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LOC124403938 Sharpr-MPRA regulatory region 1021 [ Homo sapiens (human) ]

Gene ID: 124403938, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403938
Gene description
Sharpr-MPRA regulatory region 1021
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124403938 in Genome Data Viewer
Location:
10p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (35379401..35379695)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (35408001..35408295)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (35668329..35668623)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene cyclin Y Neighboring gene uncharacterized LOC107984220 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:35588522-35589721 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2304 Neighboring gene Sharpr-MPRA regulatory region 12265 Neighboring gene CCNY antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2305 Neighboring gene Sharpr-MPRA regulatory region 675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2306 Neighboring gene uncharacterized LOC124902410 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:35736957-35737627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2307 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:35751098-35751642 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:35751643-35752185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:35752610-35753110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3265 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:35806272-35806772 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:35806773-35807273 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:35819404-35820603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3268 Neighboring gene uncharacterized LOC107984221

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_079018.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    35379401..35379695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    35408001..35408295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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