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 = 26383311

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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
146244273 GT-AG 0 1.000000099473604e-05 132 rna-gnl|WGS:JXTB|PanWU01x14_001720.1 26383311 1 2016201 2016332 Parasponia andersonii 3476 AAG|GTTGGTTTGT...ATTTTGTTGATT/TAATTTTTCATC...ATTAG|ACT 0 1 9.288
146244274 GT-AG 0 0.001326748292618 326 rna-gnl|WGS:JXTB|PanWU01x14_001720.1 26383311 2 2016554 2016879 Parasponia andersonii 3476 CAG|GTACCACTTT...TAATATTTAATT/ATTTAATTAATT...TTCAG|GGA 2 1 32.095
146244275 GT-AG 0 1.000000099473604e-05 586 rna-gnl|WGS:JXTB|PanWU01x14_001720.1 26383311 3 2017106 2017691 Parasponia andersonii 3476 AAG|GTACTACTGT...GATTCTCTAATT/GATTCTCTAATT...TCCAG|ATC 0 1 55.418
146244276 GT-AG 0 0.1026197209333592 349 rna-gnl|WGS:JXTB|PanWU01x14_001720.1 26383311 4 2017778 2018126 Parasponia andersonii 3476 CTG|GTCTCTCTCT...AATCTTTTGATG/TTTTGGTTTATA...TTCAG|GTA 2 1 64.293
146244277 GT-AG 0 0.0001636837812645 104 rna-gnl|WGS:JXTB|PanWU01x14_001720.1 26383311 5 2018219 2018322 Parasponia andersonii 3476 TAG|GTAACAAATA...AAAGCTTTAAAT/AATATATTTATG...TTCAG|ACA 1 1 73.787

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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]);