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)

7 rows where transcript_id = 9992780

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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
54888841 GT-AG 0 0.0001896613334585 4113 rna-XM_009564092.1 9992780 1 1841956 1846068 Cuculus canorus 55661 CAA|GTACTTCTAT...AAACTATTAATT/AAACTATTAATT...TGCAG|GAT 0 1 2.5
54888842 GT-AG 0 2.77842558329742e-05 385 rna-XM_009564092.1 9992780 2 1841462 1841846 Cuculus canorus 55661 TTG|GTAGGATTGC...GCCTTTTTAATT/TTGATTTTAATG...TCTAG|CAT 1 1 11.583
54888843 GT-AG 0 1.3445632538872672e-05 2570 rna-XM_009564092.1 9992780 3 1838786 1841355 Cuculus canorus 55661 CAG|GTATGACCTA...ATGTTATTATCA/ACTGTTTTCATT...GTAAG|ACT 2 1 20.417
54888844 GT-AG 0 1.000000099473604e-05 1644 rna-XM_009564092.1 9992780 4 1836931 1838574 Cuculus canorus 55661 AAG|GTAAGTAATG...ACCCTCTTAATT/AGTTTTTTAAAT...CTCAG|GAT 0 1 38.0
54888845 GT-AG 0 0.0004884171868353 704 rna-XM_009564092.1 9992780 5 1836134 1836837 Cuculus canorus 55661 GAG|GTATGGTTTA...GCTTCCTTTCCT/AAATCAATTATC...TGTAG|GTG 0 1 45.75
54888846 GT-AG 0 1.000000099473604e-05 898 rna-XM_009564092.1 9992780 6 1835175 1836072 Cuculus canorus 55661 TTG|GTGAGTAAGA...TTCTTCTTATCT/TTTCTTCTTATC...TTCAG|TGA 1 1 50.833
54888847 GT-AG 0 1.000000099473604e-05 859 rna-XM_009564092.1 9992780 7 1834196 1835054 Cuculus canorus 55661 TTG|GTAAGTGCTG...TTTCCCTTTTCT/TGGATGTTCACA...TACAG|CTC 1 1 60.833

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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]);