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LOC123575583 Sharpr-MPRA regulatory region 14811 [ Homo sapiens (human) ]

Gene ID: 123575583, updated on 12-Sep-2024

Summary

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Gene symbol
LOC123575583
Gene description
Sharpr-MPRA regulatory region 14811
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 3:PromF, promoter flanking) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123575583 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (146185266..146185560)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (146720811..146721105)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (145564829..145565123)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene leucyl-tRNA synthetase 1 Neighboring gene ribosomal protein L35a pseudogene 16 Neighboring gene ribosomal protein L35a pseudogene 17 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81447 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81571 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81597 Neighboring gene MPRA-validated peak5520 silencer Neighboring gene MPRA-validated peak5521 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:145562805-145563651 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23360 Neighboring gene RBM27-POU4F3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23361 Neighboring gene Sharpr-MPRA regulatory region 15600 Neighboring gene RNA binding motif protein 27 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81701 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81715 Neighboring gene RNA, U7 small nuclear 180 pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_81725 Neighboring gene MPRA-validated peak5522 silencer Neighboring gene POU class 4 homeobox 3

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_077844.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    146185266..146185560
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    146720811..146721105
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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