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LOC122757939 Sharpr-MPRA regulatory region 9679 [ Homo sapiens (human) ]

Gene ID: 122757939, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757939
Gene description
Sharpr-MPRA regulatory region 9679
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Sep 2021]
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Genomic context

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See LOC122757939 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (47869890..47870184)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (47875834..47876128)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (48097029..48097323)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374589 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48008525-48008706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11469 Neighboring gene mutS homolog 6 Neighboring gene ribosomal protein L36a pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15742 Neighboring gene F-box protein 11 Neighboring gene RPS27A pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:48129098-48129367 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48131440-48132226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11471 Neighboring gene uncharacterized LOC100506235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11473 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:48133799-48134583

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_076931.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    47869890..47870184
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    47875834..47876128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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