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LOC114004400 Sharpr-MPRA regulatory region 15272 [ Homo sapiens (human) ]

Gene ID: 114004400, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004400
Gene description
Sharpr-MPRA regulatory region 15272
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114004400 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (34132572..34132866)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (33956146..33956440)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (34100349..34100643)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33922205-33922705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33925615-33926355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33926356-33927095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33961394-33962166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33967681-33968182 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33973921-33974803 Neighboring gene microRNA 1275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33993583-33994310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33999095-33999617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24375 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34015538-34016092 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:34016093-34016646 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:34016647-34017200 Neighboring gene glutamate metabotropic receptor 4 Neighboring gene Sharpr-MPRA regulatory region 5466 Neighboring gene Sharpr-MPRA regulatory region 4098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34031248-34031829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34044839-34045669 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34046709-34047454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34050139-34050978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34050979-34051818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34074290-34074790 Neighboring gene MPRA-validated peak5759 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34087978-34088766 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:34099315-34100141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:34121411-34122268 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24379 Neighboring gene keratin 18 pseudogene 9 Neighboring gene CYCS pseudogene 55

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_063900.1 

    Range
    101..395
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    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    34132572..34132866
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33956146..33956440
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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