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 = 3611869

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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
18021405 GT-AG 0 0.000117936137944 218 rna-XM_020415354.1 3611869 1 2551829 2552046 Asparagus officinalis 4686 TCT|GTAAGTACTT...TTTACTTTATTT/TATGTATTTACT...TACAG|GTC 0 1 11.215
18021406 GT-AG 0 2.0463421888469764 122 rna-XM_020415354.1 3611869 2 2553184 2553305 Asparagus officinalis 4686 CAG|GTATCTTATT...TAACTTTTGAAT/AAAATTCTAACT...TTTAG|ATA 0 1 29.0
18021407 GT-AG 0 1.000000099473604e-05 1540 rna-XM_020415354.1 3611869 3 2554035 2555574 Asparagus officinalis 4686 TTG|GTAAGGAAAC...GCATTTTTAATA/TTATGACTGATA...ACCAG|CTT 0 1 40.404
18021408 GT-AG 0 0.000840602204882 6128 rna-XM_020415354.1 3611869 4 2555881 2562008 Asparagus officinalis 4686 AAG|GTAAGCTATC...TTTTCCTTATTA/ATTTTCCTTATT...TGCAG|AAA 0 1 45.19
18021409 GT-AG 0 0.0129651460406559 2824 rna-XM_020415354.1 3611869 5 2562345 2565168 Asparagus officinalis 4686 GAG|GTATGTTTTC...CTTTCCTTTCCG/GCATAAATAACT...GTCAG|GTT 0 1 50.446
18021410 GT-AG 0 0.0226582529068569 1009 rna-XM_020415354.1 3611869 6 2565268 2566276 Asparagus officinalis 4686 GAG|GTCTCTATAA...ATTTTCATGATT/TACATTTTCATG...TGCAG|ATT 0 1 51.994
18021411 GT-AG 0 5.235114023997013e-05 2491 rna-XM_020415354.1 3611869 7 2566709 2569199 Asparagus officinalis 4686 CAG|GTTTGTTAAC...ATATTTTTATCT/TTTTGTTTTATT...TGCAG|AGG 0 1 58.752
18021412 GT-AG 0 1.000000099473604e-05 1066 rna-XM_020415354.1 3611869 8 2571564 2572629 Asparagus officinalis 4686 GAG|GTGAGTAGGA...TCCCCCTTTTTT/GTGTACCTGATA...CATAG|ATG 0 1 95.73

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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]);