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 = 10378393

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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
57022116 GT-AG 0 1.000000099473604e-05 100 rna-XM_025114029.1 10378393 1 14245289 14245388 Cynara cardunculus 4265 ATG|GTGATTAATC...TTTGTTTTGACT/TTTGTTTTGACT...GGCAG|CTC 1 1 6.282
57022117 GT-AG 0 1.000000099473604e-05 1464 rna-XM_025114029.1 10378393 2 14245503 14246966 Cynara cardunculus 4265 TAG|GTAAAAATTT...ACGGTATTAATA/AATACGTTCACT...TCCAG|ATG 1 1 8.389
57022118 GT-AG 0 2.746641553647654e-05 143 rna-XM_025114029.1 10378393 3 14247587 14247729 Cynara cardunculus 4265 GGG|GTGTGTTCTC...GAAACATTAATG/ATCCTATTCATG...GACAG|GAT 0 1 19.845
57022119 GT-AG 0 1.7699419598479644e-05 580 rna-XM_025114029.1 10378393 4 14247927 14248506 Cynara cardunculus 4265 AAA|GTAATCAAAA...TTTATTTGAACC/AAGATATTTATA...CTCAG|GCT 2 1 23.485
57022120 GT-AG 0 1.000000099473604e-05 152 rna-XM_025114029.1 10378393 5 14248727 14248878 Cynara cardunculus 4265 GTG|GTGAGTATTA...AACTTTCTATTG/GGCAAACTGATT...TTCAG|CAT 0 1 27.55
57022121 GT-AG 0 7.465664380305177e-05 409 rna-XM_025114029.1 10378393 6 14248999 14249407 Cynara cardunculus 4265 AAG|GTATGGGTTC...AGTATCTTATTT/AAGTATCTTATT...TGCAG|TCT 0 1 29.767
57022122 GT-AG 0 1.000000099473604e-05 1331 rna-XM_025114029.1 10378393 7 14250161 14251491 Cynara cardunculus 4265 CAG|GTAAGACATC...TATATCGTATCA/TTGGTTATGATA...TTCAG|TGC 0 1 43.681

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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]);