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 = 32094428

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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
179201412 GT-AG 0 9.095598187521644e-05 48 rna-XM_012338189.1 32094428 1 215597 215644 Saprolegnia parasitica 101203 AAG|GTGTCGAATG...TGCTTCTTGCCT/TCTTGCCTCACT...ACTAG|CTC 0 1 25.119
179201413 GT-AG 0 0.0005037843461797 50 rna-XM_012338189.1 32094428 2 215789 215838 Saprolegnia parasitica 101203 GGT|GTACGCACGC...CGCAACTTGGCT/GCAGGTGTGATT...AGTAG|AGT 0 1 29.704
179201414 GT-AG 0 0.0001272439237693 47 rna-XM_012338189.1 32094428 3 215968 216014 Saprolegnia parasitica 101203 AAC|GTACTTTGTA...TGTCAAATGACG/TGTCAAATGACG...TCTAG|CTC 0 1 33.811
179201415 GT-AG 0 1.6793737911740592e-05 44 rna-XM_012338189.1 32094428 4 216318 216361 Saprolegnia parasitica 101203 AAG|GTAGACCTTT...AAAATGTAAATC/CAAAATGTAAAT...GTTAG|GTG 0 1 43.457
179201416 GT-AG 0 0.000312571155318 55 rna-XM_012338189.1 32094428 5 216485 216539 Saprolegnia parasitica 101203 CGG|GTTTCTCACC...CTCATGTGAATT/GATGCGCTCATG...TATAG|ATG 0 1 47.373
179201417 GT-AG 0 0.0001019645519075 46 rna-XM_012338189.1 32094428 6 216663 216708 Saprolegnia parasitica 101203 AAG|GTATTCGACC...CGGCTTGGGACC/CTTGGGACCACC...TCTAG|ATC 0 1 51.289
179201418 GT-AG 0 0.0001863367047536 45 rna-XM_012338189.1 32094428 7 216750 216794 Saprolegnia parasitica 101203 TCG|GTATTACTTC...ACATCTTTCAGG/ACATCTTTCAGG...GCTAG|AAA 2 1 52.595
179201419 GT-AG 0 2.040513569259053e-05 45 rna-XM_012338189.1 32094428 8 217191 217235 Saprolegnia parasitica 101203 CCG|GTACTTCCTC...CAACCCGCAACA/GCAACACTGAAT...TGTAG|GCT 2 1 65.202

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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]);