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LOC124403959 Sharpr-MPRA regulatory region 6982 [ Homo sapiens (human) ]

Gene ID: 124403959, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124403959
Gene description
Sharpr-MPRA regulatory region 6982
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, Feb 2022]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (59832491..59832785)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (60686219..60686513)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (61592249..61592543)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3387 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2383 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2384 Neighboring gene solute carrier family 16 member 9 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61521925-61522472 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:61529872-61530061 Neighboring gene NANOG hESC enhancer GRCh37_chr10:61549690-61550191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:61562933-61563434 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61607379-61608319 Neighboring gene myoregulin Neighboring gene Sharpr-MPRA regulatory region 3861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3390 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2385 Neighboring gene coiled-coil domain containing 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2387 Neighboring gene Sharpr-MPRA regulatory region 3982 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:61667949-61668742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2386 Neighboring gene long intergenic non-protein coding RNA 1553 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:61763136-61763882 Neighboring gene NANOG hESC enhancer GRCh37_chr10:61788258-61788759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3394 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:61889195-61889380 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:61889679-61890254 Neighboring gene ankyrin 3 Neighboring gene NANOG hESC enhancer GRCh37_chr10:62018096-62018597 Neighboring gene Sharpr-MPRA regulatory region 14495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2388 Neighboring gene uncharacterized LOC124902430

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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_079038.1 

    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
    59832491..59832785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    60686219..60686513
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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Other Literature Sources
Molecular Biology Databases