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LOC122149310 Sharpr-MPRA regulatory region 15603 [ Homo sapiens (human) ]

Gene ID: 122149310, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122149310
Gene description
Sharpr-MPRA regulatory region 15603
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122149310 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 (175152053..175152347)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (174505796..174506090)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (175121189..175121483)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:175013231-175013766 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:175023596-175024795 Neighboring gene ENTR1 pseudogene 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:175036290-175037489 Neighboring gene MPRA-validated peak471 silencer Neighboring gene tenascin N Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:175098412-175099320 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:175099321-175100227 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:175123083-175123582 Neighboring gene KIAA0040 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2132 Neighboring gene Sharpr-MPRA regulatory region 6447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2134 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:175238074-175239273 Neighboring gene uncharacterized LOC105371623 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1567 Neighboring gene ribosomal protein S29 pseudogene 4

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_076502.1 

    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
    175152053..175152347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    174505796..174506090
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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