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LOC124625877 Sharpr-MPRA regulatory region 6010 [ Homo sapiens (human) ]

Gene ID: 124625877, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625877
Gene description
Sharpr-MPRA regulatory region 6010
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 non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [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 (991743..992037)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (987636..987930)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene RNA, U4atac small nuclear 16, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5791 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr12:917646-918146 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr12:918147-918647 Neighboring gene WNK lysine deficient protein kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5792 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:1023012-1024211 Neighboring gene uncharacterized LOC124902855 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1058032-1058690 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:1058691-1059349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1067429-1067930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1067931-1068430 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:1083331-1083878 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:1092618-1092819 Neighboring gene RAD52 homolog, DNA repair protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:1099220-1099782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4110 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:1100344-1100905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1115216-1115716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1115717-1116217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:1181067-1181567 Neighboring gene ELKS/RAB6-interacting/CAST family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5795 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:1224566-1225765 Neighboring gene uncharacterized LOC124902857 Neighboring gene 5-hydroxytryptamine receptor 1D 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

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_079477.1 

    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
    991743..992037
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    987636..987930
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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