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LOC124629339 Sharpr-MPRA regulatory region 7044 [ Homo sapiens (human) ]

Gene ID: 124629339, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629339
Gene description
Sharpr-MPRA regulatory region 7044
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 unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (31066315..31066609)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (30940805..30941099)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902911 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28199 Neighboring gene tetraspanin 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31117766-31118266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31130578-31131412 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31133507-31134008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31134009-31134508 Neighboring gene TSPAN11 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6161 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31140539-31141040 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31141041-31141540 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:31165500-31165701 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:31181720-31181949 Neighboring gene DDX11 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:31226445-31226976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:31227509-31228038 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31232984-31233540 Neighboring gene DEAD/H-box helicase 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31256969-31257468 Neighboring gene MPRA-validated peak1651 silencer Neighboring gene uncharacterized LOC124902912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31270198-31270728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:31270729-31271258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:31273911-31274440 Neighboring gene alpha-2-macroglobulin like 1 pseudogene

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

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_079618.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    31066315..31066609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    30940805..30941099
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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