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LOC112163535 Sharpr-MPRA regulatory region 5794 [ Homo sapiens (human) ]

Gene ID: 112163535, updated on 17-Sep-2024

Summary

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Gene symbol
LOC112163535
Gene description
Sharpr-MPRA regulatory region 5794
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 HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Mar 2018]
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Genomic context

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See LOC112163535 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (123907842..123908136)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (123906968..123907262)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (124392389..124392683)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370042 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:124206184-124206364 Neighboring gene ATPase H+ transporting V0 subunit a2 Neighboring gene ribosomal protein L27 pseudogene 12 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124232793-124233992 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5050 Neighboring gene uncharacterized LOC105370044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7275 Neighboring gene dynein axonemal heavy chain 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124383373-124383873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:124401655-124402156 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:124402328-124403527 Neighboring gene uncharacterized LOC124903043 Neighboring gene dynein axonemal heavy chain 10 opposite strand

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_056560.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    123907842..123908136
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187590.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    81334..81628
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    123906968..123907262
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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