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LOC113839547 Sharpr-MPRA regulatory region 8519 [ Homo sapiens (human) ]

Gene ID: 113839547, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839547
Gene description
Sharpr-MPRA regulatory region 8519
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 the Sharpr-MPRA technique (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 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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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 (34992452..34992746)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (35011634..35011928)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (34992449..34992743)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene PHD finger protein 24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34926275-34926796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34926797-34927317 Neighboring gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34989927-34990856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34990857-34991786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34992717-34993646 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:34994577-34995506 Neighboring gene DNAJB5 divergent transcript Neighboring gene SPATA31 subfamily D member 1 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:35003321-35003821 Neighboring gene DnaJ heat shock protein family (Hsp40) member B5 Neighboring gene SYF2 pre-mRNA splicing factor pseudogene 2

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

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)

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_063158.1 

    Range
    101..395
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    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
    34992452..34992746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    35011634..35011928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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