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LOC123924898 Sharpr-MPRA regulatory region 15593 [ Homo sapiens (human) ]

Gene ID: 123924898, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123924898
Gene description
Sharpr-MPRA regulatory region 15593
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (6228298..6228592)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (6347677..6347971)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (6267929..6268223)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 2 alpha kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17932 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17933 Neighboring gene RNA, U6 small nuclear 218, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:6116071-6116985 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:6116986-6117899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17934 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:6141129-6141352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6143513-6144112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17937 Neighboring gene ubiquitin specific peptidase 42 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:6189130-6190329 Neighboring gene cytohesin 3 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6262905-6263525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6310870-6311592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:6311593-6312314 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6322371-6323253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6323254-6324135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6362882-6363382 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6387689-6388190 Neighboring gene small integral membrane protein 10 like 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:6388191-6388690 Neighboring gene family with sequence similarity 220 member A Neighboring gene ribosomal protein SA pseudogene 73

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_078290.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    6228298..6228592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    6347677..6347971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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