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LOC125177478 Sharpr-MPRA regulatory region 2167 [ Homo sapiens (human) ]

Gene ID: 125177478, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125177478
Gene description
Sharpr-MPRA regulatory region 2167
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 DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177478 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (42072471..42072765)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (42928980..42929274)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (40224489..40224783)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:40168666-40169865 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8510 Neighboring gene NFKB inhibitor interacting Ras like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40180775-40181563 Neighboring gene zinc finger protein 385C Neighboring gene chromosome 17 open reading frame 113 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40203397-40203898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40214064-40214654 Neighboring gene Sharpr-MPRA regulatory region 8946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8513 Neighboring gene Sharpr-MPRA regulatory region 13373 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40220039-40220539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40223445-40224418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40256421-40257354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40257355-40258286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12183 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:40259930-40260442 Neighboring gene DExH-box helicase 58 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:40267799-40268334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8516 Neighboring gene lysine acetyltransferase 2A

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_080533.1 

    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
    42072471..42072765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    42928980..42929274
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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