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LOC123956261 Sharpr-MPRA regulatory region 13519 [ Homo sapiens (human) ]

Gene ID: 123956261, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123956261
Gene description
Sharpr-MPRA regulatory region 13519
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 DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Jan 2022]
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Genomic context

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See LOC123956261 in Genome Data Viewer
Location:
7q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (144513336..144513630)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (145693795..145694089)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (144210429..144210723)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene RNA, U6atac small nuclear 40, pseudogene Neighboring gene peptidylprolyl isomerase A pseudogene 83 Neighboring gene NANOG hESC enhancer GRCh37_chr7:144172657-144173158 Neighboring gene thiamin pyrophosphokinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18730 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:144231635-144232508 Neighboring gene NANOG hESC enhancer GRCh37_chr7:144262663-144263224 Neighboring gene NANOG hESC enhancer GRCh37_chr7:144316313-144316842 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26797 Neighboring gene RN7SK pseudogene 174

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_078452.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    144513336..144513630
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654715.1 Reference GRCh38.p14 PATCHES

    Range
    563074..563368
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    145693795..145694089
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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