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LOC113839557 Sharpr-MPRA regulatory region 12362 [ Homo sapiens (human) ]

Gene ID: 113839557, updated on 17-Sep-2024

Summary

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Gene symbol
LOC113839557
Gene description
Sharpr-MPRA regulatory region 12362
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 3:PromF, promoter flanking) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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See LOC113839557 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (70438573..70438867)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (82605370..82605664)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (73053489..73053783)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72888582-72889082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:72889083-72889583 Neighboring gene structural maintenance of chromosomes 5 Neighboring gene uncharacterized LOC124900273 Neighboring gene KLF9-II enhancer Neighboring gene ReSE screen-validated silencer GRCh37_chr9:73027338-73027530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:73028054-73028907 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:73033721-73034442 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19943 Neighboring gene uncharacterized LOC105376079 Neighboring gene KLF9-I enhancer Neighboring gene KLF9 divergent transcript Neighboring gene MPRA-validated peak7263 silencer Neighboring gene KLF transcription factor 9 Neighboring gene RNA, 7SL, cytoplasmic 726, pseudogene Neighboring gene transient receptor potential cation channel subfamily M member 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

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_063166.1 

    Range
    101..395
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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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    70438573..70438867
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    82605370..82605664
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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