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 = 23220223

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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
126296628 GT-AG 0 0.000366204887673 326 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 1 188900 189225 Neocallimastix sp. jgi-2020a 2767002 GCT|GTAAGTTTCC...AAATACTTATAT/TAAATACTTATA...AAAAG|GAT 0 1 11.813
126296629 GT-AG 0 0.0006019055120793 330 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 2 188289 188618 Neocallimastix sp. jgi-2020a 2767002 AAA|GTAATTTGAA...TTATTTTTAATT/TTATTTTTAATT...TAAAG|TTA 2 1 22.768
126296630 GT-AG 0 0.0343880280811494 226 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 3 187879 188104 Neocallimastix sp. jgi-2020a 2767002 GAA|GTATGTTTTT...ATTTTTTCAAAA/CATTTATTCAAT...AATAG|CAT 0 1 29.942
126296631 GT-AG 0 0.0032331365480863 212 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 4 187523 187734 Neocallimastix sp. jgi-2020a 2767002 AAA|GTAATTTTTT...TCTATTTTAATT/TCTATTTTAATT...ATTAG|GTA 0 1 35.556
126296632 GT-AG 0 1.000000099473604e-05 387 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 5 186945 187331 Neocallimastix sp. jgi-2020a 2767002 AAG|GTAAAACTAA...CTTTTTTTAATT/CTTTTTTTAATT...GGTAG|ACC 2 1 43.002
126296633 GT-AG 0 0.0025696306971525 167 rna-gnl|WGS:JACVTC|H8356DRAFT_mRNA972339 23220223 6 185397 185563 Neocallimastix sp. jgi-2020a 2767002 AAG|GTAACTTAAA...TTTTTTTTATAT/TTTTTTTTTATA...TATAG|TTT 0 1 96.842

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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]);