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 = 1076612

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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
5510139 GT-AG 0 9.845867156717494e-05 724 rna-XM_006257951.3 1076612 1 626638 627361 Alligator mississippiensis 8496 CAG|GTACGCGTCC...ATTGCCTTGGCT/TGTGATCTCATT...TGCAG|GTG 0 1 3.271
5510140 GT-AG 0 1.000000099473604e-05 1386 rna-XM_006257951.3 1076612 2 625199 626584 Alligator mississippiensis 8496 CAG|GTAAATATTC...CAGATTTTAATT/TTAATTTTCATC...TTTAG|GTC 2 1 11.526
5510141 GT-AG 0 1.000000099473604e-05 1111 rna-XM_006257951.3 1076612 3 624050 625160 Alligator mississippiensis 8496 TAG|GTAAGAACTC...ATTTCTTTGTTT/TGGTATTTAATT...TTAAG|GTG 1 1 17.445
5510142 GT-AG 0 1.000000099473604e-05 1285 rna-XM_006257951.3 1076612 4 622679 623963 Alligator mississippiensis 8496 CAG|GTAGGCAGTT...CTGGTTTCAATC/GCTGGTTTCAAT...TACAG|GTC 0 1 30.841
5510143 GT-AG 0 1.000000099473604e-05 2721 rna-XM_006257951.3 1076612 5 619785 622505 Alligator mississippiensis 8496 AAG|GTACAAAAAG...GACAGCTGAACT/TGGGTGCTGACA...GGCAG|CTA 2 1 57.788
5510144 GT-AG 0 1.000000099473604e-05 1769 rna-XM_006257951.3 1076612 6 617913 619681 Alligator mississippiensis 8496 CAG|GTAGGACATT...CTTTTCTTTTCA/TTTCTTTTCACC...TTCAG|ATC 0 1 73.832
5510145 GT-AG 0 1.6252837985777455e-05 4923 rna-XM_006257951.3 1076612 7 612900 617822 Alligator mississippiensis 8496 GAG|GTACGTTGGG...AAACTCTGATTT/CAAACTCTGATT...TGCAG|CAC 0 1 87.85

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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]);