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 = 33469729

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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
187538736 GT-AG 0 1.000000099473604e-05 615 rna-XM_021447504.1 33469729 1 60061132 60061746 Sorghum bicolor 4558 AAG|GTGAGGACCT...ACATCTATGATT/CTATGATTCATG...TACAG|GTG 0 1 5.307
187538737 GT-AG 0 1.000000099473604e-05 767 rna-XM_021447504.1 33469729 2 60062476 60063242 Sorghum bicolor 4558 TAT|GTGAGTTTTT...AAGTTTTTGAAT/TTTATGTTCATT...TGCAG|GCT 0 1 22.277
187538738 GT-AG 0 0.0007260765048448 119 rna-XM_021447504.1 33469729 3 60064401 60064519 Sorghum bicolor 4558 AAG|GTATGTTATG...GCCTCCTTGCAA/CAAATGCTCATA...GCTAG|ATT 0 1 49.232
187538739 GT-AG 0 0.0022468290495361 661 rna-XM_021447504.1 33469729 4 60064848 60065508 Sorghum bicolor 4558 AAG|GTACATTTTA...GTATCCTTTTCT/ATAAAGCTAACT...TGTAG|AGT 1 1 56.867
187538740 GT-AG 0 0.0019413433980003 97 rna-XM_021447504.1 33469729 5 60065765 60065861 Sorghum bicolor 4558 CAA|GTATGTTGCC...GCATTTTCAGTT/TGCATTTTCAGT...AACAG|GTA 2 1 62.826
187538741 GT-AG 0 0.0213471738105914 613 rna-XM_021447504.1 33469729 6 60066040 60066652 Sorghum bicolor 4558 CAG|GTATTCTGGA...GTTCTGTTGATC/GTTCTGTTGATC...ATCAG|AGT 0 1 66.969

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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]);