U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC108353820 JPH2 intron CAGE-defined T cell enhancer [ Homo sapiens (human) ]

Gene ID: 108353820, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC108353820
Gene description
JPH2 intron CAGE-defined T cell enhancer
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 element is located in an intron of the JPH2 (junctophilin 2) gene. It was defined as a tissue-specific transcribed enhancer based on the co-occurrence of H3K4me1, H3K27ac and DNase hypersensitive epigenetic marks with the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE) in T cells. It was validated as a functional enhancer by reporter assays in Jurkat T cells. [provided by RefSeq, Jul 2016]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
20q13.12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (44153318..44154567)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (45887955..45889204)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (42781958..42783207)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543229-42543946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42543947-42544664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42564724-42565224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42565225-42565725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42571264-42571764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17918 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:42583279-42584478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42584612-42585246 Neighboring gene TOX high mobility group box family member 2 Neighboring gene Sharpr-MPRA regulatory region 6747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42634840-42635340 Neighboring gene RNA, 7SL, cytoplasmic 443, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42696545-42697061 Neighboring gene Sharpr-MPRA regulatory region 7745 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42739928-42740441 Neighboring gene Sharpr-MPRA regulatory region 3924 Neighboring gene junctophilin 2 Neighboring gene uncharacterized LOC124904909 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:42795218-42795478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42806021-42806521 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:42809003-42809909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42810816-42811722 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:42832370-42833569 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42838821-42839440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12940 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:42860439-42861068 Neighboring gene OSER1 divergent transcript Neighboring gene oxidative stress responsive serine rich 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:42875650-42876448 Neighboring gene Sharpr-MPRA regulatory region 13448 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:42900885-42901394 Neighboring gene Sharpr-MPRA regulatory region 2613 Neighboring gene ganglioside induced differentiation associated protein 1 like 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

Go to the top of the page Help

Other Names

  • JPH2 intron FANTOM5 blood enhancer

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_051216.1 

    Range
    101..1350
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    44153318..44154567
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    45887955..45889204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases