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)

7 rows where transcript_id = 2158740

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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
11719839 GT-AG 0 1.000000099473604e-05 61 rna-XM_008863050.1 2158740 1 1125484 1125544 Aphanomyces invadans 157072 TGG|GTAAGTTGTG...CTGGGTTTATTC/GGTTTATTCACC...GCTAG|GCT 1 1 41.509
11719840 GT-AG 0 0.0135423030043964 60 rna-XM_008863050.1 2158740 2 1125707 1125766 Aphanomyces invadans 157072 AAG|GTATTCTGAC...CTCTCCCTGATG/CCGCATCTTATG...GCTAG|GCC 1 1 45.768
11719841 GT-AG 0 4.915673710836368e-05 47 rna-XM_008863050.1 2158740 3 1126614 1126660 Aphanomyces invadans 157072 AGG|GTACGTTGCC...GACAACTTACTG/AACTTACTGACA...TGCAG|ATT 2 1 68.034
11719842 GT-AG 0 1.000000099473604e-05 53 rna-XM_008863050.1 2158740 4 1126883 1126935 Aphanomyces invadans 157072 CGG|GTACGAACGC...GTTGTTTTCGCA/CATGTGCTCACG...GACAG|GCA 2 1 73.87
11719843 GT-AG 0 5.340506574675898e-05 57 rna-XM_008863050.1 2158740 5 1127582 1127638 Aphanomyces invadans 157072 GAG|GTACCACACG...GGCGTTTTCTTT/CGACAGCTGAAA...TCTAG|GTC 0 1 90.852
11719844 GT-AG 0 0.0002193967733214 50 rna-XM_008863050.1 2158740 6 1127752 1127801 Aphanomyces invadans 157072 CCC|GTACGTACCC...CGTGCCTTGTTT/CCTTGTTTCAAT...TGTAG|GGA 2 1 93.822
11719845 GT-AG 0 0.151586537133613 60 rna-XM_008863050.1 2158740 7 1127931 1127990 Aphanomyces invadans 157072 GCT|GTATGCACCA...CCATGCTTGACT/CCATGCTTGACT...TATAG|GTA 2 1 97.213

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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]);