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LOC108348031 GNG7 intron CAGE-defined B cell enhancer [ Homo sapiens (human) ]

Gene ID: 108348031, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108348031
Gene description
GNG7 intron CAGE-defined B 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 GNG7 (G protein subunit gamma 7) 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 B cells. It was validated as a functional enhancer by reporter assays in DAUDI B cells. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
19p13.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2667814..2669082)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2644023..2645289)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (2667812..2669080)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:2603289-2604055 Neighboring gene RNA, 7SL, cytoplasmic 121, pseudogene Neighboring gene H3K4me1 hESC enhancers GRCh37_chr19:2607315-2608169 and GRCh37_chr19:2608170-2609023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9803 Neighboring gene Sharpr-MPRA regulatory region 3019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13710 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:2626979-2628178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2643435-2643934 Neighboring gene microRNA 7850 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2650512-2650687 Neighboring gene MPRA-validated peak3237 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2678080-2678228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2723575-2724487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13715 Neighboring gene DIRAS family GTPase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2734868-2735368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2735369-2735869 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2739111-2739378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9805 Neighboring gene solute carrier family 39 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. An atlas of active enhancers across human cell types and tissues. Andersson R, et al. Nature, 2014 Mar 27. PMID 24670763, Free PMC Article
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 13712
  • GNG7 intron FANTOM5 blood enhancer

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_051193.1 

    Range
    101..1369
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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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    2667814..2669082
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2644023..2645289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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