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LOC108254685 PDXK-CSTB intergenic CAGE-defined low expression enhancer [ Homo sapiens (human) ]

Gene ID: 108254685, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108254685
Gene description
PDXK-CSTB intergenic CAGE-defined low expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
regulatory: enhancer, transcriptional_cis_regulatory_region
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 is located in the intergenic region between the PDXK [pyridoxal (pyridoxine, vitamin B6) kinase] and CSTB (cystatin B) genes on chromosome 21. A subregion was defined as a low expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE), and was validated as a functional enhancer by reporter assays in both HeLa and HepG2 cells. Two subregions marked by the H3K27ac and H3K4me1 histone modifications were also shown to be active enhancers by ChIP-STARR-seq in human embryonic stem cells. Another subregion was validated as a high-confidence cis-regulatory element for the CSTB gene based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Nov 2022]
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Genomic context

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Location:
21q22.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (43767823..43769207)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42123432..42124816)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45187704..45188752)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18546 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13365 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45139703-45140612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18547 Neighboring gene pyridoxal kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45146555-45147396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45148239-45149080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45149081-45149922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45151396-45151896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45152891-45153850 Neighboring gene uncharacterized LOC105372824 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45157073-45157572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45159504-45160242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45160243-45160981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45183829-45184574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45184575-45185320 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45186633-45187246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45189831-45190753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45190754-45191675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13368 Neighboring gene cystatin B upstream repeat instability region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45198401-45199200 Neighboring gene uncharacterized LOC105372825 Neighboring gene cystatin B

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  3. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  4. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article
  5. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • CRISPRi-validated cis-regulatory element chr21.1148
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45187861-45188474
  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45188475-45189088
  • PDXK-CSTB interval low CAGE FANTOM5 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_051032.3 

    Range
    101..1485
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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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    43767823..43769207
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42123432..42124816
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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