NCBI taxid 1192867
✓ Has minor (U12-type) introns
665 high-confidence minor introns · 694 including lower-confidence candidates (score 50–90) · snRNA machinery: corroborated· proteome BUSCO 98.8%
Download this genome's introns: minor introns (CSV) · all introns (BED)

genomes: 1192867

One row per species (2,634 genomes) — start here to look up an organism. Each row carries its minor-intron verdict (u12_status), high-confidence and total U12-type intron counts, snRNA status, and proteome completeness (BUSCO); click the taxonomy_id or species name to open its full genome page. Featured views: U12-type loss landscape U12-type % vs genome size U12-type intron count vs proteome BUSCO Minor vs total introns

Data license: ODbL · Data source: Larue & Roy, 2023

This data as json

taxonomy_id species common_name group phylum order family u12_status n_minor_introns percent_minor_introns u12_density_percentile n_u12_all n_major_introns motif_category z_excess hc_u12_cds hc_u12_exon snrna_status minor_snrnas n_minor_snrna u11_E u12_E u4atac_E u6atac_E total_genes total_introns_scored genome_size_bp gc_content coding_gc_content n_contigs assembly_n50 assembly_l50 busco_score accession genome_version source assembly_url ncbi_taxonomy_url wikipedia_url common_name_level taxonomy genome_path annotation_path
1192867 Chroicocephalus ridibundus black-headed gull vertebrates Chordata Charadriiformes Laridae U12_POSITIVE 665 0.40% 97.99 694 174,250 DETECTED 330.5754346992208 656 9 corroborated U11, U12, U4atac, U6atac 4 2.3e-22 8.5e-36 3.1e-14 1e-33 19,454 174,944 1,417,554,307 44.662 52.094 728 83,755,488 6 98.8 GCF_963924245.1 bChrRid1.1 refseq https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_963924245.1/ https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1192867 https://en.wikipedia.org/wiki/Black-headed_gull species
Chroicocephalus ridibundus;Chroicocephalus;Laridae;Charadriiformes;Neognathae;Aves;Coelurosauria;Theropoda;Saurischia;Dinosauria;Archosauria;Archelosauria;Sauria;Sauropsida;Amniota;Tetrapoda;Dipnotetrapodomorpha;Sarcopterygii;Euteleostomi;Teleostomi;Gnathostomata;Vertebrata;Craniata;Chordata;Deuterostomia;Bilateria;Eumetazoa;Metazoa;Opisthokonta;Eukaryota;cellular organisms
 vertebrates/refseq/chroicocephalus_ridibundus-bChrRid1.1/chroicocephalus_ridibundus.GCF_963924245.1_bChrRid1.1_genomic.fna.gz vertebrates/refseq/chroicocephalus_ridibundus-bChrRid1.1/chroicocephalus_ridibundus.GCF_963924245.1_bChrRid1.1_genomic.gff.gz

Links from other tables

Filter introns: U12-type set: Introns are called on the longest isoform per gene.

Splice-site logos for Chroicocephalus ridibundus

Rendered in the browser from motif_pwm counts via the Schneider-Stephens / WebLogo 3 information formula. The U12-type set control in the filter bar above switches the U12-type population — in these logos and every distribution chart below — between high-confidence calls (adjusted score ≥ 90) and motif-positive introns (p_motif ≥ 0.5: every intron whose splice-signal motif is U12-like, even where the genome made few or no calls). U2-type is the fixed genome-wide background.

Y-axis:

U12-type introns

U2-type introns

Intron distributions for Chroicocephalus ridibundus

Pre-aggregated from the full intron set (intron_stats); rendered client-side with Vega-Lite. Bars are grouped by set (U12-type = green, U2-type = gray).

Phase
Intron termini
Intron location
CDSexon
Score (intronIC, 0-100)
Intron length
Branch-point offset (nt to 3′SS)
Relative position in transcript (%)

Motif-score model for Chroicocephalus ridibundus

intronIC's per-species tail model: the U2-type (major) background motif-score distribution (gray, log-scaled) in p_motif space, its extrapolated exponential tail (dashed — how far U2-type scores are expected to reach by chance), and the U12-type calls (green, p_motif ≥ 0.9). Calls sitting far to the right of the U2-type tail are the evidence for a genuine minor-spliceosome population.