introns

Data license: ODbL · Data source: Larue & Roy, 2023 · About: Minor Intron Database (WtMTA)

id
INTEGER (primary key), globally unique identifier for each intron
dinucleotide_pair
TEXT, terminal dinucleotide sequences of the intron
is_minor
INTEGER, indicates if the intron is a minor intron (1) or not (0)
score
REAL, score representing the probability (0-100%) of the intron being minor
length
INTEGER, length of the intron in base pairs
transcript_id
INTEGER (foreign key referencing transcripts(id)), parent transcript
ordinal_index
INTEGER, ordinal position of the intron within the transcript (e.g., 3 for the third intron)
start
INTEGER, start position of the intron in the genome
end
INTEGER, end position of the intron in the genome
taxonomy_id
INTEGER (foreign key referencing genomes(taxonomy_id)), NCBI taxonomy identifier for species
scored_motifs
TEXT, motifs scored for the intron
phase
INTEGER, phase of the intron in coding sequence (0, 1, or 2 or null for introns outside of coding sequence)
in_cds
INTEGER, indicates if the intron is within the coding sequence (1) or not (0; e.g., UTR introns)
relative_position
REAL, relative position of the intron within the transcript (as a percentage of coding length)

6 rows where transcript_id = 5879244

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id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
29939458 GT-AG 0 1.000000099473604e-05 14817 rna-XM_014963994.1 5879244 1 62217 77033 Calidris pugnax 198806 CAG|GTAGGTGGCG...CCTTTCTTATTT/TCCTTTCTTATT...CTCAG|GAG 1 1 4.738
29939459 GT-AG 0 0.0007455873777627 2114 rna-XM_014963994.1 5879244 2 59973 62086 Calidris pugnax 198806 AGT|GTAAGTTGAC...TTTTCTTTATTT/TTTTTCTTTATT...TATAG|ATA 2 1 11.984
29939460 GT-AG 0 1.000000099473604e-05 825 rna-XM_014963994.1 5879244 3 58969 59793 Calidris pugnax 198806 ACA|GTAAGGAAAG...CTGCATTTGATA/CTGCATTTGATA...TCCAG|CTA 1 1 21.962
29939461 GT-AG 0 1.000000099473604e-05 1209 rna-XM_014963994.1 5879244 4 57584 58792 Calidris pugnax 198806 AGG|GTAAGATCTG...TTTTCCTTTTTT/TGAGGAGTTAGA...TCCAG|TGG 0 1 31.773
29939462 GT-AG 0 0.0001853112722118 753 rna-XM_014963994.1 5879244 5 56686 57438 Calidris pugnax 198806 AAG|GTATGTGTAA...TTTTCTTTTGTT/AAGTTGCTCAGT...AACAG|ATA 1 1 39.855
29939463 GT-AG 0 1.000000099473604e-05 1053 rna-XM_014963994.1 5879244 6 55493 56545 Calidris pugnax 198806 CTG|GTAAGTGTTC...TTTTCATTATAT/TTATATTTCACT...TCCAG|GTA 0 1 47.659

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CREATE TABLE "introns" (
"id" INTEGER,
  "dinucleotide_pair" TEXT,
  "is_minor" INTEGER,
  "score" REAL,
  "length" INTEGER,
  "transcript_id" INTEGER,
  "ordinal_index" INTEGER,
  "start" INTEGER,
  "end" INTEGER,
  "taxonomy_id" INTEGER,
  "scored_motifs" TEXT,
  "phase" INTEGER,
  "in_cds" INTEGER,
  "relative_position" REAL
  ,PRIMARY KEY ([id]),
   FOREIGN KEY([transcript_id]) REFERENCES [transcripts]([id]),
   FOREIGN KEY([taxonomy_id]) REFERENCES [genomes]([taxonomy_id])
);
CREATE INDEX [idx_introns_transcript_id]
    ON [introns] ([transcript_id]);
CREATE INDEX [idx_introns_taxonomy_id]
    ON [introns] ([taxonomy_id]);
CREATE INDEX [idx_introns_phase]
    ON [introns] ([phase]);
CREATE INDEX [idx_introns_is_minor]
    ON [introns] ([is_minor]);
CREATE INDEX [idx_introns_dinucleotide_pair]
    ON [introns] ([dinucleotide_pair]);
CREATE INDEX [idx_introns_score]
    ON [introns] ([score]);
CREATE INDEX [idx_introns_in_cds]
    ON [introns] ([in_cds]);