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LOC125418086 Sharpr-MPRA regulatory region 7423 [ Homo sapiens (human) ]

Gene ID: 125418086, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125418086
Gene description
Sharpr-MPRA regulatory region 7423
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 DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125418086 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (45596755..45597049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43965775..43966069)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene collagen type XVIII alpha 1 chain Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46908672-46909202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46912122-46912622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46934825-46935332 Neighboring gene microRNA 6815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46935840-46936346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18591 Neighboring gene Sharpr-MPRA regulatory region 1559 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46948644-46948814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46954106-46954980 Neighboring gene solute carrier family 19 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46962482-46962994 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46970045-46970201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46975660-46976554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46980259-46980968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46998853-46999354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47001008-47001944 Neighboring gene uncharacterized LOC107985485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47009554-47010054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47015623-47016124 Neighboring gene MPRA-validated peak4424 silencer Neighboring gene MPRA-validated peak4426 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47031725-47032226 Neighboring gene long intergenic non-protein coding RNA 1694 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:47053121-47054320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47057095-47057612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13411 Neighboring gene poly(rC) binding protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47204393-47205264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47236921-47237422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47237423-47237922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47241669-47242354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47244540-47245132 Neighboring gene MPRA-validated peak4427 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47255439-47255946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47257017-47257560 Neighboring gene PCBP3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47274544-47275220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47275221-47275896 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:47278335-47279534 Neighboring gene uncharacterized LOC124905044

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

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_081112.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    45596755..45597049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43965775..43966069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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