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LOC113939930 Sharpr-MPRA regulatory region 11085 [ Homo sapiens (human) ]

Gene ID: 113939930, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939930
Gene description
Sharpr-MPRA regulatory region 11085
Gene type
biological region
Feature type(s)
regulatory: silencer
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 repressive element 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 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites), with weaker repression in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2019]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (102824491..102824785)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (102785620..102785914)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (103218269..103218563)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2456 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23056 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:102814900-102816099 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_23075/23079 Neighboring gene insulin like growth factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:102869029-102869530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:102869531-102870030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6885 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:102933234-102934433 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:103115830-103116467 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:103218752-103218929 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:103226259-103226804 Neighboring gene long intergenic non-protein coding RNA 485 Neighboring gene NANOG hESC enhancer GRCh37_chr12:103232984-103233485 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:103244689-103245888 Neighboring gene uncharacterized LOC124902999 Neighboring gene phenylalanine hydroxylase Neighboring gene uncharacterized LOC112267865 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:103343731-103344658

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_063715.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    102824491..102824785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    102785620..102785914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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