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 = 29501511

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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
164359238 GT-AG 0 1.000000099473604e-05 3914 rna-XM_014249182.1 29501511 1 59238990 59242903 Pseudopodoces humilis 181119 CAG|GTAGGTACGG...TCTGCCTTCACA/TCTGCCTTCACA...AGCAG|ATT 1 1 3.754
164359239 GT-AG 0 3.649741195722954e-05 4927 rna-XM_014249182.1 29501511 2 59243069 59247995 Pseudopodoces humilis 181119 AGG|GTACAGTACT...CTCCTTTTAAAT/CTCCTTTTAAAT...TTTAG|GTT 1 1 6.649
164359240 GT-AG 0 1.000000099473604e-05 2515 rna-XM_014249182.1 29501511 3 59248122 59250636 Pseudopodoces humilis 181119 CAG|GTAATGCCTG...TAATCCTTGCTG/CTGTTTGTGAAT...TCCAG|GTT 1 1 8.86
164359241 GT-AG 0 1.000000099473604e-05 3047 rna-XM_014249182.1 29501511 4 59250778 59253824 Pseudopodoces humilis 181119 CAG|GTACTGAGTC...GCGTCATTAATT/AATGTTCTCAAA...TTCAG|AAT 1 1 11.333
164359242 GT-AG 0 0.0001088053989151 2923 rna-XM_014249182.1 29501511 5 59253953 59256875 Pseudopodoces humilis 181119 AAG|GTAACTGCAA...CCTGCCCTGACG/CCTGCCCTGACG...CACAG|ACG 0 1 13.579
164359243 GT-AG 0 1.000000099473604e-05 1065 rna-XM_014249182.1 29501511 6 59257009 59258073 Pseudopodoces humilis 181119 GAG|GTGAGGGTCC...TTGTGCTTAATC/TTGTGCTTAATC...TGCAG|GGG 1 1 15.912
164359244 GT-AG 0 1.000000099473604e-05 5812 rna-XM_014249182.1 29501511 7 59258228 59264039 Pseudopodoces humilis 181119 AAA|GTAAAGCAGT...ACAATGTTGACG/ACAATGTTGACG...CACAG|CAC 2 1 18.614

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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]);