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 = 32094480

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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
179201783 GT-AG 0 40.51430723769808 46 rna-XM_012338704.1 32094480 1 1428961 1429006 Saprolegnia parasitica 101203 AGA|GTATCCGTCG...TCCTCTTTACTT/TTCCTCTTTACT...CGTAG|GCT 2 1 47.852
179201784 GT-AG 0 1.000000099473604e-05 47 rna-XM_012338704.1 32094480 2 1429098 1429144 Saprolegnia parasitica 101203 AAC|GTAAGCGCTG...CCACTCGTGGCT/GCTCGCCTCACG...CGTAG|TTT 0 1 52.101
179201785 GT-AG 0 0.003505282317963 50 rna-XM_012338704.1 32094480 3 1429349 1429398 Saprolegnia parasitica 101203 CGG|GTCTCTCGCA...GAAACATTGATA/TAGATATTTATG...GATAG|GCG 0 1 61.625
179201786 GT-AG 0 1.000000099473604e-05 49 rna-XM_012338704.1 32094480 4 1429498 1429546 Saprolegnia parasitica 101203 CAG|GTGATCGCCA...ATGTCATTGACA/ATGTCATTGACA...GACAG|ATG 0 1 66.246
179201787 GT-AG 0 0.0049801621194253 52 rna-XM_012338704.1 32094480 5 1429865 1429916 Saprolegnia parasitica 101203 GTC|GTACGCTCAT...TTTTCGGTACCA/TACCACCCCATT...AGTAG|GCG 0 1 81.092
179201788 GT-AG 0 4.987225741605904e-05 47 rna-XM_012338704.1 32094480 6 1430282 1430328 Saprolegnia parasitica 101203 GAG|GTATGCGCGG...AGGGTGGTAGCG/TGGAGAGAGACA...TGTAG|ATC 2 1 98.133

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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]);