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)

5 rows where transcript_id = 23121141

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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
125746512 GT-AG 0 0.0002481676578789 2482 rna-XM_010251908.2 23121141 1 9957023 9959504 Nelumbo nucifera 4432 GAG|GTATGTTCCG...TCAGTTTAGATA/AAATAGTTGATA...TGTAG|GCT 0 1 58.667
125746513 GT-AG 0 1.000000099473604e-05 134 rna-XM_010251908.2 23121141 2 9956833 9956966 Nelumbo nucifera 4432 CGG|GTAAGAATGT...TTCTCTTTGTTT/TGTTTGTTTACT...TGTAG|TGA 2 1 61.156
125746514 GT-AG 0 0.1149285032593156 177 rna-XM_010251908.2 23121141 3 9956425 9956601 Nelumbo nucifera 4432 GAG|GTAGCTTTCT...TTTTTTTTACAA/TTTATATTAAAC...TGCAG|ATA 2 1 71.422
125746515 GT-AG 0 3.004802249510867e-05 182 rna-XM_010251908.2 23121141 4 9955951 9956132 Nelumbo nucifera 4432 GAG|GTAAATAATA...TTTTTCTTAATC/CTTTTTCTTAAT...TCCAG|GTG 0 1 84.4
125746516 GT-AG 0 3.348629014081296e-05 362 rna-XM_010251908.2 23121141 5 9955392 9955753 Nelumbo nucifera 4432 ATG|GTAAGCCAGC...TTCCCTTTGATT/TTTTTCCTGATA...TGTAG|GTA 2 1 93.156

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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]);