CXCL2 proximal 3′-UTR all-single-nucleotide-substitution fast-UTR library
Massively parallel functional annotation of 3′ untranslated regionsA 67-nt CXCL2 3′-UTR segment containing ARE1 and flanking sequence was tested with all 201 possible single-nucleotide substitutions in BEAS-2B-tTA cells. Reporter steady-state mRNA effects were reported as variant-versus-reference delta mRNA from pooled RNA/DNA clone measurements.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
Basal / Untreated
The BTV reporter is a bidirectional tetracycline-regulated viral reporter delivered by lentivirus. Oligonucleotide-pool clones were indexed and analyzed by paired-end Illumina sequencing of reporter RNA/cDNA and genomic DNA; the table uses the paper’s published WIG effect and significance tracks.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 16 definitions
- variant_id
- Stable variant identifier composed of CXCL2, coordinate, and RNA reference/alternate bases.
- gene
- Tested gene, CXCL2.
- chromosome
- Chromosome containing the tested sequence.
- genomic_coordinate_1based
- 1-based hg19 genomic coordinate of the substituted base.
- reference_genome
- Assembly used for genomic coordinates.
- strand
- Genomic strand of CXCL2; negative strand.
- reference_genomic_base
- Reference hg19 base on the genomic plus-strand representation.
- alternate_genomic_base
- Genomic complement of the tested RNA alternate base.
- reference_rna_base
- Reference base in the reporter/RNA orientation.
- alternate_rna_base
- Tested alternate base in the reporter/RNA orientation.
- rna_substitution
- Reference→alternate substitution in RNA orientation.
- delta_mrna
- Published difference in steady-state reporter mRNA between variant and reference, expressed as a fraction (e.g. 0.74 = 74%).
- neg_log10_p
- Published −log10 p-value for the variant-versus-reference delta mRNA comparison.
- p_value
- p-value reconstructed as 10^(−neg_log10_p).
- known_population_snp
- dbSNP identifier for the population SNPs listed in Supplementary Table 1; blank otherwise.
- reported_population_substitution
- Substitution notation printed in Supplementary Table 1; blank for unlisted substitutions.
Quality control
The authors removed clone indexes with mean <10 reads and excluded segments represented by fewer than 10 clones. The published WIG tracks are downstream of those filters; the processed table retains all 201 finite non-reference substitutions. Reference RNA alleles were checked against the UCSC hg19 sequence and the negative-strand orientation.
Curation notes
The original WIG contains RNA>A/C/G/U tracks; entries where the alternate matched the reference were excluded, leaving the 201 possible substitutions. The paper prints T in its population-SNP table while the fast-UTR tracks use U, so the processed RNA-oriented fields use U and retain the printed notation separately. Raw read counts are not supplied by the paper.