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 = 23121110

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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
125746241 GT-AG 0 2.396027982796223e-05 94 rna-XM_010254298.2 23121110 2 13975824 13975917 Nelumbo nucifera 4432 TAG|GTAAACAGAA...GTTCTCTTACTT/CTCTTACTTATC...TCTAG|GCT 1 1 48.817
125746242 GT-AG 0 1.000000099473604e-05 1801 rna-XM_010254298.2 23121110 3 13973901 13975701 Nelumbo nucifera 4432 AAG|GTGATGTCAT...GCTTTTTTATTG/TGCTTTTTTATT...TGCAG|GGT 0 1 52.517
125746243 GT-AG 0 1.000000099473604e-05 85 rna-XM_010254298.2 23121110 4 13973537 13973621 Nelumbo nucifera 4432 AGA|GTGAGTACCT...TAGTTCTTGATA/TGGATTCTGATT...AACAG|GAC 0 1 60.976
125746244 GT-AG 0 8.221186473530906e-05 535 rna-XM_010254298.2 23121110 5 13972618 13973152 Nelumbo nucifera 4432 GAG|GTAAATTTCC...CTATGCTTAATG/CTTTTTTTTATG...TTCAG|GTT 0 1 72.62
125746245 GT-AG 0 0.0011985595440871 76 rna-XM_010254298.2 23121110 6 13972432 13972507 Nelumbo nucifera 4432 CAG|GTATGTCTCT...TTCTGCTTAGTT/CTTCTGCTTAGT...TGCAG|GTA 2 1 75.955
125746246 GT-AG 0 1.000000099473604e-05 395 rna-XM_010254298.2 23121110 7 13971808 13972202 Nelumbo nucifera 4432 ATG|GTGAGCACTG...GTTGTTCTAATA/GTTGTTCTAATA...GGCAG|GTA 0 1 82.899
125748224 GT-AG 0 1.000000099473604e-05 338 rna-XM_010254298.2 23121110 1 13977463 13977800 Nelumbo nucifera 4432 GTG|GTTAGTAATT...GTATTTTTAATT/GTATTTTTAATT...TGCAG|GGA   0 4.124

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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]);