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LOC121627962 Sharpr-MPRA regulatory region 15471 [ Homo sapiens (human) ]

Gene ID: 121627962, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627962
Gene description
Sharpr-MPRA regulatory region 15471
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [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 (20252951..20253245)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (19835846..19836140)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (20271069..20271363)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29480 Neighboring gene EIF1AX antisense RNA 1 Neighboring gene small Cajal body-specific RNA 9 like Neighboring gene eukaryotic translation initiation factor 1A X-linked Neighboring gene ribosomal protein S6 kinase A3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29481 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20696 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20697 Neighboring gene Sharpr-MPRA regulatory region 100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29483 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29484 Neighboring gene RN7SK pseudogene 183 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:20504565-20505764 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:20532054-20533253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20698 Neighboring gene uncharacterized LOC124905257

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_075442.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    20252951..20253245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    19835846..19836140
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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