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LOC112272566 Sharpr-MPRA regulatory region 5900 [ Homo sapiens (human) ]

Gene ID: 112272566, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272566
Gene description
Sharpr-MPRA regulatory region 5900
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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also represents an accessible chromatin region 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:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (90396721..90397140)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (84621448..84621867)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (90863169..90863463)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, ATPase 1 Neighboring gene NRDE-2, necessary for RNA interference, domain containing Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:90757747-90758946 Neighboring gene Sharpr-MPRA regulatory region 379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90792221-90792722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90792723-90793222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6006 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:90819601-90819793 Neighboring gene uncharacterized LOC105370618 Neighboring gene ribosomal protein L21 pseudogene 11 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:90848618-90849145 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:90849146-90849672 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:90849673-90850199 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8879 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6010 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8881 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:90870785-90871984 Neighboring gene calmodulin 1 Neighboring gene MPRA-validated peak2228 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90905675-90906438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8882 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr14:90920205-90920822 and GRCh37_chr14:90920823-90921440 Neighboring gene long intergenic non-protein coding RNA 2317 Neighboring gene long intergenic non-protein coding RNA 642

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 6007

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_056700.2 

    Range
    101..520
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    90396721..90397140
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    84621448..84621867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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