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)

6 rows where transcript_id = 6092550

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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
31463534 GT-AG 0 0.0001170077346956 17204 rna-XM_030954579.1 6092550 1 73466113 73483316 Camarhynchus parvulus 87175 CAG|GTACCAGCTT...TTTTTTTTTTCC/TAATATCTAAAA...TTTAG|CAA 2 1 1.991
31463535 GT-AG 0 1.000000099473604e-05 3978 rna-XM_030954579.1 6092550 2 73483475 73487452 Camarhynchus parvulus 87175 CCA|GTGAGTTACA...TACATTTTGAAA/TACATTTTGAAA...TCTAG|TTA 1 1 4.635
31463536 GT-AG 0 1.000000099473604e-05 102 rna-XM_030954579.1 6092550 3 73487525 73487626 Camarhynchus parvulus 87175 AAG|GTAAGCAAAA...CTACTTTTATCA/ACTGTATTTATT...TTTAG|ATC 1 1 5.84
31463537 GT-AG 0 1.000000099473604e-05 4600 rna-XM_030954579.1 6092550 4 73487772 73492371 Camarhynchus parvulus 87175 ACG|GTGAGCTATA...AGTTCCTTTTCA/TTCCTTTTCAAA...TACAG|ATA 2 1 8.266
31463538 GT-AG 0 1.000000099473604e-05 1584 rna-XM_030954579.1 6092550 5 73492421 73494004 Camarhynchus parvulus 87175 ACG|GTAAGTAGCT...GTTACTTTACAA/GGTTACTTTACA...AACAG|GCT 0 1 9.086
31463539 GT-AG 0 1.000000099473604e-05 1588 rna-XM_030954579.1 6092550 6 73494132 73495719 Camarhynchus parvulus 87175 GTG|GTAAGTGTGT...TTTTTTTTTTCC/AGATTATTAAAG...TGCAG|TTC 1 1 11.212

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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]);