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LOC112543482 Sharpr-MPRA regulatory region 5698 [ Homo sapiens (human) ]

Gene ID: 112543482, updated on 10-Oct-2023

Summary

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Gene symbol
LOC112543482
Gene description
Sharpr-MPRA regulatory region 5698
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 DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, May 2018]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (3691011..3691305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (3669413..3669707)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (3691009..3691303)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3605850-3606424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3606998-3607571 Neighboring gene thromboxane A2 receptor Neighboring gene CACTIN antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3618043-3618915 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3623949-3624450 Neighboring gene cactin, spliceosome C complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3624451-3624950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3625177-3625738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3625739-3626300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:3626301-3626862 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 gamma Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3643569-3644108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3644109-3644646 Neighboring gene MPRA-validated peak3250 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3665265-3666095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3672153-3672828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3673765-3674558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3675389-3675890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3679833-3680333 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3681521-3682070 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682071-3682618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3682619-3683168 Neighboring gene Sharpr-MPRA regulatory region 323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9859 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13743 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3699523-3700306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3707827-3708490 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:3708491-3709152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3709988-3710533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3712547-3713048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:3713049-3713548 Neighboring gene tight junction protein 3 Neighboring gene MPRA-validated peak3252 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:3761575-3761892 Neighboring gene uncharacterized LOC105372248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13744 Neighboring gene amyloid beta precursor protein binding family A member 3

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_057569.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    3691011..3691305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    3669413..3669707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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