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 = 34724137

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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
195653568 GT-AG 0 0.0101882786804783 318 rna-XM_010530954.2 34724137 2 2377973 2378290 Tarenaya hassleriana 28532 AAG|GTATACTAGA...GGCTTCTGATTT/TTTATTTTCATG...TGCAG|ATA 1 1 51.217
195653569 GT-AG 0 0.0055408448288029 102 rna-XM_010530954.2 34724137 3 2377576 2377677 Tarenaya hassleriana 28532 AAG|GTATTCACCT...TTTATGTTATCA/CTTTATGTTATC...TGCAG|ATT 2 1 58.123
195653570 GT-AG 0 1.000000099473604e-05 121 rna-XM_010530954.2 34724137 4 2376683 2376803 Tarenaya hassleriana 28532 GAT|GTGAGGATCT...TCTTCTTTGATG/TATTTGTTGATC...TACAG|CTT 0 1 76.194
195653571 GT-AG 0 1.000000099473604e-05 86 rna-XM_010530954.2 34724137 5 2376473 2376558 Tarenaya hassleriana 28532 ATG|GTAAGTGATG...TTTTGCATGATT/TTTTGCATGATT...GTCAG|GGG 1 1 79.096
195653572 GT-AG 0 2.708588448871697e-05 489 rna-XM_010530954.2 34724137 6 2375764 2376252 Tarenaya hassleriana 28532 CTG|GTAAGTATTT...CAACTCTTAACA/TTTACATTGATA...GGTAG|GTA 2 1 84.246
195653573 GT-AG 0 1.000000099473604e-05 98 rna-XM_010530954.2 34724137 7 2375207 2375304 Tarenaya hassleriana 28532 TGG|GTTAGCTCCC...TCTAGTTTGATG/TCTAGTTTGATG...GACAG|GAC 2 1 94.991

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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]);