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LOC114004370 Sharpr-MPRA regulatory region 3202 [ Homo sapiens (human) ]

Gene ID: 114004370, updated on 10-Oct-2023

Summary

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Gene symbol
LOC114004370
Gene description
Sharpr-MPRA regulatory region 3202
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 21:Repr, strong Polycomb repression), with weak repression in HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2019]
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Genomic context

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See LOC114004370 in Genome Data Viewer
Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (25105720..25106014)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (25140168..25140462)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (25328589..25328883)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene EFR3 homolog B Neighboring gene RNA, 7SL, cytoplasmic 856, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25293144-25293286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25311273-25312272 Neighboring gene SUCLA2 pseudogene 3 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:25312273-25313271 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:25320574-25320751 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58220 Neighboring gene Sharpr-MPRA regulatory region 11705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25359725-25360226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:25360227-25360726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:25383210-25384066 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11245 Neighboring gene POMC promoter region Neighboring gene POMC distal enhancer region Neighboring gene proopiomelanocortin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11246 Neighboring gene long intergenic non-protein coding RNA 1381

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_063789.1 

    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
    25105720..25106014
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    25140168..25140462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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