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)

5 rows where transcript_id = 4520933

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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
23578122 GT-AG 0 1.000000099473604e-05 2437 rna-XM_019954497.1 4520933 1 67804742 67807178 Bos indicus 9915 CAG|GTAAAGTCAG...CATTTCTTCTTT/AAAAAGTTGACC...TCCAG|GTA 2 1 5.776
23578123 GT-AG 0 0.0453035323879034 4138 rna-XM_019954497.1 4520933 3 67807485 67811622 Bos indicus 9915 CAG|GTACCCATGC...CTTCCCTCACTC/ACTTCCCTCACT...TCCAG|GTC 0 1 15.115
23578124 GT-AG 0 0.0009634114631991 13439 rna-XM_019954497.1 4520933 4 67812508 67825946 Bos indicus 9915 CAG|GTACCTCCTT...TTTGTGTTAAGA/AGAGTATTCATC...TTTAG|GTC 0 1 42.304
23578125 GT-AG 0 3.806068306959567e-05 5615 rna-XM_019954497.1 4520933 5 67826178 67831792 Bos indicus 9915 GAG|GTATGTGCTG...TCTGTTGTGATC/TCTGTTGTGATC...CTCAG|GTG 0 1 49.401
23578126 GT-AG 0 1.000000099473604e-05 2218 rna-XM_019954497.1 4520933 6 67831917 67834134 Bos indicus 9915 CAG|GTAAAGGAGC...AACCCCTTCACT/GCAGTACTAACC...TACAG|ATG 1 1 53.21

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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]);