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LOC124946339 Sharpr-MPRA regulatory region 13414 [ Homo sapiens (human) ]

Gene ID: 124946339, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124946339
Gene description
Sharpr-MPRA regulatory region 13414
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (110412202..110412496)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (109642287..109642581)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene collagen type IV alpha 1 chain Neighboring gene uncharacterized LOC124903212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:110935768-110936268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110959260-110960093 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110960094-110960926 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:110971991-110973190 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110979365-110980133 Neighboring gene collagen type IV alpha 2 chain Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:110990505-110991006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5501 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:110994550-110995499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:110995500-110996448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:110999397-111000255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111005255-111005767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111012706-111013206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111013207-111013707 Neighboring gene microRNA 8073 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111031805-111032755 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:111039396-111040260 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7992 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111098314-111098814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111098815-111099315 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:111100302-111101501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111110079-111110888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:111110889-111111697 Neighboring gene COL4A2 antisense RNA 2

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_080045.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    110412202..110412496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    109642287..109642581
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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