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 = 29940939

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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
167734737 GT-AG 0 1.897677262402418e-05 16576 rna-XM_041474601.1 29940939 2 7313885 7330460 Pyrgilauda ruficollis 221976 AGG|GTAAGTATGA...TTTTCTTTATCT/CTTTATCTAATT...TATAG|AGG 1 1 20.19
167734738 GT-AG 0 1.000000099473604e-05 3849 rna-XM_041474601.1 29940939 3 7309953 7313801 Pyrgilauda ruficollis 221976 GAG|GTAATTATAT...ATTTCAGTAACT/GTATATTTCAGT...TATAG|GTG 0 1 22.911
167734739 GT-AG 0 2.3946451882543724e-05 841 rna-XM_041474601.1 29940939 4 7308967 7309807 Pyrgilauda ruficollis 221976 GAG|GTATGGGTTC...TATTTTTTCTTT/GAGTGTGTAATG...TTGAG|GCA 1 1 27.663
167734740 GT-AG 0 0.0002526457216651 590 rna-XM_041474601.1 29940939 5 7308206 7308795 Pyrgilauda ruficollis 221976 AAG|GTTTGTTCAT...ACTGCTTTGACT/CTTTAATTGACT...AACAG|ATG 1 1 33.268
167734741 GT-AG 0 1.000000099473604e-05 3720 rna-XM_041474601.1 29940939 6 7304405 7308124 Pyrgilauda ruficollis 221976 AAT|GTGAGTGCAT...TTCGTTTTATCT/TTTCGTTTTATC...TTTAG|CTA 1 1 35.923
167734742 GT-AG 0 1.000000099473604e-05 1358 rna-XM_041474601.1 29940939 7 7302901 7304258 Pyrgilauda ruficollis 221976 AAG|GTAAAAGGCA...TGCTTGTTAATA/TGCTTGTTAATA...TCCAG|GTT 0 1 40.708
167736149 GT-AG 0 1.000000099473604e-05 1194 rna-XM_041474601.1 29940939 1 7330653 7331846 Pyrgilauda ruficollis 221976 GAG|GTGAGCTCCT...TTATCATTATTT/TAATTTATCATT...GGCAG|CTA   0 14.061

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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]);