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LOC122861268 Sharpr-MPRA regulatory region 10664 [ Homo sapiens (human) ]

Gene ID: 122861268, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861268
Gene description
Sharpr-MPRA regulatory region 10664
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (187530022..187530316)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (188018957..188019251)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (188394749..188395043)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene CALCRL and TFPI antisense RNA 1 Neighboring gene RNA, U6 small nuclear 989, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15572 Neighboring gene MPRA-validated peak3978 silencer Neighboring gene MPRA-validated peak3980 silencer Neighboring gene MPRA-validated peak3982 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:188273472-188274250 Neighboring gene calcitonin receptor like receptor Neighboring gene Sharpr-MPRA regulatory region 13492 Neighboring gene MPRA-validated peak3983 silencer Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene 59 Neighboring gene MPRA-validated peak3984 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:188384681-188385366 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:188411556-188412755 Neighboring gene tissue factor pathway inhibitor Neighboring gene NANOG hESC enhancer GRCh37_chr2:188422204-188422788 Neighboring gene NANOG hESC enhancer GRCh37_chr2:188422789-188423371 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:188430328-188430906 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:188430907-188431484 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:188480540-188481090 Neighboring gene NANOG hESC enhancer GRCh37_chr2:188483510-188484011 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:188535284-188535785 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:188540495-188541307 Neighboring gene MPRA-validated peak3986 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:188565262-188565763 Neighboring gene uncharacterized LOC105373788 Neighboring gene ST13, Hsp70 interacting protein pseudogene 2

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_077084.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    187530022..187530316
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    188018957..188019251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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