genomes: 9915

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
9915	Bos indicus	zebu cattle	vertebrates	Chordata	Artiodactyla	Bovidae	U12_POSITIVE	702	0.43%	99.47	745	171,995	DETECTED	348.3897534353251	658	44	corroborated	U11, U12, U4atac, U6atac	4	2.3e-26	6.2e-37	1.9e-21	8.8e-33	26,229	172,740	2,673,965,444	41.742	53.384	32	106,310,653	11	93.8	GCF_000247795.1	Bos_indicus_1.0	refseq	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000247795.1/	https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9915	https://en.wikipedia.org/wiki/Zebu	species	bos indicus;bos;bovinae;bovidae;pecora;ruminantia;artiodactyla;laurasiatheria;boreoeutheria;eutheria;theria;mammalia;amniota;tetrapoda;dipnotetrapodomorpha;sarcopterygii;euteleostomi;teleostomi;gnathostomata;vertebrata;craniata;chordata;deuterostomia;bilateria;eumetazoa;metazoa;opisthokonta;eukaryota;cellular organisms	vertebrates/refseq/bos_indicus-Bos_indicus_1.0/bos_indicus.GCF_000247795.1_Bos_indicus_1.0_genomic.fna.gz	vertebrates/refseq/bos_indicus-Bos_indicus_1.0/bos_indicus.GCF_000247795.1_Bos_indicus_1.0_genomic.gff.gz

Links from other tables

20,967 rows from taxonomy_id in transcripts
172,740 rows from taxonomy_id in introns
745 rows from taxonomy_id in minor_introns

Filter introns: All CDS only Exon only U12-type set: High-confidence Motif-positive Introns are called on the longest isoform per gene.

Splice-site logos for Bos indicus

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 Bos indicus

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 Bos indicus

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.

5′SS vs BPS motif scores for Bos indicus

Every intron's raw 5′ splice-site vs branch-point motif score (log-odds, robust-standardized per genome). The U2-type (major) background is a log-scaled density (far too many introns to plot individually); U12-type calls are points, colored by confidence like intronIC (green > 90, amber / red = lower tiers set from the per-genome score spread). Minor introns separate into the high-score corner.