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LOC112272581 Sharpr-MPRA regulatory region 3573 [ Homo sapiens (human) ]

Gene ID: 112272581, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112272581
Gene description
Sharpr-MPRA regulatory region 3573
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 matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 12:CtcfO). [provided by RefSeq, Mar 2018]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (29613965..29614259)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (27404675..27404969)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (29906169..29906463)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene endosomal transmembrane epsin interactor 2 Neighboring gene DDB1 and CUL4 associated factor 6 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:29561321-29561822 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:29561823-29562322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9166 Neighboring gene NSE3 homolog, SMC5-SMC6 complex component Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:29611925-29612479 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:29637062-29638044 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:29699994-29700185 Neighboring gene MPRA-validated peak2283 silencer Neighboring gene Sharpr-MPRA regulatory region 8593 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr15:29903026-29903716 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr15:29903717-29904407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:29924029-29924548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:29943839-29944339 Neighboring gene tubulin beta class I pseudogene 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:29967552-29968082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:29968083-29968613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:29970293-29970793 Neighboring gene uncharacterized LOC105370743 Neighboring gene lung cancer immune cell infiltration associated lncRNA

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_056718.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    29613965..29614259
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    1785602..1785896
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1898086..1898380
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    27404675..27404969
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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