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LOC121079960 Sharpr-MPRA regulatory region 12197 [ Homo sapiens (human) ]

Gene ID: 121079960, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121079960
Gene description
Sharpr-MPRA regulatory region 12197
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [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 (132098176..132098470)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132618046..132618340)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131433869..131434163)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379174 Neighboring gene enhancer-blocking elements downstream of IL3 Neighboring gene origin of replication downstream of CSF2 Neighboring gene interleukin 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131423316-131423538 Neighboring gene colony stimulating factor 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:131429841-131431040 Neighboring gene Sharpr-MPRA regulatory region 14284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131517361-131517888 Neighboring gene NANOG hESC enhancer GRCh37_chr5:131520231-131520732 Neighboring gene Sharpr-MPRA regulatory region 7421 Neighboring gene P4HA2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543137-131543638 Neighboring gene prolyl 4-hydroxylase subunit alpha 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543639-131544138 Neighboring gene microRNA 6830

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_074178.1 

    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
    132098176..132098470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132618046..132618340
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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