 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:206861417-206861978 Neighboring gene MAPK activated protein kinase 2 Neighboring gene ribosomal protein S14 pseudogene 1

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_076551.1 

    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
    206680264..206680558
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    205944444..205944738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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