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)

7 rows where transcript_id = 29163164

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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
162621424 GT-AG 0 1.000000099473604e-05 3021 rna-XM_015813318.1 29163164 1 1135471 1138491 Protobothrops mucrosquamatus 103944 AAG|GTAGCGGGAG...GGATCCATAGTT/CATAGTTTGATT...TACAG|GCT 0 1 17.787
162621425 GT-AG 0 1.000000099473604e-05 1725 rna-XM_015813318.1 29163164 2 1133559 1135283 Protobothrops mucrosquamatus 103944 AAG|GTAGGGCTGC...CTATTTTTACAA/AGTTATATAAAC...TACAG|GAT 1 1 31.309
162621426 GT-AG 0 2.1003922805078464e-05 1288 rna-XM_015813318.1 29163164 3 1132182 1133469 Protobothrops mucrosquamatus 103944 CAG|GTATGACCCT...GATATTTTAATA/TTTTTAGTAACT...TACAG|GTG 0 1 37.744
162621427 GT-AG 0 1.000000099473604e-05 3746 rna-XM_015813318.1 29163164 4 1128294 1132039 Protobothrops mucrosquamatus 103944 ATG|GTAAGACATT...TTTTTTTTTTTT/GTCGGGTTCATT...AGTAG|GTT 1 1 48.012
162621428 GT-AG 0 7.000462798437364e-05 2453 rna-XM_015813318.1 29163164 5 1125733 1128185 Protobothrops mucrosquamatus 103944 CAG|GTATGTACAC...TGTCCATTACCA/TTAAAAATAATT...TTCAG|ATT 1 1 55.821
162621429 GT-AG 0 0.0001345046531069 3431 rna-XM_015813318.1 29163164 6 1121948 1125378 Protobothrops mucrosquamatus 103944 CAG|GTAATTTTTA...TAATCCTTAAGG/CTAAATTTAATC...TCTAG|AAC 1 1 81.417
162621430 GT-AG 0 1.0458178873072143e-05 1146 rna-XM_015813318.1 29163164 7 1120689 1121834 Protobothrops mucrosquamatus 103944 CAC|GTAAGTATAT...TTTTTCTGATTT/CTTTTTCTGATT...TTAAG|GTT 0 1 89.588

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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]);