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 = 8713670

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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
46842262 GT-AG 0 1.000000099473604e-05 881 rna-gnl|WGS:VZRZ|CLIRUF_R11544_mrna 8713670 1 26187 27067 Climacteris rufus 47695 TCG|GTAATGTGAC...TCTCTCTGAGCC/TTCTCTCTGAGC...TGCAG|TAC 0 1 31.225
46842263 GT-AG 0 1.000000099473604e-05 93 rna-gnl|WGS:VZRZ|CLIRUF_R11544_mrna 8713670 2 26003 26095 Climacteris rufus 47695 TCG|GTGCGTGGGG...CCCTCCCTGATG/CCCTCCCTGATG...ACAAG|GCG 1 1 43.215
46842264 GT-AG 0 1.000000099473604e-05 166 rna-gnl|WGS:VZRZ|CLIRUF_R11544_mrna 8713670 3 25762 25927 Climacteris rufus 47695 GCG|GTGAGCGCGA...AAACGTTTGACC/AAACGTTTGACC...TCCAG|CCC 1 1 53.096
46842265 GT-AG 0 1.000000099473604e-05 73 rna-gnl|WGS:VZRZ|CLIRUF_R11544_mrna 8713670 4 25613 25685 Climacteris rufus 47695 CCT|GTGAGTGCGG...CGGGCCCTGACC/CGGGCCCTGACC...CGCAG|GCT 2 1 63.109
46842266 GT-AG 0 1.000000099473604e-05 857 rna-gnl|WGS:VZRZ|CLIRUF_R11544_mrna 8713670 5 24629 25485 Climacteris rufus 47695 CTG|GTGAGCGAGG...TGCTTTTTATTG/GTGCTTTTTATT...TGCAG|GTC 0 1 79.842

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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]);