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LOC122819157 Sharpr-MPRA regulatory region 6492 [ Homo sapiens (human) ]

Gene ID: 122819157, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819157
Gene description
Sharpr-MPRA regulatory region 6492
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [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 (134432238..134432532)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (134871816..134872110)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135189809..135190103)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135002234-135002734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135002735-135003235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16551 Neighboring gene RNA, 5S ribosomal pseudogene 104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16561 Neighboring gene epididymal protein 3C, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:135129934-135130438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135201292-135201792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135217811-135218312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135218313-135218812 Neighboring gene Sharpr-MPRA regulatory region 15464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135240067-135240597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135240598-135241127 Neighboring gene uncharacterized LOC124906076 Neighboring gene transmembrane protein 163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135293574-135294074 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:135318760-135318939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16563 Neighboring gene MPRA-validated peak3868 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11977 Neighboring gene uncharacterized LOC105373629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11978 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:135478596-135479795

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_077017.1 

    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
    134432238..134432532
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    134871816..134872110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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