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 = 37986750

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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
209726976 GT-AG 0 0.0005216234790013 509 rna-XM_047298966.1 37986750 3 84193 84701 Vigna umbellata 87088 CCG|GTATGTGATT...AATGACTTAACT/TTGTTTTTCAAT...TGCAG|TTC 2 1 59.532
209726977 GT-AG 0 0.4916659465017022 171 rna-XM_047298966.1 37986750 4 83949 84119 Vigna umbellata 87088 GAG|GTATCTTTAG...ATTGTTTTGTTT/TTGGTATTCATT...GACAG|GAC 0 1 68.07
209726978 GT-AG 0 0.0003086144142522 356 rna-XM_047298966.1 37986750 5 83545 83900 Vigna umbellata 87088 GGG|GTATGGATTC...TTATTTTTATAT/GTTATTTTTATA...TTCAG|AAT 0 1 73.684
209726979 GT-AG 0 0.000309417616114 895 rna-XM_047298966.1 37986750 6 82555 83449 Vigna umbellata 87088 GAG|GTATTGTGTA...ATTATCTGGATG/CCTTGAATTATC...TGCAG|TGG 2 1 84.795
209726982 GT-AG 0 1.000000099473604e-05 1211 rna-XM_047298966.1 37986750 1 85153 86363 Vigna umbellata 87088 TAG|GTGAGTTTTC...AAATTTTTAAGC/TTTAAGCTAACC...TACAG|GTC   0 21.637
209726983 GT-AG 0 0.016380947999173 110 rna-XM_047298966.1 37986750 2 84952 85061 Vigna umbellata 87088 TAG|GTATATTCAT...ATATTTTTAACA/ATATTTTTAACA...TGCAG|CTG   0 32.281

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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]);