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 = 38062814

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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
210096407 GT-AG 0 1.000000099473604e-05 1474 rna-XM_034826934.1 38062814 1 9826296 9827769 Vitis riparia 96939 CGG|GTGGGTTCTC...TTTTTTTTTTCT/CCTGCTCTGATA...TGCAG|GAG 1 1 17.866
210096408 GT-AG 0 3.4775055415740754e-05 145 rna-XM_034826934.1 38062814 2 9828030 9828174 Vitis riparia 96939 CAA|GTAAGTTTGG...GAATCTGTATTT/CATCTGTTCACT...TGAAG|GTT 0 1 26.903
210096409 GT-AG 0 0.0023377637653983 350 rna-XM_034826934.1 38062814 3 9828328 9828677 Vitis riparia 96939 GTG|GTATGATTTG...TAATTATTATTT/TTATTATTTATA...ATCAG|TTA 0 1 32.221
210096410 GT-AG 0 1.000000099473604e-05 182 rna-XM_034826934.1 38062814 4 9829093 9829274 Vitis riparia 96939 ATG|GTGAGTTTTA...ATCTCTCTGACA/TTTTTGCTCATG...TGCAG|ATG 1 1 46.646
210096411 GT-AG 0 0.0001529594604042 111 rna-XM_034826934.1 38062814 5 9829968 9830078 Vitis riparia 96939 TTG|GTAATTTTTT...CTCCCCATGATG/CTCCTGTTAATG...GGCAG|GTG 1 1 70.733
210096412 GT-AG 0 1.000000099473604e-05 5885 rna-XM_034826934.1 38062814 6 9830669 9836553 Vitis riparia 96939 AAG|GTAAGCAATG...GTTGTCTTATGA/TGTTGTCTTATG...TACAG|CAT 0 1 91.241

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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]);