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LOC122819156 Sharpr-MPRA regulatory region 5769 [ Homo sapiens (human) ]

Gene ID: 122819156, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122819156
Gene description
Sharpr-MPRA regulatory region 5769
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122819156 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 (134206618..134206912)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (134646142..134646436)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (134964189..134964483)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16543 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:134821977-134822608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16544 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:134864951-134865484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134866541-134867202 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134867203-134867862 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11971 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134891163-134891785 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:134891786-134892407 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16545 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134915432-134916037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134916038-134916642 Neighboring gene microRNA 3679 Neighboring gene alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16546 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_52692 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134960700-134961201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16547 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 16551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16550 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 epididymal protein 3C, 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_077016.1 

    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
    134206618..134206912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    134646142..134646436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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