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)

8 rows where transcript_id = 12758643

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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
67905233 GT-AG 0 0.002115405604129 112 rna-XM_022865981.1 12758643 1 2794394 2794505 Durio zibethinus 66656 AAG|GTTTGCTTCA...TATTCTTCAATC/CTATTCTTCAAT...AAAAG|GGA 1 1 15.738
67905234 GT-AG 0 1.1735783012665308e-05 218 rna-XM_022865981.1 12758643 2 2795173 2795390 Durio zibethinus 66656 CAG|GTCAGCTCCT...TAACCTTTATCA/TTTTCTCTGAAT...ACCAG|ACA 2 1 48.338
67905235 GT-AG 0 1.528580067475975e-05 152 rna-XM_022865981.1 12758643 3 2795474 2795625 Durio zibethinus 66656 AAG|GTTTGTTTAC...GGCATTTCAATC/AATCAACTCATG...TTCAG|TTT 1 1 52.395
67905236 GT-AG 0 1.5236191331861134e-05 92 rna-XM_022865981.1 12758643 4 2795635 2795726 Durio zibethinus 66656 TGG|GTAAGCCAAG...ATAATCTTGATT/CTTTTATTAATC...TTCAG|GTG 1 1 52.835
67905237 GT-AG 0 1.000000099473604e-05 115 rna-XM_022865981.1 12758643 5 2795816 2795930 Durio zibethinus 66656 CCA|GTAAGTCAAA...TGCTCATTGCTC/TGGTTGCTCATT...GGCAG|CTT 0 1 57.185
67905238 GT-AG 0 1.000000099473604e-05 98 rna-XM_022865981.1 12758643 6 2796005 2796102 Durio zibethinus 66656 AAG|GTTGGTTTCT...TATGTCTTGATG/TTCCTTTTTATT...TACAG|AAA 2 1 60.802
67905239 GT-AG 0 0.0337782915413669 100 rna-XM_022865981.1 12758643 7 2796154 2796253 Durio zibethinus 66656 AAG|GTTTCTATTG...TTTTTCTTTTTT/CATGTAATGATT...TGTAG|ACA 2 1 63.294
67905240 GT-AG 0 1.000000099473604e-05 386 rna-XM_022865981.1 12758643 8 2796331 2796716 Durio zibethinus 66656 TTA|GTGAGTTCTT...AATCTTTTGACC/AATCTTTTGACC...TTCAG|GCA 1 1 67.058

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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]);