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 = 8594570

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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
46265854 GT-AG 0 0.0015999876338049 757 rna-XM_006466764.3 8594570 1 26758995 26759751 Citrus sinensis 2711 TTG|GTACATTTTA...GCAGCATTGATA/TTGTTCCACATT...TGTAG|GAC 2 1 9.307
46265855 GT-AG 0 1.000000099473604e-05 67 rna-XM_006466764.3 8594570 2 26763146 26763212 Citrus sinensis 2711 TCT|GTGAGTATAC...AGGACTTTAACA/ATTTTTATGACT...TGCAG|GAC 0 1 87.491
46265856 GT-AG 0 0.0002599675032299 133 rna-XM_006466764.3 8594570 3 26763289 26763421 Citrus sinensis 2711 TTG|GTATGTAATT...TCATTCTAAAAC/TTTTGACTGACT...TGAAG|CTT 1 1 89.242
46265857 GT-AG 0 0.0002386263408375 74 rna-XM_006466764.3 8594570 4 26763520 26763593 Citrus sinensis 2711 GCG|GTATGACTTC...GTCTGCTTATTT/AGTCTGCTTATT...TGCAG|GCA 0 1 91.5
46265858 GT-AG 0 1.7738656481693603e-05 91 rna-XM_006466764.3 8594570 5 26763660 26763750 Citrus sinensis 2711 AAT|GTAAAATCTT...CTCTGCTTATTT/CATATATTCATT...TGCAG|AGA 0 1 93.02
46265859 GT-AG 0 0.0168502722132234 558 rna-XM_006466764.3 8594570 6 26763841 26764398 Citrus sinensis 2711 TAT|GTATGTGTTA...ACCTCCTGAACC/TTAGTATTTACC...GGCAG|ATA 0 1 95.093
46265860 GT-AG 0 0.6614372040708985 526 rna-XM_006466764.3 8594570 7 26764576 26765101 Citrus sinensis 2711 AAG|GTATCTCTTT...TTTCTGTTAATT/TTTCTGTTAATT...TTCAG|GAA 0 1 99.171

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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]);