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LOC122819161 Sharpr-MPRA regulatory region 1885 [ Homo sapiens (human) ]

Gene ID: 122819161, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819161
Gene description
Sharpr-MPRA regulatory region 1885
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (137190899..137191193)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (137636862..137637156)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (137948469..137948763)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:137165304-137165804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:137165805-137166305 Neighboring gene RN7SK pseudogene 141 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:137240685-137240943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16591 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:137267551-137268375 Neighboring gene NANOG hESC enhancer GRCh37_chr2:137275190-137275696 Neighboring gene MPRA-validated peak3883 silencer Neighboring gene uncharacterized LOC105373633 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:137303752-137303922 Neighboring gene structural maintenance of chromosomes 4 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:137523097-137523598 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:137605714-137605949 Neighboring gene thrombospondin type 1 domain containing 7B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:138072328-138072828 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:138155943-138156474 Neighboring gene uncharacterized LOC105373634 Neighboring gene RNA, 5S ribosomal pseudogene 105

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_077021.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    137190899..137191193
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    137636862..137637156
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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