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LOC108348029 CAGE-defined B cell enhancer in LOC101928911-SPACA1 intergenic region [ Homo sapiens (human) ]

Gene ID: 108348029, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108348029
Gene description
CAGE-defined B cell enhancer in LOC101928911-SPACA1 intergenic region
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 the intergenic region between the uncharacterized LOC101928911 and SPACA1 (sperm acrosome associated 1) genes. 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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See LOC108348029 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (87925246..87926335)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (89133696..89134785)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (88634964..88636053)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24805 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:88445010-88445674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24808 Neighboring gene uncharacterized LOC101928911 Neighboring gene FOXA motif-containing MPRA enhancer 167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88505589-88506090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:88506091-88506590 Neighboring gene NANOG hESC enhancer GRCh37_chr6:88508442-88508943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24810 Neighboring gene RNA, 7SL, cytoplasmic 183, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:88571406-88572219 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24812 Neighboring gene uncharacterized LOC105377882 Neighboring gene uncharacterized LOC107986541

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 24813
  • LOC101928911-SPACA1 interval 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_051191.1 

    Range
    101..1190
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    87925246..87926335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    89133696..89134785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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