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LOC112081405 Sharpr-MPRA regulatory region 730 [ Homo sapiens (human) ]

Gene ID: 112081405, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112081405
Gene description
Sharpr-MPRA regulatory region 730
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 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Feb 2018]
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Genomic context

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See LOC112081405 in Genome Data Viewer
Location:
11p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (6606959..6607253)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (6665427..6665721)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (6628189..6628483)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene dynein heavy chain domain 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:6589123-6589980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:6592335-6592842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:6607422-6608410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:6608411-6609399 Neighboring gene Sharpr-MPRA regulatory region 2811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:6624079-6624620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4344 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4347 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:6632062-6632650 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:6632651-6633238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3106 Neighboring gene ribosomal RNA processing 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4350 Neighboring gene TATA-box binding protein associated factor 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4351 Neighboring gene integrin linked kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4352 Neighboring gene tripeptidyl peptidase 1 Neighboring gene dachsous cadherin-related 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:6662561-6663130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:6668387-6668887

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_056466.1 

    Range
    101..395
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    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    6606959..6607253
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    6665427..6665721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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