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 = 3380126

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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
16590586 GT-AG 0 1.000000099473604e-05 10814 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 1 1584633 1595446 Ardeotis kori 89386 CAG|GTAATCCGAA...ATTGTCTTCTCT/TACTTGTTCATT...TGTAG|AAA 0 1 37.241
16590587 GT-AG 0 1.000000099473604e-05 1830 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 2 1595508 1597337 Ardeotis kori 89386 GAG|GTGGGTTAAT...TTTTTCCTATTG/TTTTTTCCTATT...TGCAG|AAT 1 1 44.253
16590588 GT-AG 0 1.000000099473604e-05 2023 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 3 1597451 1599473 Ardeotis kori 89386 CAG|GTGAATATTC...TACGACTTAAAT/TTAAATATAACA...TCTAG|GAC 0 1 57.241
16590589 GT-AG 0 3.5864458353762105e-05 1761 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 4 1599511 1601271 Ardeotis kori 89386 AAG|GTATGACTTT...TGTGCTTTGGTT/AAATGTTTCAAG...TCTAG|CAG 1 1 61.494
16590590 GT-AG 0 3.680914560260786e-05 6103 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 5 1601421 1607523 Ardeotis kori 89386 ATG|GTAAGCCTTT...GTATTATTGAAA/ATGGGTCTGATT...CACAG|CGA 0 1 78.621
16590591 GT-AG 0 1.000000099473604e-05 7224 rna-gnl|WGS:VWPR|ARDKOR_R10121_mrna 3380126 6 1607579 1614802 Ardeotis kori 89386 TAG|GTAAGTAGTA...CTCTGCTTAATA/TTAATACTGAAC...TTCAG|GCA 1 1 84.943

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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]);