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LOC122861275 Sharpr-MPRA regulatory region 7560 [ Homo sapiens (human) ]

Gene ID: 122861275, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861275
Gene description
Sharpr-MPRA regulatory region 7560
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122861275 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (198309705..198309999)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (198793456..198793750)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (199174429..199174723)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12217 Neighboring gene PLCL1 intron CAGE-defined T cell enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:198737772-198738272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16948 Neighboring gene Sharpr-MPRA regulatory region 13904 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:198773623-198774822 Neighboring gene Sharpr-MPRA regulatory region 14302 Neighboring gene phospholipase C like 1 (inactive) Neighboring gene ReSE screen-validated silencer GRCh37_chr2:198803213-198803426 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12218 Neighboring gene long intergenic non-protein coding RNA 1923 Neighboring gene uncharacterized LOC105373831 Neighboring gene uncharacterized LOC105373830 Neighboring gene MIA SH3 domain ER export factor 2 pseudogene

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_077091.1 

    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
    198309705..198309999
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    198793456..198793750
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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