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LOC123575582 Sharpr-MPRA regulatory region 7053 [ Homo sapiens (human) ]

Gene ID: 123575582, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123575582
Gene description
Sharpr-MPRA regulatory region 7053
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 unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (142867024..142867318)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (143398335..143398629)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (142246589..142246883)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA36 family Neighboring gene FGF1 promoter C Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:142024170-142025369 Neighboring gene Sharpr-MPRA regulatory region 3450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142039508-142040008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142040009-142040509 Neighboring gene fibroblast growth factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142047003-142047511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142047512-142048019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142049247-142049746 Neighboring gene NANOG hESC enhancer GRCh37_chr5:142052360-142052880 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:142064129-142064998 Neighboring gene FGF1 promoter B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16475 Neighboring gene long intergenic non-protein coding RNA 1844 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16476 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142150581-142151416 Neighboring gene NANOG hESC enhancer GRCh37_chr5:142176991-142177492 Neighboring gene Rho GTPase activating protein 26 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16477 Neighboring gene ARHGAP26 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:142242364-142242980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142242981-142243597 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142243598-142244214 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142275426-142276332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23320 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:142296188-142296688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:142296689-142297189 Neighboring gene uncharacterized LOC107986457 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142361413-142362255 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:142362256-142363097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23321 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:142388320-142389519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23324 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:142416478-142417238 Neighboring gene uncharacterized LOC124901097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23326

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_077843.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    142867024..142867318
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    143398335..143398629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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