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 = 30001222

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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
168078090 GT-AG 0 4.9220869315494894e-05 238 rna-XM_009377574.2 30001222 1 1933707 1933944 Pyrus x bretschneideri 225117 CAG|GTGACTTTTT...TGTTGTTTATTG/ATGTTGTTTATT...TGCAG|TGT 2 1 5.895
168078091 GT-AG 0 1.000000099473604e-05 429 rna-XM_009377574.2 30001222 2 1933202 1933630 Pyrus x bretschneideri 225117 GTT|GTAAGACATT...TGTTTCTTACTT/ATGTTTCTTACT...AACAG|GTT 0 1 9.859
168078092 GT-AG 0 0.0211362563230527 127 rna-XM_009377574.2 30001222 3 1933016 1933142 Pyrus x bretschneideri 225117 AAG|GTATCAACCC...TTGTTCTTATAA/TTTGTTCTTATA...AATAG|CAG 2 1 12.937
168078093 GT-AG 0 1.000000099473604e-05 85 rna-XM_009377574.2 30001222 4 1932434 1932518 Pyrus x bretschneideri 225117 AAT|GTGAGTTAAT...CCTTTGTTAGTT/TGTTAGTTGAAA...TACAG|TAT 1 1 38.863
168078094 GT-AG 0 1.6525699297722856e-05 78 rna-XM_009377574.2 30001222 5 1932195 1932272 Pyrus x bretschneideri 225117 AAT|GTAAGATTTT...CAATTCCTAATA/AATATTTTTATG...GATAG|ATT 0 1 47.261
168078095 GT-AG 0 5.340872275869491e-05 336 rna-XM_009377574.2 30001222 6 1931655 1931990 Pyrus x bretschneideri 225117 AAG|GTATATGACT...TGAGTCATGACC/AAGTGGTTGATT...TACAG|GTC 0 1 57.903
168078096 GT-AG 0 0.0015672338724024 233 rna-XM_009377574.2 30001222 7 1931190 1931422 Pyrus x bretschneideri 225117 GAG|GTATATCTTG...TGCTCTTTTTCT/CCGTTGCTAATG...TCTAG|GTT 1 1 70.005

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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]);