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LOC123956250 Sharpr-MPRA regulatory region 2153 [ Homo sapiens (human) ]

Gene ID: 123956250, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956250
Gene description
Sharpr-MPRA regulatory region 2153
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Jan 2022]
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Genomic context

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Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (140640709..140641003)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (141954886..141955180)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (140340509..140340803)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140143760-140144260 Neighboring gene nucleoside diphosphate kinase, mitochondrial-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140156257-140157110 Neighboring gene makorin ring finger protein 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140178571-140179411 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140179742-140180652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26782 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140206498-140207088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140207089-140207678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140227087-140227701 Neighboring gene DENN domain containing 2A Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140244505-140245005 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140253137-140253867 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140255121-140255621 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140269202-140269702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:140269703-140270203 Neighboring gene Sharpr-MPRA regulatory region 5784 Neighboring gene Sharpr-MPRA regulatory region 9531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140324769-140325360 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140325951-140326542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140327133-140327724 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140327725-140328314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140332981-140333481 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140334787-140335394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140335395-140336002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:140336003-140336609 Neighboring gene uncharacterized LOC105375535 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:140346933-140347108 Neighboring gene RNA, 7SL, cytoplasmic 771, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18715 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140378691-140379191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:140389463-140389963 Neighboring gene aarF domain containing kinase 2

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_078444.1 

    Range
    101..395
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    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
    140640709..140641003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    141954886..141955180
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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