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LOC121009674 Sharpr-MPRA regulatory region 380 [ Homo sapiens (human) ]

Gene ID: 121009674, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121009674
Gene description
Sharpr-MPRA regulatory region 380
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 enhancer 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 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2021]
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Genomic context

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See LOC121009674 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57969842..57970136)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (58010232..58010526)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57955569..57955863)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene sarcolemma associated protein Neighboring gene uncharacterized LOC105377103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57944346-57944927 Neighboring gene uncharacterized LOC105377104 Neighboring gene PPIAP16-FLNB intergenic CAGE-defined mid-level expression enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57946764-57947718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57947719-57948671 Neighboring gene peptidylprolyl isomerase A pseudogene 16 Neighboring gene uncharacterized LOC124909385 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57958837-57959340 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57959341-57959842 Neighboring gene PPIAP16-FLNB intergenic CAGE-defined low expression enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57983544-57984119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:57999317-57999817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:57999844-58000357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58000358-58000870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58000871-58001384 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58005500-58006482 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58006483-58007463 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58007464-58008445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58020595-58021094 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58023882-58024382 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58025201-58025780 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58027143-58027657 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58028173-58028686 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:58034417-58035616 Neighboring gene Sharpr-MPRA regulatory region 2534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58040937-58041474 Neighboring gene filamin B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58051153-58052030 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14485 Neighboring gene Sharpr-MPRA regulatory region 3708 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:58147281-58148480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58149790-58150603 Neighboring gene Sharpr-MPRA regulatory region 1271 Neighboring gene FLNB antisense RNA 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_074065.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    57969842..57970136
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    58010232..58010526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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