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LOC108348028 TBCD intron CAGE-defined B cell enhancer [ Homo sapiens (human) ]

Gene ID: 108348028, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108348028
Gene description
TBCD intron CAGE-defined B cell enhancer
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
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 TBCD (tubulin folding cofactor D) 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, and it also had some enhancer activity in Jurkat T cells and THP-1 monocytes. This locus also includes two accessible chromatin subregions, one of which was validated as an enhancer and the other as a silencer based on their ability to activate or repress 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:
17q25.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82870853..82872050)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83745968..83747167)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80828729..80829926)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80693947-80694659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80694660-80695371 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80701509-80702145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9229 Neighboring gene Sharpr-MPRA regulatory region 591 Neighboring gene fructosamine 3 kinase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13015 Neighboring gene tubulin folding cofactor D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80747669-80748170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80751687-80752407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80786629-80787475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80795429-80795930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80802695-80803196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80803197-80803696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80807949-80808451 Neighboring gene zinc finger protein 750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80817109-80817884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80824049-80824550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80824551-80825050 Neighboring gene uncharacterized LOC124904096 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:80833329-80834528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80840561-80841358 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80842957-80843755 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:80853679-80853938 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80856643-80857144 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:80877734-80878933 Neighboring gene uncharacterized LOC124904095 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:80935960-80937159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80942083-80942584 Neighboring gene Sharpr-MPRA regulatory region 7018 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80968063-80968585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80975436-80976388 Neighboring gene uncharacterized LOC124904094

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 13018
  • ATAC-STARR-seq lymphoblastoid silent region 9231
  • TBCD 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_051187.1 

    Range
    101..1298
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82870853..82872050
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83745968..83747167
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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