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LOC121627965 Sharpr-MPRA regulatory region 12649 [ Homo sapiens (human) ]

Gene ID: 121627965, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121627965
Gene description
Sharpr-MPRA regulatory region 12649
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 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 6:EnhF, candidate strong enhancer, flanking 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 (39853315..39853609)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (39253532..39253826)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (39712569..39712863)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373177 Neighboring gene OOEP pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39675935-39676850 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39676851-39677768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39686865-39687366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39687367-39687866 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:39699064-39699252 Neighboring gene microRNA 1587 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39717183-39717683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39734537-39735038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39735039-39735538 Neighboring gene ribosomal protein S11 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:39756695-39757676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39765114-39765903 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:39766731-39767930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39787967-39788468 Neighboring gene uncharacterized LOC105373180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39788469-39788968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29533

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_075445.1 

    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
    39853315..39853609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    39253532..39253826
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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