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LOC114022700 Sharpr-MPRA regulatory region 3625 [ Homo sapiens (human) ]

Gene ID: 114022700, updated on 17-Sep-2024

Summary

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Gene symbol
LOC114022700
Gene description
Sharpr-MPRA regulatory region 3625
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 DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114022700 in Genome Data Viewer
Location:
9q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129790430..129790724)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141995007..141995301)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (132552709..132553003)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902284 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132489030-132489223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132504976-132505476 Neighboring gene prostaglandin E synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132537345-132537911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132539303-132539818 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132543973-132544473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29120 Neighboring gene UBE2V1 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20389 Neighboring gene torsin family 1 member B

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_063917.1 

    Range
    101..395
    Download
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    129790430..129790724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141995007..141995301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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