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LOC125078022 Sharpr-MPRA regulatory region 3148 [ Homo sapiens (human) ]

Gene ID: 125078022, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078022
Gene description
Sharpr-MPRA regulatory region 3148
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 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125078022 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (91156325..91156619)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (85381787..85382081)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene D-glutamate cyclase Neighboring gene RNA, U7 small nuclear 30 pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91579864-91580776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91582717-91583218 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:91585689-91586888 Neighboring gene Sharpr-MPRA regulatory region 15407 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8894 Neighboring gene small nucleolar RNA, H/ACA box 11B Neighboring gene ReSE screen-validated silencer GRCh37_chr14:91619068-91619346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8895 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8896 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8899 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91710745-91711246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91719939-91720470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91720471-91721002 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1904 Neighboring gene Sharpr-MPRA regulatory region 4292 Neighboring gene G protein-coupled receptor 68 Neighboring gene CRISPRi-validated cis-regulatory element chr14.1906 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:91749514-91749720 Neighboring gene coiled-coil domain containing 88C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6023 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91771631-91772466 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91772467-91773300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8904 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8906 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8905 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:91818809-91819780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91821242-91821752 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826469-91826970 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:91826971-91827470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8908 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8910 Neighboring gene uncharacterized LOC107984673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:91838097-91838709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8911

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_080158.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    91156325..91156619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    85381787..85382081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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