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LOC125177407 Sharpr-MPRA regulatory region 3058 [ Homo sapiens (human) ]

Gene ID: 125177407, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125177407
Gene description
Sharpr-MPRA regulatory region 3058
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177407 in Genome Data Viewer
Location:
17p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (4648114..4648408)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (4537843..4538137)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (4551409..4551703)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371498 Neighboring gene RNA, U6 small nuclear 955, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4534741-4535270 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:4535271-4535798 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:4541217-4542416 Neighboring gene arachidonate 15-lipoxygenase Neighboring gene uncharacterized LOC105371499 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:4552879-4553094 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47177/47178 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47179 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47181 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47184 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47187 Neighboring gene proline, glutamate and leucine rich protein 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47196 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47199 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47200 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47201 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47204 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47205 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47206 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47207 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11544 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47211 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47214 Neighboring gene PELP1 divergent transcript Neighboring gene ribosomal protein S12 pseudogene 29

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_080464.1 

    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
    4648114..4648408
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    4537843..4538137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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