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 = 23617111

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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
128510971 GT-AG 0 1.000000099473604e-05 134 rna-XM_019408417.1 23617111 2 13412649 13412782 Nicotiana attenuata 49451 TTG|GTAAGATATC...CTCCCCTTGTCC/AACAAAATCATG...TGCAG|ATT 1 1 27.487
128510972 GT-AG 0 1.000000099473604e-05 155 rna-XM_019408417.1 23617111 3 13412429 13412583 Nicotiana attenuata 49451 GAG|GTGTGTTATG...TTTTGTTTATCC/TTTTTGTTTATC...TTTAG|GAT 0 1 29.206
128510973 GT-AG 0 0.0016230734196551 108 rna-XM_019408417.1 23617111 4 13410697 13410804 Nicotiana attenuata 49451 AAG|GTGTTCTTCT...CAATTTTTAAAT/CAATTTTTAAAT...TGCAG|GAG 1 1 72.169
128510974 GT-AG 0 1.000000099473604e-05 847 rna-XM_019408417.1 23617111 5 13409665 13410511 Nicotiana attenuata 49451 GAA|GTAAGTAGTG...ATATCTATAATC/ATATCTATAATC...TTCAG|GAT 0 1 77.063
128510975 GT-AG 0 1.000000099473604e-05 76 rna-XM_019408417.1 23617111 6 13409402 13409477 Nicotiana attenuata 49451 CAG|GTTAACCTGT...ATTTTCTTATAT/TATATGCTCACC...TGTAG|ATG 1 1 82.011
128517215 GT-AG 0 6.643502233241838e-05 527 rna-XM_019408417.1 23617111 1 13413005 13413531 Nicotiana attenuata 49451 TAG|GTAAGTCTAC...ATGTCCTTAATC/CTTAATCTAAAT...ATCAG|ACT   0 23.492

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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]);