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LOC122152319 Sharpr-MPRA regulatory region 11146 [ Homo sapiens (human) ]

Gene ID: 122152319, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122152319
Gene description
Sharpr-MPRA regulatory region 11146
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, Jul 2021]
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Genomic context

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Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (229240682..229240976)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (228619346..228619640)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (229376429..229376723)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene iron-sulfur cluster assembly 1 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229194589-229195089 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229195717-229196216 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229223803-229224521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229227240-229228172 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229228173-229229104 Neighboring gene long intergenic non-protein coding RNA 2815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229243991-229244514 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229244515-229245036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229251653-229252154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229252155-229252654 Neighboring gene Sharpr-MPRA regulatory region 2560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229295511-229296011 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229297904-229298404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229298405-229298905 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:229309691-229310255 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:229313110-229314036 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:229314037-229314963 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:229314964-229315890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2699 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:229333469-229333968 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229338935-229339572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229341375-229341982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229356687-229357188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229357189-229357688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:229360637-229361210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:229363801-229364526 Neighboring gene uncharacterized LOC102723935 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:229388645-229389519 Neighboring gene uncharacterized LOC124904540 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:229389520-229390393 Neighboring gene RAB4A antisense RNA 1 Neighboring gene transmembrane protein 78

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_076593.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    229240682..229240976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    228619346..228619640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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