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)

7 rows where transcript_id = 1565097

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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
8696117 GT-AG 0 8.104736561329719e-05 357 rna-XM_020230769.1 1565097 2 189180 189536 Ananas comosus 4615 AAG|GTGTGTTATT...AACTTTTTAATG/AACTTTTTAATG...TGCAG|ATG 0 1 62.455
8696118 GT-AG 0 0.0778575429534381 116 rna-XM_020230769.1 1565097 3 188931 189046 Ananas comosus 4615 AAT|GTATGCTGCT...ATCATCTTGTTT/GCAAATCTTATG...TCTAG|TTC 1 1 64.993
8696119 GT-AG 0 1.1552054520497206 387 rna-XM_020230769.1 1565097 4 188455 188841 Ananas comosus 4615 AAG|GTATTCTTCC...AACACTTTGACT/CTGGAACTAATA...TTTAG|CTA 0 1 66.692
8696120 GT-AG 0 2.919631498559856e-05 1151 rna-XM_020230769.1 1565097 5 187065 188215 Ananas comosus 4615 CGG|GTAAGCATCA...GTTGATTTGACT/ATTATGTTGATT...CACAG|ATC 2 1 71.254
8696121 GT-AG 0 0.0050630902739152 649 rna-XM_020230769.1 1565097 6 186329 186977 Ananas comosus 4615 TAG|GTAACTTGCT...ATATCCTTCTTT/TCGATTCTAATT...AACAG|ATT 2 1 72.915
8696122 GT-AG 0 1.000000099473604e-05 196 rna-XM_020230769.1 1565097 7 186033 186228 Ananas comosus 4615 TCG|GTAATAACAA...AATTTCTTGATT/AATTTCTTGATT...TTCAG|ATT 0 1 74.823
8696123 GT-AG 0 1.000000099473604e-05 85 rna-XM_020230769.1 1565097 8 185734 185818 Ananas comosus 4615 AAG|GTAAGGATGT...TTCTTTTTAATA/TTCTTTTTAATA...CACAG|CTG 1 1 78.908

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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]);