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)

9 rows where transcript_id = 25340401

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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
139664978 GT-AG 0 1.000000099473604e-05 18939 rna-XM_007934695.1 25340401 1 9756112 9775050 Orycteropus afer 9818 GAA|GTGAGTACCC...TATGCTTTTTCT/GATATTTTTATG...TTTAG|GAC 0 1 5.869
139664979 GT-AG 0 1.000000099473604e-05 8289 rna-XM_007934695.1 25340401 2 9747721 9756009 Orycteropus afer 9818 CAG|GTAAATAATT...ACAGTCTTATTA/AACAGTCTTATT...TATAG|GTA 0 1 13.85
139664980 GT-AG 0 0.0001842276979408 866 rna-XM_007934695.1 25340401 3 9746743 9747608 Orycteropus afer 9818 AAG|GTAAACTTTA...TTTCCTATAGAT/CCGTATATCATT...CATAG|GTG 1 1 22.613
139664981 GT-AG 0 0.0433540216127007 412 rna-XM_007934695.1 25340401 4 9746178 9746589 Orycteropus afer 9818 AAG|GTATATTTTT...AAAATTTTAGTA/TTAATGTTCATA...TTTAG|ATA 1 1 34.585
139664982 GT-AG 0 0.0009645119930211 1307 rna-XM_007934695.1 25340401 5 9744779 9746085 Orycteropus afer 9818 ATA|GTATGTCCTT...CTACTTGTGAAT/TTGTGAATAATA...TATAG|GTA 0 1 41.784
139664983 GT-AG 0 0.0013270139265092 1655 rna-XM_007934695.1 25340401 6 9742941 9744595 Orycteropus afer 9818 GAG|GTAACTAGTA...AACACTTTATCT/TTATTGGTGACC...TGCAG|CGT 0 1 56.103
139664984 GT-AG 0 0.0006014459627466 154 rna-XM_007934695.1 25340401 7 9742640 9742793 Orycteropus afer 9818 GTG|GTATGTCCCA...TGCATTTTATAA/TTGCATTTTATA...AACAG|ATC 0 1 67.606
139664985 GT-AG 0 1.000000099473604e-05 695 rna-XM_007934695.1 25340401 8 9741843 9742537 Orycteropus afer 9818 GAG|GTAAGAGGAA...TTGCTCTTAATT/TTGCTCTTAATT...TAAAG|GTT 0 1 75.587
139664986 GT-AG 0 2.4151082826567585e-05 2703 rna-XM_007934695.1 25340401 9 9739016 9741718 Orycteropus afer 9818 ATG|GTAAGTATGC...GCCTTCTTAATT/TAATTCTTTATT...TTTAG|ATA 1 1 85.29

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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]);