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LOC108281139 RRP1B-PDXK intergenic CAGE-defined mid-level expression enhancer [ Homo sapiens (human) ]

Gene ID: 108281139, updated on 10-Oct-2023

Summary

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Gene symbol
LOC108281139
Gene description
RRP1B-PDXK intergenic CAGE-defined mid-level expression enhancer
Gene type
biological region
Feature type(s)
misc_feature: CAGE_cluster
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 RRP1B (ribosomal RNA processing 1B) and PDXK [pyridoxal (pyridoxine, vitamin B6) kinase] genes. It was defined as a mid-level expression actively transcribed enhancer based on the presence of balanced bidirectional capped transcripts by cap analysis of gene expression (CAGE). It was validated as a functional enhancer by reporter assays in HeLa cells. [provided by RefSeq, Jul 2016]
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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 (43712088..43712709)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42067630..42068251)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45131969..45132590)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18545 Neighboring gene ribosomal RNA processing 1B Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:45094121-45094620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13363 Neighboring gene uncharacterized LOC124905030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45127109-45127642 Neighboring gene uncharacterized LOC124905031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45131022-45131903 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 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 pyridoxal kinase 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

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

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

  • RRP1B-PDXK interval mid 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_051095.1 

    Range
    101..722
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    43712088..43712709
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    42067630..42068251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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