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LOC122757966 Sharpr-MPRA regulatory region 1834 [ Homo sapiens (human) ]

Gene ID: 122757966, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122757966
Gene description
Sharpr-MPRA regulatory region 1834
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 22:ReprW, weaker Polycomb repression). [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 (69961517..69961811)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (69973241..69973535)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (70188649..70188943)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11602 Neighboring gene Sharpr-MPRA regulatory region 10436 Neighboring gene MAX dimerization protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70164441-70164976 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:70173615-70174814 Neighboring gene aspartic peptidase retroviral like 1 Neighboring gene small nucleolar RNA U13 Neighboring gene PCBP1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70199285-70200162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70202867-70203378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70203379-70203889 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70211622-70212122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70212123-70212623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:70220299-70220798 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:70224580-70224834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15983 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:70256223-70257094 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15984 Neighboring gene Sharpr-MPRA regulatory region 12254 Neighboring gene RNA, 7SL, cytoplasmic 470, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11604 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:70315031-70315675 Neighboring gene conserved acetylation island sequence C15 enhancer Neighboring gene poly(rC) binding protein 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_076958.1 

    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
    69961517..69961811
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    69973241..69973535
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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