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LOC124418416 Sharpr-MPRA regulatory region 11059 [ Homo sapiens (human) ]

Gene ID: 124418416, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124418416
Gene description
Sharpr-MPRA regulatory region 11059
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124418416 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 (2463139..2463433)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (2552465..2552759)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (2484369..2484663)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2422141-2422641 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2421638-2422140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2435338-2435838 Neighboring gene Sharpr-MPRA regulatory region 9407 Neighboring gene tumor suppressing subtransferable candidate 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3070 Neighboring gene transient receptor potential cation channel subfamily M member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2482166-2482666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4304 Neighboring gene potassium voltage-gated channel subfamily Q member 1 Neighboring gene uncharacterized LOC124902613 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2540941-2541442 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2541443-2541942 Neighboring gene MPRA-validated peak1163 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4305 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:2554792-2554952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:2556786-2557286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2582101-2582884 Neighboring gene Sharpr-MPRA regulatory region 10946 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:2590869-2591089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2600763-2601368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4306 Neighboring gene KCNQ1 opposite strand/antisense transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2706658-2707620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:2709545-2710505 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:2714101-2714968

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_079161.1 

    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
    2463139..2463433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    2552465..2552759
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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