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LOC121725105 Sharpr-MPRA regulatory region 13798 [ Homo sapiens (human) ]

Gene ID: 121725105, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121725105
Gene description
Sharpr-MPRA regulatory region 13798
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes two accessible chromatin subregions that were validated as silencers based on their 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:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (157876162..157876681)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (158329236..158329755)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (158732789..158733083)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907898 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:158590437-158591636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:158605968-158606478 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:158606479-158606988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:158608073-158608572 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:158616153-158616973 Neighboring gene activin A receptor type 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:158617891-158618482 Neighboring gene NANOG hESC enhancer GRCh37_chr2:158687547-158688048 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:158694657-158695856 Neighboring gene uncharacterized LOC124907899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12031 Neighboring gene uncharacterized LOC105373714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12034 Neighboring gene RNA, U6 small nuclear 436, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:158789161-158789872 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:158789873-158790582 Neighboring gene MTA3 pseudogene 1

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 12032
  • ATAC-STARR-seq lymphoblastoid silent region 12033

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_075574.2 

    Range
    101..620
    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
    157876162..157876681
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    158329236..158329755
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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