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)

9 rows where transcript_id = 35515720

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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
199620478 GT-AG 0 1.000000099473604e-05 4797 rna-XM_010215070.1 35515720 1 150728 155524 Tinamus guttatus 94827 AAG|GTGAGCGGGG...TTTTGTTTATTT/TTTTTGTTTATT...ACCAG|AAA 0 1 2.251
199620479 GT-AG 0 0.0471411759343673 2118 rna-XM_010215070.1 35515720 2 155636 157753 Tinamus guttatus 94827 AGT|GTATGCATGC...TTTGTTTTTCCT/AAGGTACTGATT...TGCAG|CTT 0 1 14.148
199620480 GT-AG 0 1.000000099473604e-05 3378 rna-XM_010215070.1 35515720 3 157853 161230 Tinamus guttatus 94827 GAG|GTAGGAGAAG...GTTGTTTTAATC/GTTGTTTTAATC...TACAG|TCA 0 1 24.759
199620481 GT-AG 0 0.0003356636164145 7020 rna-XM_010215070.1 35515720 4 161330 168349 Tinamus guttatus 94827 AAA|GTAAGCTCAT...CTCCCCTTACTG/TCTCCCCTTACT...CACAG|GAC 0 1 35.37
199620482 GT-AG 0 1.000000099473604e-05 2593 rna-XM_010215070.1 35515720 5 168449 171041 Tinamus guttatus 94827 TAT|GTGAGTTTAT...ATCATTTTAACA/ATCATTTTAACA...CTCAG|GAT 0 1 45.981
199620483 GT-AG 0 1.000000099473604e-05 3750 rna-XM_010215070.1 35515720 6 171141 174890 Tinamus guttatus 94827 CAG|GTAATGCTCA...GAAGCCTTGAGC/GAAGCCTTGAGC...TGCAG|GAT 0 1 56.592
199620484 GT-AG 0 1.000000099473604e-05 421 rna-XM_010215070.1 35515720 7 174990 175410 Tinamus guttatus 94827 GAT|GTGAGTAGCG...CTCAACTTACCT/ACTCAACTTACC...TACAG|GAT 0 1 67.203
199620485 GT-AG 0 1.000000099473604e-05 1072 rna-XM_010215070.1 35515720 8 175507 176578 Tinamus guttatus 94827 AAG|GTTAGTAGTG...TCTGGCTTCACG/TCTGGCTTCACG...TGCAG|AAC 0 1 77.492
199620486 GT-AG 0 1.000000099473604e-05 1459 rna-XM_010215070.1 35515720 9 176678 178136 Tinamus guttatus 94827 AAG|GTACGAGCGG...GCTTTTCTAACT/GCTTTTCTAACT...CACAG|GCA 0 1 88.103

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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]);