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)

8 rows where transcript_id = 12947856

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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
69094785 GT-AG 0 1.000000099473604e-05 120 rna-XM_010942424.3 12947856 1 50114709 50114828 Elaeis guineensis 51953 AAG|GTGAGTATGC...TTTTTCTTTTCC/CTTTTCCACATT...CACAG|ACA 2 1 14.186
69094786 GT-AG 0 1.000000099473604e-05 473 rna-XM_010942424.3 12947856 2 50115522 50115994 Elaeis guineensis 51953 CGT|GTAAGGCTTT...CATGTTTTCATT/CATGTTTTCATT...TGCAG|GTC 2 1 27.311
69094787 GT-AG 0 1.000000099473604e-05 3908 rna-XM_010942424.3 12947856 3 50117358 50121265 Elaeis guineensis 51953 GAG|GTTGGTATTC...TCTGACTTATTT/CTGATTCTGACT...GGCAG|CTT 0 1 53.125
69094788 GT-AG 0 1.000000099473604e-05 91 rna-XM_010942424.3 12947856 4 50121561 50121651 Elaeis guineensis 51953 AGG|GTAATGTTGC...TATCTCTTTCAT/ATAAAGCTGATG...GCCAG|GTG 1 1 58.712
69094789 GT-AG 0 1.000000099473604e-05 97 rna-XM_010942424.3 12947856 5 50121777 50121873 Elaeis guineensis 51953 CAG|GTTAGTTCTC...CCTTTCCTAACA/CCTTTCCTAACA...ATCAG|GTC 0 1 61.08
69094790 GT-AG 0 5.7718856846331686e-05 126 rna-XM_010942424.3 12947856 6 50122344 50122469 Elaeis guineensis 51953 AAG|GTAATTTGTT...CTGTTTTTAATG/CTGTTTTTAATG...TTTAG|GGA 2 1 69.981
69094791 GT-AG 0 2.8223127595679865e-05 118 rna-XM_010942424.3 12947856 7 50122499 50122616 Elaeis guineensis 51953 AAG|GTATGATCAT...AAAACCTTGTTT/TTTCCCCTTACC...TTCAG|GTA 1 1 70.53
69094792 GT-AG 0 0.0001375042021815 80 rna-XM_010942424.3 12947856 8 50123106 50123185 Elaeis guineensis 51953 AAA|GTAAGCCTAT...TTGTCTTTTGCT/AATATCTCCATC...TGCAG|ATT 1 1 79.792

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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]);