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LOC121627967 Sharpr-MPRA regulatory region 10897 [ Homo sapiens (human) ]

Gene ID: 121627967, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627967
Gene description
Sharpr-MPRA regulatory region 10897
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer 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 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jun 2021]
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Genomic context

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Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (41327396..41327690)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (40729481..40729775)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (41186649..41186943)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 502 Neighboring gene NANOG hESC enhancer GRCh37_chrX:41163312-41163875 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:41165064-41165269 Neighboring gene SHISA5 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29554 Neighboring gene DEAD-box helicase 3 X-linked Neighboring gene RNA, 7SL, cytoplasmic 15, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15169 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:41244756-41245273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29559 Neighboring gene nyctalopin Neighboring gene GEMIN7 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

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_075447.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    41327396..41327690
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    40729481..40729775
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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