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LOC123497975 Sharpr-MPRA regulatory region 15161 [ Homo sapiens (human) ]

Gene ID: 123497975, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123497975
Gene description
Sharpr-MPRA regulatory region 15161
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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See LOC123497975 in Genome Data Viewer
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (137635600..137635894)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (138156729..138157023)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (136971289..136971583)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 193 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:136372100-136372962 Neighboring gene SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:136385493-136386121 Neighboring gene uncharacterized LOC105379192 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:136481153-136482352 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:136536474-136537125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16381 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:136570305-136571504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:136655443-136655942 Neighboring gene MPRA-validated peak5485 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16383 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:136965897-136966647 Neighboring gene MPRA-validated peak5486 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr5:137020129-137020374 Neighboring gene Sharpr-MPRA regulatory region 14679 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137023227-137023961 Neighboring gene kelch like family member 3 Neighboring gene VISTA enhancer hs2181 Neighboring gene microRNA 874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:137071377-137072045 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:137088711-137089402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23186 Neighboring gene heterogeneous nuclear ribonucleoprotein A0

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_077826.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    137635600..137635894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    138156729..138157023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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