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)

8 rows where transcript_id = 4181787

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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
21587214 GT-AG 0 0.0003675573114327 100 rna-XM_010680271.2 4181787 1 1218120 1218219 Beta vulgaris 161934 AAC|GTAAATTTTG...TGTGTCTAATTT/TTGTGTCTAATT...ATTAG|GGT 2 1 3.435
21587215 GT-AG 0 1.000000099473604e-05 1987 rna-XM_010680271.2 4181787 2 1216026 1218012 Beta vulgaris 161934 AAG|GTTGTTGTTA...GTATTTTTTGTG/TGAGGGCTGACT...CGCAG|GTT 1 1 5.853
21587216 GT-AG 0 1.000000099473604e-05 80 rna-XM_010680271.2 4181787 3 1215738 1215817 Beta vulgaris 161934 TGG|GTCAGTTTTT...TTAGTTTTGATC/ATTTTATTGACA...CTCAG|GCC 2 1 10.554
21587217 GT-AG 0 9.369102586512312e-05 89 rna-XM_010680271.2 4181787 4 1215108 1215196 Beta vulgaris 161934 CAG|GTTTGTATTA...TGCTTCTTATTC/CTTTTATTTACT...ATCAG|GTC 0 1 22.78
21587218 GT-AG 0 10.594379381696442 108 rna-XM_010680271.2 4181787 5 1214748 1214855 Beta vulgaris 161934 TGG|GTATCTTGTC...TCTGACTTGATT/TGTTCTCTGACT...CTCAG|CTA 0 1 28.475
21587219 GT-AG 0 0.0033150865757088 102 rna-XM_010680271.2 4181787 6 1214454 1214555 Beta vulgaris 161934 TTG|GTAACTCTTC...TGTTCTGTGATG/TCTGTGATGATC...TGCAG|GCT 0 1 32.814
21587220 GT-AG 0 1.0271890627372056e-05 175 rna-XM_010680271.2 4181787 7 1214204 1214378 Beta vulgaris 161934 TTG|GTAAAATCGT...ATTTTTTTGACC/ATTTTTTTGACC...GATAG|GTC 0 1 34.508
21587221 GT-AG 0 0.0752996538350706 1262 rna-XM_010680271.2 4181787 8 1210416 1211677 Beta vulgaris 161934 TCG|GTATGTTTCC...TATTTGTTGACG/TATTTGTTGACG...TGCAG|ATG 0 1 91.593

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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]);