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 = 20936989

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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
112209066 GT-AG 0 0.0003549041873668 89589 rna-XM_027949350.1 20936989 1 29916964 30006552 Marmota flaviventris 93162 AAC|GTAAGTTTTC...GTGTCCCTGATT/GTGTCCCTGATT...TCAAG|GGC 1 1 1.159
112209067 GT-AG 0 0.0001368894315922 22847 rna-XM_027949350.1 20936989 2 30006712 30029558 Marmota flaviventris 93162 AAG|GTAATCATTG...AGGGCTTTGATC/GCTTTGATCATT...TTCAG|GTG 1 1 5.768
112209068 GT-AG 0 1.000000099473604e-05 99144 rna-XM_027949350.1 20936989 3 30029658 30128801 Marmota flaviventris 93162 CAG|GTAGGACAGA...GTGTTCTAAACA/AGTGTTCTAAAC...TGCAG|GAG 1 1 8.638
112209069 GT-AG 0 0.0002308377350063 67010 rna-XM_027949350.1 20936989 4 30128921 30195930 Marmota flaviventris 93162 TTG|GTATGTGAAT...AAGTTTTTAATC/AAGTTTTTAATC...TACAG|AAG 0 1 12.087
112209070 GT-AG 0 1.000000099473604e-05 138544 rna-XM_027949350.1 20936989 5 30196043 30334586 Marmota flaviventris 93162 AAG|GTAAATGCAG...TCTTCCTTTTTT/GAGAGTCCCATG...AATAG|GGG 1 1 15.333
112209071 GT-AG 0 1.000000099473604e-05 3455 rna-XM_027949350.1 20936989 6 30334794 30338248 Marmota flaviventris 93162 ACA|GTAAGTGCTG...TACGTTTTTGCC/CAGTAGCTAATG...TGCAG|AAG 1 1 21.333
112209072 GT-AG 0 1.000000099473604e-05 1973 rna-XM_027949350.1 20936989 7 30338474 30340446 Marmota flaviventris 93162 GTG|GTAAGGGGCA...GTGTTTTTATTT/AGTGTTTTTATT...TCCAG|GAG 1 1 27.855

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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]);