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LOC121627932 Sharpr-MPRA regulatory region 14215 [ Homo sapiens (human) ]

Gene ID: 121627932, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627932
Gene description
Sharpr-MPRA regulatory region 14215
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). This locus also includes an accessible chromatin subregion that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (21816660..21816954)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (22230140..22230434)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (22170949..22171243)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22077940-22078170 Neighboring gene yippee like 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22084296-22084483 Neighboring gene RNA, 7SL, cytoplasmic 280, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13514 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18707 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22112788-22113234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18710 Neighboring gene mitogen-activated protein kinase 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22144051-22144194 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:22145734-22146933 Neighboring gene MPRA-validated peak4466 silencer Neighboring gene RNA, 5S ribosomal pseudogene 493 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22165820-22166034 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22192349-22192556 Neighboring gene MPRA-validated peak4467 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:22210131-22210632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13517 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:22237113-22237874 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63076 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:22254563-22254749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22271290-22272100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22274276-22274935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22275597-22276255 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22292226-22293032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22293033-22293840 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22293841-22294647 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:22298307-22298806 Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1F Neighboring gene PPM1F antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18712 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:22306489-22307009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13519 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:22318681-22319182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:22319183-22319682 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63111 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:22336585-22337571 Neighboring gene DNA topoisomerase III beta

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid silent region 13516

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_075123.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    21816660..21816954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    22230140..22230434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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