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LOC112340379 Sharpr-MPRA regulatory region 1380 [ Homo sapiens (human) ]

Gene ID: 112340379, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112340379
Gene description
Sharpr-MPRA regulatory region 1380
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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2018]
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Genomic context

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Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (15502292..15502586)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (15507086..15507380)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (15596149..15596443)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene nuclear pore complex interacting protein family member A5 Neighboring gene MPV17L-BMERB1 readthrough Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15506027-15506244 Neighboring gene MPV17 mitochondrial inner membrane protein like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15528749-15529371 Neighboring gene bMERB domain containing 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15587399-15588598 Neighboring gene uncharacterized LOC105371102 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15603978-15604478 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:15607777-15607948 Neighboring gene NANOG hESC enhancer GRCh37_chr16:15632973-15633474 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:15636050-15636595 Neighboring gene Sharpr-MPRA regulatory region 9672 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:15673003-15673503 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:15680941-15681442 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:15684383-15685582 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:15693082-15694281 Neighboring gene Sharpr-MPRA regulatory region 10508 Neighboring gene meiosis regulator and mRNA stability factor 1 Neighboring gene microRNA 6506

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_056779.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    15502292..15502586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187607.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1160284..1160578
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    15507086..15507380
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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