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LOC125177409 Sharpr-MPRA regulatory region 10924 [ Homo sapiens (human) ]

Gene ID: 125177409, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125177409
Gene description
Sharpr-MPRA regulatory region 10924
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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Location:
17p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4903634..4903928)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4793882..4794176)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4806929..4807223)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene misshapen like kinase 1 Neighboring gene Sharpr-MPRA regulatory region 481 Neighboring gene ATPase H+ transporting V0 subunit c pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11550 Neighboring gene RNA, 7SL, cytoplasmic 784, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8049 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4805105-4805746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4805747-4806388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11552 Neighboring gene chromosome 17 open reading frame 107 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4811144-4811970 Neighboring gene cholinergic receptor nicotinic epsilon subunit Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4811971-4812796 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4812797-4813623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4841097-4841622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:4841623-4842148 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4842149-4842674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8051 Neighboring gene glycoprotein Ib platelet subunit alpha Neighboring gene solute carrier family 25 member 11

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_080466.1 

    Range
    101..395
    Download
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    4903634..4903928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4793882..4794176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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