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LOC122889006 Sharpr-MPRA regulatory region 12909 [ Homo sapiens (human) ]

Gene ID: 122889006, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122889006
Gene description
Sharpr-MPRA regulatory region 12909
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122889006 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (235643785..235644079)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (236133265..236133559)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (236552429..236552723)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene AGAP1 intronic transcript 1 Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_57171 Neighboring gene trinucleotide repeat containing 17 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236475811-236476311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236494510-236495010 Neighboring gene Sharpr-MPRA regulatory region 15430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236505422-236506274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236539863-236540736 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:236567081-236567736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236599338-236599838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236599839-236600339 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236617362-236618561 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236632223-236632790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236632791-236633358 Neighboring gene uncharacterized LOC105373942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236696882-236697382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236701667-236702167 Neighboring gene Sharpr-MPRA regulatory region 1374 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:236735809-236737008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236757968-236758468 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:236763280-236764479 Neighboring gene VISTA enhancer hs521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236784736-236785236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:236785237-236785737 Neighboring gene thymosin beta 10 pseudogene 1

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_077138.1 

    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
    235643785..235644079
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    236133265..236133559
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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