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LOC124421492 Sharpr-MPRA regulatory region 9596 [ Homo sapiens (human) ]

Gene ID: 124421492, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124421492
Gene description
Sharpr-MPRA regulatory region 9596
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124421492 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 (12750002..12750296)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (12842501..12842795)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (12771549..12771843)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene parvin alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12474119-12474620 Neighboring gene Sharpr-MPRA regulatory region 15612/8581 Neighboring gene Sharpr-MPRA regulatory region 1666 Neighboring gene uncharacterized LOC105376556 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12658187-12658688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12658689-12659188 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3162 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12696795-12697609 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12697610-12698423 Neighboring gene TEAD1 intron CAGE-defined low expression enhancer 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:12701865-12702582 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12702583-12703300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12703301-12704018 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:12714955-12716154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:12736558-12737398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3163 Neighboring gene Sharpr-MPRA regulatory region 14023 Neighboring gene TEA domain transcription factor 1 Neighboring gene Sharpr-MPRA regulatory region 5264 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12788587-12789086 Neighboring gene Sharpr-MPRA regulatory region 13244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12809225-12809732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12809733-12810240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12810874-12811512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12830522-12831193 Neighboring gene uncharacterized LOC107984313 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:12849868-12850506 Neighboring gene VISTA enhancer hs1314 Neighboring gene Sharpr-MPRA regulatory region 11610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:12897776-12898276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12902094-12903038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:12910458-12910966 Neighboring gene uncharacterized LOC124900312

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_079181.1 

    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
    12750002..12750296
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    12842501..12842795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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