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LOC113839558 Sharpr-MPRA regulatory region 9116 [ Homo sapiens (human) ]

Gene ID: 113839558, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113839558
Gene description
Sharpr-MPRA regulatory region 9116
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 K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (72477053..72477347)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (84627889..84628183)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (75091969..75092263)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene hESC enhancers GRCh37_chr9:74979127-74979830 and GRCh37_chr9:74979831-74980535 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19949 Neighboring gene zinc finger AN1-type containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28458 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:75069728-75070499 Neighboring gene ribosomal protein S12 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28459 Neighboring gene uncharacterized LOC105376080 Neighboring gene uncharacterized LOC101927234 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:75139667-75140228 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:75140229-75140790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28460 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28461 Neighboring gene transmembrane channel like 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

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_063167.1 

    Range
    101..395
    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
    72477053..72477347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    84627889..84628183
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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