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 = 36995250

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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
204419641 GT-AG 0 0.000300787667868 387 rna-XM_038844908.1 36995250 1 1898433 1898819 Tripterygium wilfordii 458696 GAG|GTTTGTTTCT...CTTTCTGTAATT/CTTGTTTTCAAT...TTTAG|AGG 0 1 31.867
204419642 GT-AG 0 1.000000099473604e-05 79 rna-XM_038844908.1 36995250 2 1899349 1899427 Tripterygium wilfordii 458696 TAG|GTATGGCAAC...AGATGCTTAGTT/TGGTTGCTTATG...GCCAG|GTA 1 1 50.787
204419643 GT-AG 0 1.000000099473604e-05 1225 rna-XM_038844908.1 36995250 3 1899559 1900783 Tripterygium wilfordii 458696 AAG|GTAATGGAAG...AATCTTCTATCT/AAATATATAATC...TTCAG|AAA 0 1 55.472
204419644 GT-AG 0 7.318207690830921e-05 228 rna-XM_038844908.1 36995250 4 1901135 1901362 Tripterygium wilfordii 458696 TTC|GTAAATATCT...GAACTCTCATTT/TGAACTCTCATT...GTCAG|GCT 0 1 68.026
204419645 GT-AG 0 6.515935244931498e-05 82 rna-XM_038844908.1 36995250 5 1901520 1901601 Tripterygium wilfordii 458696 TTG|GTAATCAATC...CAACTTTTAGTT/CTTTTAGTTATT...TTCAG|GTA 1 1 73.641
204419646 GT-AG 0 0.3292199969071178 357 rna-XM_038844908.1 36995250 6 1901895 1902251 Tripterygium wilfordii 458696 GAG|GTATCTCTAC...ATTTCCTGATTT/AATTTCCTGATT...AACAG|GCC 0 1 84.12
204419647 GT-AG 0 0.0006830190647863 94 rna-XM_038844908.1 36995250 7 1902312 1902405 Tripterygium wilfordii 458696 CTT|GTACGTATTC...TCATGCTTACCC/CAATTTTTCATG...GCTAG|GAA 0 1 86.266
204419648 GT-AG 0 0.0042332936170918 93 rna-XM_038844908.1 36995250 8 1902496 1902588 Tripterygium wilfordii 458696 GAG|GTTTTTTTTT...AACGCCTTAATC/TCTATTTTAACG...TCTAG|GAG 0 1 89.485

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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]);