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 = 34107420

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
190903474 GT-AG 0 1.000000099473604e-05 1939 Sbene_T00738-R1 34107420 1 22297236 22299174 Streblospio benedicti 95538 GTG|GTAAGACATA...AATCCATTCATT/AATCCATTCATT...TATAG|ATA 1 1 13.459
190903475 GT-AG 0 0.0003877731460745 165 Sbene_T00738-R1 34107420 2 22299261 22299425 Streblospio benedicti 95538 AGT|GTAAGCCAAA...TATTTTTTATCT/TTATTTTTTATC...TACAG|CAA 0 1 19.456
190903476 GT-AG 0 1.3367774930952269e-05 117 Sbene_T00738-R1 34107420 3 22299498 22299614 Streblospio benedicti 95538 TTG|GTAAGGTTTT...TATGCTTTACTC/ATATGCTTTACT...TTCAG|CCT 0 1 24.477
190903477 GT-AG 0 1.000000099473604e-05 294 Sbene_T00738-R1 34107420 4 22299772 22300065 Streblospio benedicti 95538 TTG|GTAAGTTGGA...AAAAGTTTAATA/AAAAGTTTAATA...TTTAG|GTC 1 1 35.425
190903478 GT-AG 0 1.000000099473604e-05 278 Sbene_T00738-R1 34107420 5 22300146 22300423 Streblospio benedicti 95538 AGG|GTAAGTTAAT...TTTTTTCTAATA/TTTTTTCTAATA...AATAG|GTA 0 1 41.004
190903479 GT-AG 0 3.5809227205600514e-05 404 Sbene_T00738-R1 34107420 6 22300494 22300897 Streblospio benedicti 95538 CAG|GTAAGCTATT...TAATATTTAATA/ATATTTCTAATA...TTCAG|AAA 1 1 45.886
190903480 GT-AG 0 0.0001070964981129 36 Sbene_T00738-R1 34107420 7 22301147 22301182 Streblospio benedicti 95538 AGA|GTAACGAGTT...TAGAGCTGAACA/ATAGAGCTGAAC...CAAAG|TAA 1 1 63.25
190903481 CT-AA 0 1.000000099473604e-05 93 Sbene_T00738-R1 34107420 8 22301513 22301605 Streblospio benedicti 95538 AAG|CTGTTTCAGG...AACTTCAAGATA/TAGAACTTCAAG...TCCAA|ATA 1 1 86.262

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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]);