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)

8 rows where transcript_id = 5530412

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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
28484121 GT-AG 0 1.000000099473604e-05 11239 rna-XM_044274114.1 5530412 1 493330143 493341381 Bufo gargarizans 30331 GGG|GTGAGTGTGT...TTTTCTTTTTCA/TTCTTTTTCAAT...TTCAG|GCT 0 1 2.403
28484122 GT-AG 0 0.0024310249850782 3601 rna-XM_044274114.1 5530412 2 493341448 493345048 Bufo gargarizans 30331 CAG|GTATGTATTG...TTGTCCTTTATA/TTGTCCTTTATA...TGCAG|ATG 0 1 3.552
28484123 GT-AG 0 0.0001538145704345 3745 rna-XM_044274114.1 5530412 3 493345161 493348905 Bufo gargarizans 30331 AAG|GTACACCAGT...TGTCTCTTTGCT/GACTGTTTGATT...TACAG|AAA 1 1 5.501
28484124 GT-AG 0 0.0043384861070892 4786 rna-XM_044274114.1 5530412 4 493349023 493353808 Bufo gargarizans 30331 CTA|GTATGTATAT...TTATCTTGGATA/AAAGTATTTATC...TACAG|AAA 1 1 7.538
28484125 GT-AG 0 0.1529038805337084 77 rna-XM_044274114.1 5530412 5 493353898 493353974 Bufo gargarizans 30331 CAG|GTACCTCTTC...TTGTCTTTACTT/TTTGTCTTTACT...TTCAG|ACC 0 1 9.088
28484126 GT-AG 0 1.000000099473604e-05 18529 rna-XM_044274114.1 5530412 6 493358610 493377138 Bufo gargarizans 30331 AAG|GTTAGGTTCT...TAATCTTTAAAA/GCTTTACTTATA...TCAAG|GAT 0 1 89.781
28484127 GT-AG 0 1.000000099473604e-05 259 rna-XM_044274114.1 5530412 7 493377361 493377619 Bufo gargarizans 30331 CAA|GTGAGTGAAT...TTTCCTTTATTC/TTTTCCTTTATT...AACAG|AGT 0 1 93.646
28484128 GT-AG 0 1.7801263268161287e-05 23982 rna-XM_044274114.1 5530412 8 493377727 493401708 Bufo gargarizans 30331 TGT|GTAAGTGTCA...TGTCCTTTCATC/TGTCCTTTCATC...TACAG|TGC 2 1 95.508

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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]);