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)

8 rows where transcript_id = 5981972

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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
30724769 GT-AG 0 1.892639193862286e-05 5410 rna-XM_025852756.1 5981972 1 12693319 12698728 Callorhinus ursinus 34884 AGG|GTAAGTATTG...CATTTTTTATCA/TCATTTTTTATC...TACAG|ACG 0 1 7.061
30724770 GT-AG 0 1.000000099473604e-05 41462 rna-XM_025852756.1 5981972 2 12699845 12741306 Callorhinus ursinus 34884 CAG|GTAAAGTATG...CATACCTTACTG/GCATACCTTACT...CACAG|ATT 0 1 60.663
30724771 GT-AG 0 0.0002301212377505 79210 rna-XM_025852756.1 5981972 3 12741361 12820570 Callorhinus ursinus 34884 GCA|GTAAGTAATC...TTTCCTTTGATT/ATTATTCTAATT...AACAG|CTA 0 1 63.256
30724772 GT-AG 0 1.000000099473604e-05 66941 rna-XM_025852756.1 5981972 4 12820718 12887658 Callorhinus ursinus 34884 CGG|GTAAGACATT...AGTTCTATATTT/TCTATATTTACA...ATAAG|ACT 0 1 70.317
30724773 GT-AG 0 0.0004816323638215 10465 rna-XM_025852756.1 5981972 5 12887867 12898331 Callorhinus ursinus 34884 AAG|GTATTTCATA...CTTTTTTTGTTT/AATGAAATCATA...CATAG|AGG 1 1 80.307
30724774 GT-AG 0 1.000000099473604e-05 3145 rna-XM_025852756.1 5981972 6 12898409 12901553 Callorhinus ursinus 34884 GTG|GTACGTACAT...ATTTCTCTACTT/TATATATTTATG...TACAG|AAA 0 1 84.006
30724775 GT-AG 0 1.000000099473604e-05 10578 rna-XM_025852756.1 5981972 7 12901638 12912215 Callorhinus ursinus 34884 AAG|GTGAAAGTAA...TACTGTTTGATG/TACTGTTTGATG...TTCAG|AAT 0 1 88.04
30724776 GT-AG 0 1.000000099473604e-05 4048 rna-XM_025852756.1 5981972 8 12912339 12916386 Callorhinus ursinus 34884 CAG|GTAGGTGCCA...TAATTCTAAAAA/CACATACTAATT...CTCAG|GCG 0 1 93.948

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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]);