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LOC121099716 Sharpr-MPRA regulatory region 13731 [ Homo sapiens (human) ]

Gene ID: 121099716, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121099716
Gene description
Sharpr-MPRA regulatory region 13731
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 non-DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 25:Art). [provided by RefSeq, Apr 2021]
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Genomic context

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Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177317928..177318222)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177861161..177861455)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176744929..176745223)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:176728411-176729610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16677 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176730775-176731652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23701 Neighboring gene RAB24, member RAS oncogene family Neighboring gene PRELI domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176737000-176737866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23705 Neighboring gene MAX dimerization protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176746939-176747440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176747441-176747940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176751079-176751579 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:176753137-176754080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176763024-176763649 Neighboring gene lectin, mannose binding 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176765883-176766836 Neighboring gene ribosomal protein S20 pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23706 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:176778754-176778968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176784977-176785477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23710 Neighboring gene regulator of G protein signaling 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176793955-176794594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176794595-176795233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176796333-176797184

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_074196.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    177317928..177318222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177861161..177861455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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