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 = 8855915

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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
47813296 GT-AG 0 0.0446239551863277 79 rna-XM_027258542.1 8855915 1 47847437 47847515 Coffea arabica 13443 CAT|GTATGTTTCG...TTTTTTTTTGTT/TTTCTGTTTACC...TGCAG|CTC 1 1 9.136
47813297 GT-AG 0 0.0002251090634513 97 rna-XM_027258542.1 8855915 2 47847669 47847765 Coffea arabica 13443 AAG|GTCTTCATCC...ATTGTTCTAACA/ATTGTTCTAACA...TGCAG|GTA 1 1 13.559
47813298 GT-AG 0 1.000000099473604e-05 134 rna-XM_027258542.1 8855915 3 47847829 47847962 Coffea arabica 13443 CAG|GTGGACCACT...TTATTCTTTATG/TACTTATTCATT...TACAG|CTA 1 1 15.38
47813299 GT-AG 0 5.056381388993662e-05 95 rna-XM_027258542.1 8855915 4 47848026 47848120 Coffea arabica 13443 CAG|GTATTTGATG...GTTTGTTTACTG/AGTTTGTTTACT...TATAG|AAC 1 1 17.202
47813300 GT-AG 0 1.06798659220212e-05 94 rna-XM_027258542.1 8855915 5 47848199 47848292 Coffea arabica 13443 TAG|GTTGTCCTCT...ATCTTCTGAATA/CTACTTCTCACC...TACAG|CCA 1 1 19.456
47813301 GT-AG 0 0.000650208860219 87 rna-XM_027258542.1 8855915 6 47849361 47849447 Coffea arabica 13443 AAG|GTATGCATAG...ATATACTTATAA/TATATACTTATA...TGCAG|GTT 1 1 50.332
47813302 GT-AG 0 0.0961116508589784 367 rna-XM_027258542.1 8855915 7 47851127 47851493 Coffea arabica 13443 CTG|GTACACTTTC...GTTTTTTTATTG/TGTTTTTTTATT...CCCAG|GCG 0 1 98.873

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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]);