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 = 35781924

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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
201285604 GT-AG 0 1.000000099473604e-05 15160 rna-XM_004368596.3 35781924 1 30824452 30839611 Trichechus manatus 9778 ATG|GTGAGGGCCG...TGTTTCTTGTTC/TGCCTGCTCAGC...TGTAG|CCG 1 1 0.629
201285605 GT-AG 0 1.000000099473604e-05 2358 rna-XM_004368596.3 35781924 2 30822016 30824373 Trichechus manatus 9778 ACG|GTGAGTGCCC...CCCTCCTTGGCT/CCTTGGCTCACC...CCTAG|AGC 1 1 2.593
201285606 GT-AG 0 1.000000099473604e-05 451 rna-XM_004368596.3 35781924 3 30821386 30821836 Trichechus manatus 9778 CCA|GTGAGTCTGA...GAAGCCGTGCCC/AGGGGTCTCACA...TTCAG|GTG 0 1 7.1
201285607 GT-AG 0 0.0029561948070403 208 rna-XM_004368596.3 35781924 4 30821082 30821289 Trichechus manatus 9778 AAG|GTAGCCCTCG...CTCTCCATCCCC/GAGGTGCCCATT...GGCAG|GAT 0 1 9.517
201285608 GT-AG 0 1.000000099473604e-05 144 rna-XM_004368596.3 35781924 5 30820833 30820976 Trichechus manatus 9778 GAG|GTGGGTTGGG...ATCTGCTTCCTC/GCCTGGCTCACC...CCCAG|GTA 0 1 12.16
201285609 GT-AG 0 1.000000099473604e-05 733 rna-XM_004368596.3 35781924 6 30819974 30820706 Trichechus manatus 9778 CTG|GTGGGCGCCC...GGTGCCCTGACA/GGTGCCCTGACA...GGCAG|AAG 0 1 15.332
201285610 GT-AG 0 1.000000099473604e-05 117 rna-XM_004368596.3 35781924 7 30819706 30819822 Trichechus manatus 9778 TGG|GTGAGTGGCT...CCAGCCTCACCT/CCCAGCCTCACC...CGTAG|TGT 1 1 19.134
201285611 GT-AG 0 1.000000099473604e-05 5582 rna-XM_004368596.3 35781924 8 30814002 30819583 Trichechus manatus 9778 AAG|GTGGGCCCTT...GCACACTTACAC/TGCACACTTACA...CCCAG|GGC 0 1 22.205

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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]);