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 = 3380106

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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
16590477 GT-AG 0 1.000000099473604e-05 1511 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 1 451730 453240 Ardeotis kori 89386 CAG|GTACAGAGAG...GAGCCCTTGGCT/CCTTGGCTGAGC...CTCAG|GCT 1 1 6.153
16590478 GT-AG 0 1.000000099473604e-05 2083 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 2 449542 451624 Ardeotis kori 89386 AAG|GTAGGAAGCT...GTTTCCATAAAA/CAGGTTTCCATA...AACAG|AGG 1 1 10.801
16590479 GT-AG 0 0.000386244115928 1273 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 3 448151 449423 Ardeotis kori 89386 CAG|GTACCGTCCC...TGCGCAGTGACA/TGCGCAGTGACA...TGCAG|GTA 2 1 16.025
16590480 GT-AG 0 1.000000099473604e-05 565 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 4 447359 447923 Ardeotis kori 89386 GCA|GTAAGTGGCC...AGCATCTGAAAT/CAGAAACTCAAC...CACAG|AGT 1 1 26.073
16590481 GT-AG 0 1.000000099473604e-05 474 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 5 446835 447308 Ardeotis kori 89386 ATA|GTAAGTGCCA...GCTTTCTTTTTT/GAAACACTAATG...CATAG|CCG 0 1 28.287
16590482 GT-AG 0 1.000000099473604e-05 912 rna-gnl|WGS:VWPR|ARDKOR_R11655_mrna 3380106 6 445797 446708 Ardeotis kori 89386 GAG|GTGAGACTGT...GTTTCCTTTCCC/GGCTCCCTGATG...AACAG|GTT 0 1 33.865

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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]);