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LOC125146375 Sharpr-MPRA regulatory region 7653 [ Homo sapiens (human) ]

Gene ID: 125146375, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125146375
Gene description
Sharpr-MPRA regulatory region 7653
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146375 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (2005608..2005902)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (2025562..2025856)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (2055609..2055903)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7014 Neighboring gene growth factor, augmenter of liver regeneration Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:2038929-2039508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7016 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2041827-2042404 Neighboring gene synaptogyrin 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2042985-2043562 Neighboring gene zinc finger protein 598, E3 ubiquitin ligase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2056701-2057648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2059548-2060496 Neighboring gene uncharacterized LOC124903626 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:2062031-2062226 Neighboring gene RNA, 7SL, cytoplasmic 219, pseudogene

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_080305.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    2005608..2005902
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791799.1 Reference GRCh38.p14 PATCHES

    Range
    71756..72050
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    2025562..2025856
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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