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LOC125177367 Sharpr-MPRA regulatory region 6565 [ Homo sapiens (human) ]

Gene ID: 125177367, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177367
Gene description
Sharpr-MPRA regulatory region 6565
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 25:Art, potential CNV or repetitive artifacts) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84739703..84739997)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90805948..90806242)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7790 Neighboring gene kelch like family member 36 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84706085-84706586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84745056-84745556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84752587-84753087 Neighboring gene ubiquitin specific peptidase 10 Neighboring gene Sharpr-MPRA regulatory region 11774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84760363-84760863 Neighboring gene uncharacterized LOC124903737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84769037-84770002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84770003-84770968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11255 Neighboring gene Sharpr-MPRA regulatory region 1784 Neighboring gene uncharacterized LOC105371378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84828009-84828510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84837954-84838454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84839622-84840200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84840201-84840777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7795 Neighboring gene cysteine rich secretory protein LCCL domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84869778-84870346 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84878477-84879206 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84879989-84880225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84884617-84885118 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84913207-84914406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84918435-84919058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84919059-84919684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84919685-84920308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84920309-84920933

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_080435.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    84739703..84739997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90805948..90806242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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