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LOC122889005 Sharpr-MPRA regulatory region 6954 [ Homo sapiens (human) ]

Gene ID: 122889005, updated on 12-Sep-2024

Summary

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Gene symbol
LOC122889005
Gene description
Sharpr-MPRA regulatory region 6954
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889005 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (235070325..235070619)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (235559294..235559588)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (235978969..235979263)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235840873-235841418 Neighboring gene uncharacterized LOC105373938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235843604-235844104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:235861114-235861763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235873459-235874021 Neighboring gene SH3 domain binding protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235882781-235883348 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235883349-235883916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235883917-235884484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235885570-235886122 Neighboring gene uncharacterized LOC105373939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235888982-235889719 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:235892104-235892818 and GRCh37_chr2:235892819-235893532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235899889-235900660 Neighboring gene Sharpr-MPRA regulatory region 6611 Neighboring gene Sharpr-MPRA regulatory region 6657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235907423-235908052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235908168-235908844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235911298-235912136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235914015-235914602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235913425-235914014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235914603-235915192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235916550-235917186 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235920146-235920722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235920723-235921298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:235921299-235921875 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235939804-235940432 Neighboring gene OCT4 hESC enhancer GRCh37_chr2:235952107-235952608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235960919-235961880 Neighboring gene Sharpr-MPRA regulatory region 15714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235970623-235971123 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:235991995-235993194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235996100-235996600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236022675-236023222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236035311-236035906 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:236045748-236045962 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:236066308-236066890 Neighboring gene CEP19 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:236080141-236080327 Neighboring gene uncharacterized LOC124907998

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_077137.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    235070325..235070619
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    235559294..235559588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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