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LOC113839548 Sharpr-MPRA regulatory region 11996 [ Homo sapiens (human) ]

Gene ID: 113839548, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839548
Gene description
Sharpr-MPRA regulatory region 11996
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 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 4:PromP). 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:
9p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37027538..37027997)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37051255..37051714)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37027669..37027963)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene paired box 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36900581-36901081 Neighboring gene microRNA 4476 Neighboring gene MTA1-activated intronic PAX5 enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36947656-36948180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36961379-36962370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36962371-36963361 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36980425-36980924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:36986501-36987456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36996149-36996649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36997151-36997666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:36997667-36998181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28368 Neighboring gene uncharacterized LOC105376032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28371 Neighboring gene uncharacterized LOC105376031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37028766-37029440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28373 Neighboring gene PAX5 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37037999-37038576 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:37053864-37054416 Neighboring gene ribosomal protein L32 pseudogene 21 Neighboring gene MPRA-validated peak7233 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28377 Neighboring gene endogenous Bornavirus like nucleoprotein 3, 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
  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 19900

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_063160.2 

    Range
    101..560
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    37027538..37027997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    37051255..37051714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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