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LOC124500678 Sharpr-MPRA regulatory region 370 [ Homo sapiens (human) ]

Gene ID: 124500678, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124500678
Gene description
Sharpr-MPRA regulatory region 370
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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (67628478..67628772)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67623165..67623459)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67395949..67396243)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67381921-67382434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67382435-67382950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67382951-67383466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67383983-67384496 Neighboring gene double C2 domain gamma, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:67384509-67385123 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67386492-67387365 Neighboring gene uncharacterized LOC124902696 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:67388663-67389245 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:67389246-67389827 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67393084-67393613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3647 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3649 Neighboring gene nudix hydrolase 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67399437-67399966 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67400495-67401024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67401025-67401552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67401848-67402406 Neighboring gene T-box transcription factor 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67402407-67402965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67411697-67412266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67412267-67412834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5119 Neighboring gene aminoacylase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67416073-67416595

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_079335.1 

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

    Range
    67628478..67628772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    67623165..67623459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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