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LOC121967074 Sharpr-MPRA regulatory region 5895 [ Homo sapiens (human) ]

Gene ID: 121967074, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121967074
Gene description
Sharpr-MPRA regulatory region 5895
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 HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC121967074 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (10494672..10494966)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (10038279..10038573)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (10554729..10555023)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene CENPS-CORT readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10534116-10535081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 247 Neighboring gene cortistatin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 151 Neighboring gene DNA fragmentation factor subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 153 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10568725-10569413 Neighboring gene peroxisomal biogenesis factor 14 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:10588102-10589301 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10601005-10601548 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10616013-10616674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 248 Neighboring gene Sharpr-MPRA regulatory region 3136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10654141-10654658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10654659-10655176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10662571-10663072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10663073-10663572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10675589-10676274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10676275-10676958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10678456-10679010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10682167-10682666 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:10683990-10685189 Neighboring gene RNA, 7SL, cytoplasmic 614, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10693091-10694054 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10695017-10695979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10706359-10706864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10715263-10715920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10720335-10720845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10719824-10720334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10724469-10725217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10725218-10725965 Neighboring gene castor zinc finger 1 Neighboring gene VISTA enhancer hs289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10735694-10736484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10736485-10737273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10738853-10739642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10739643-10740432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10746179-10746778 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10746779-10747379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10761480-10761980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10763789-10764710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10764711-10765633 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10765634-10766555 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10772353-10772897 Neighboring gene VISTA enhancer hs389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10787641-10788438 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10788439-10789235 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 253 Neighboring gene VISTA enhancer hs2094 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:10804287-10805486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10805585-10806508 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:10814763-10814950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10821512-10822012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10822013-10822513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10845108-10845670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10845671-10846231 Neighboring gene VISTA enhancer hs408

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_076214.1 

    Range
    101..395
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    10494672..10494966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    10038279..10038573
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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