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LOC122757954 Sharpr-MPRA regulatory region 1961 [ Homo sapiens (human) ]

Gene ID: 122757954, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757954
Gene description
Sharpr-MPRA regulatory region 1961
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (62730674..62730968)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (62736974..62737257)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (62957809..62958103)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:62804913-62806112 Neighboring gene ribosomal L24 domain containing 1 pseudogene 2 Neighboring gene phosphoserine aminotransferase 1 pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr2:62874108-62874609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:62898481-62898982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11541 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11540 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15870 Neighboring gene EH domain binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:63062886-63063515 Neighboring gene VISTA enhancer hs690 Neighboring gene ribosomal protein S20 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15873 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:63270899-63271878 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:63271879-63272858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:63274968-63275716 Neighboring gene EHBP1 antisense RNA 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_076946.1 

    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
    62730674..62730968
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    62736974..62737257
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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