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)

6 rows where transcript_id = 12917223

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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
68847157 GT-AG 0 0.0001318946834193 1020 rna-XM_009635921.2 12917223 1 816179 817198 Egretta garzetta 188379 CAG|GTCGCTTCGT...CCTCCTCTGACG/ATAACTCTGATC...AACAG|AGC 1 1 0.603
68847158 GT-AG 0 0.000616256706108 1125 rna-XM_009635921.2 12917223 2 814861 815985 Egretta garzetta 188379 AAG|GTACATATTT...GTTTCCATATTT/CCATATTTAAAC...AGCAG|CTC 2 1 17.227
68847159 GT-AG 0 0.0012093395450189 796 rna-XM_009635921.2 12917223 4 813074 813869 Egretta garzetta 188379 CAG|GTACTTTTCC...TCTTCCTTTTCC/TAATTATTAATA...TACAG|GTT 0 1 47.545
68847160 GT-AG 0 8.652373935187738e-05 512 rna-XM_009635921.2 12917223 5 812391 812902 Egretta garzetta 188379 GAG|GTATGTGATA...GAGTATTTGACA/AAGTTTTTCAGA...CAAAG|CCT 0 1 62.274
68847161 GT-AG 0 7.475296881727198e-05 2652 rna-XM_009635921.2 12917223 6 809618 812269 Egretta garzetta 188379 CCA|GTAAGTGTGA...TTCTTCTTGAAT/CTGCTTCTGACC...CCAAG|GTG 1 1 72.696
68847162 GT-AG 0 0.0002001699698176 1303 rna-XM_009635921.2 12917223 7 808135 809437 Egretta garzetta 188379 AAA|GTAAGCTACA...CAGGTGTTAATC/CAGGTGTTAATC...CCCAG|AAA 1 1 88.2

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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]);