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LOC112694706 Sharpr-MPRA regulatory region 12013 [ Homo sapiens (human) ]

Gene ID: 112694706, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112694706
Gene description
Sharpr-MPRA regulatory region 12013
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. A subregion 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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or 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:
20q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (33811023..33811476)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (35537380..35537833)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (32398829..32399282)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:32321171-32321874 Neighboring gene zinc finger protein 341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32349191-32349692 Neighboring gene ribosomal protein L31 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17746 Neighboring gene Sharpr-MPRA regulatory region 4652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12823 Neighboring gene Sharpr-MPRA regulatory region 14745 Neighboring gene ZNF341 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32399709-32400549 Neighboring gene charged multivesicular body protein 4B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32441073-32441573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12826 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:32450578-32450741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32458568-32459068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:32495633-32496134 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:32507904-32508103 Neighboring gene tropomyosin 3 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:32521004-32521504 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class P pseudogene 3

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 within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. 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 active region 17747
  • ATAC-STARR-seq lymphoblastoid silent region 12824

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_060736.2 

    Range
    101..554
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    33811023..33811476
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    35537380..35537833
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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