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 = 20937021

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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
112209602 GT-AG 0 1.000000099473604e-05 21789 rna-XM_027950748.2 20937021 1 59051847 59073635 Marmota flaviventris 93162 TTG|GTAAGTGCTG...GGAACCTTGCAC/GCCCGCCTCACA...CCCAG|GGC 1 1 10.535
112209603 GT-AG 0 1.000000099473604e-05 1578 rna-XM_027950748.2 20937021 2 59050080 59051657 Marmota flaviventris 93162 TAG|GTGAGTGCTG...GCCGTCTGATCA/TGCCGTCTGATC...TCCAG|GTC 1 1 18.696
112209604 GT-AG 0 1.000000099473604e-05 466 rna-XM_027950748.2 20937021 3 59049434 59049899 Marmota flaviventris 93162 CTG|GTAACGCCTT...GGGGCCGCAGTG/CACTGGCTCACC...ACCAG|GCC 1 1 26.468
112209605 GT-AG 0 1.000000099473604e-05 700 rna-XM_027950748.2 20937021 4 59047709 59048408 Marmota flaviventris 93162 AAG|GTGAGCACCT...TTGTCCTGAGCA/TTTGTCCTGAGC...AACAG|GAC 0 1 70.725
112209606 GT-AG 0 1.000000099473604e-05 948 rna-XM_027950748.2 20937021 5 59046661 59047608 Marmota flaviventris 93162 CAG|GTAAGAGGTG...TCATCCCTGTCC/CATGAGCTCATC...TGCAG|CCT 1 1 75.043
112209607 GT-AG 0 1.000000099473604e-05 2417 rna-XM_027950748.2 20937021 6 59044032 59046448 Marmota flaviventris 93162 GAG|GTACGTCCAT...ATTCTCTTCTCT/GAACCCCTCACT...TCTAG|TAC 0 1 84.197

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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]);