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 = 24633816

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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
134640305 GT-AG 0 1.000000099473604e-05 46 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 1 513 558 Olpidium bornovanus 278681 ACC|GTCAAATTGT...TTTTCTTTCAAT/TTTTCTTTCAAT...GGTAG|GCG 0 1 7.231
134640306 GT-AG 0 0.0076824704095558 55 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 2 648 702 Olpidium bornovanus 278681 AGG|GTAGCTTCAG...GCGCCCTTCCCG/TCGTGCTCGATG...GTTAG|ATT 2 1 13.361
134640307 GT-AG 0 1.000000099473604e-05 134 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 3 1450 1583 Olpidium bornovanus 278681 CAG|GTTTTAGCGT...CCTTTCTTCTCG/ACCAATGTCACA...GTTAG|CCT 2 1 64.807
134640308 GT-AG 0 5.550285202236508e-05 48 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 4 1696 1743 Olpidium bornovanus 278681 CAG|GTACACCGGC...GGGAACTTATCG/TGGGAACTTATC...CACAG|GGT 0 1 72.521
134640309 GT-AG 0 0.0003168885337254 57 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 5 1824 1880 Olpidium bornovanus 278681 CCT|GTCTAGATTC...ACGCTCCTAACC/TGCCTACTCATT...ATTAG|TGT 2 1 78.03
134640310 GT-AG 0 1.59351022568069e-05 55 rna-gnl|WGS:JAEFCI|BJ554DRAFT_mRNA4027 24633816 6 2050 2104 Olpidium bornovanus 278681 CTC|GTTGTGTTCT...TATTCTGTATCT/TCTGTATCTATC...GTTAG|CCT 0 1 89.669

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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]);