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LOC125078034 Sharpr-MPRA regulatory region 11273 [ Homo sapiens (human) ]

Gene ID: 125078034, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125078034
Gene description
Sharpr-MPRA regulatory region 11273
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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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (99780692..99780986)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (94012129..94012423)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6067 Neighboring gene Sharpr-MPRA regulatory region 4550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100090366-100091068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9005 Neighboring gene HHIP like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118945-100119445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100118444-100118944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100128755-100129256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100129257-100129756 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130377-100130920 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100130921-100131465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100135414-100135955 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:100136897-100137496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100138099-100138698 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100137497-100138098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100141430-100141993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100142557-100143120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100143121-100143683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100174717-100175236 Neighboring gene cytochrome P450 family 46 subfamily A member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100197899-100198758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100203867-100204677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100205489-100206299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100215862-100216394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100217886-100218507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100218508-100219128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100221613-100222233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100222234-100222853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100234232-100235190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100235191-100236147 Neighboring gene EMAP like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9010 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100259671-100260502 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100304941-100305568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100342767-100343319 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:100349991-100350528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100354721-100355374 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100355375-100356028 Neighboring gene Sharpr-MPRA regulatory region 1474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9011 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:100405395-100406594 Neighboring gene uncharacterized LOC102724682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100412450-100413378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100416877-100417378 Neighboring gene RNA, U1 small nuclear 47, pseudogene Neighboring gene voltage dependent anion channel 3 pseudogene 1

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_080170.1 

    Range
    101..395
    Download
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    99780692..99780986
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    94012129..94012423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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