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LOC122056814 Sharpr-MPRA regulatory region 2241 [ Homo sapiens (human) ]

Gene ID: 122056814, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056814
Gene description
Sharpr-MPRA regulatory region 2241
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122056814 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (28437258..28437552)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (28279217..28279511)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (28763769..28764063)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28585772-28586620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 537 Neighboring gene sestrin 2 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:28616419-28617413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:28640148-28640648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28655585-28656092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:28656093-28656600 Neighboring gene mediator complex subunit 18 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:28695423-28696378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 538 Neighboring gene phosphatase and actin regulator 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:28726665-28726882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 540 Neighboring gene RNA, U6atac small nuclear 27, pseudogene Neighboring gene Sharpr-MPRA regulatory region 7965 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:28833855-28834620 Neighboring gene small nucleolar RNA, H/ACA box 73A Neighboring gene small nucleolar RNA host gene 3 Neighboring gene regulator of chromosome condensation 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_076270.1 

    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
    28437258..28437552
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    28279217..28279511
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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