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 = 5879277

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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
29939765 GT-AG 0 1.000000099473604e-05 18626 rna-XM_014966566.1 5879277 1 45088 63713 Calidris pugnax 198806 CCG|GTAAGGGGCT...CCACCCCTGTCT/TGGGGGCTCAAT...CCCAG|GGA 1 1 14.783
29939766 GT-AG 0 2.1106130290627453e-05 3854 rna-XM_014966566.1 5879277 2 40573 44426 Calidris pugnax 198806 CGG|GTAAGCTGGC...AACCCCTTCCCC/CCCTTCCCCATC...TGCAG|GGT 2 1 52.511
29939767 GT-AG 0 1.000000099473604e-05 152 rna-XM_014966566.1 5879277 3 40359 40510 Calidris pugnax 198806 CAG|GTAAGGGGGG...TCACTCTTCCCC/CCCCCCCTCACT...CACAG|GGA 1 1 56.05
29939768 GT-AG 0 1.000000099473604e-05 228 rna-XM_014966566.1 5879277 4 39969 40196 Calidris pugnax 198806 AGA|GTAAGGAGCC...CAGGCTCTGATG/CAGGCTCTGATG...GGCAG|GCA 1 1 65.297
29939769 GT-AG 0 1.000000099473604e-05 172 rna-XM_014966566.1 5879277 5 39735 39906 Calidris pugnax 198806 GAG|GTAAGTGGGC...TGCCCCTCAACC/ATGCCCCTCAAC...GTCAG|GAC 0 1 68.836
29939770 GT-AG 0 1.000000099473604e-05 92 rna-XM_014966566.1 5879277 6 39484 39575 Calidris pugnax 198806 AAG|GTGAGCTGGG...ATGTCCCTCATG/ATGTCCCTCATG...CGCAG|GAC 0 1 77.911
29939771 GT-AG 0 1.000000099473604e-05 1178 rna-XM_014966566.1 5879277 7 38144 39321 Calidris pugnax 198806 CAG|GTGAGGAACC...ATGGCCGTGCCC/GCCGTGCCCACC...CCCAG|GTG 0 1 87.158

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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]);