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 = 23121150

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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
125746586 GT-AG 0 1.000000099473604e-05 409 rna-XM_010246053.2 23121150 1 6568449 6568857 Nelumbo nucifera 4432 AGC|GTAAGAGATC...GTTCTATTGATG/AGTTTGTTCACT...TTAAG|GGT 2 1 5.469
125746587 GT-AG 0 4.046947976928295e-05 137 rna-XM_010246053.2 23121150 2 6568194 6568330 Nelumbo nucifera 4432 AAG|GTAATCTAAC...GAGTTCTTGCTT/ACAAATTTGATA...TCCAG|GCA 0 1 11.033
125746588 GT-AG 0 0.0797733853796395 139 rna-XM_010246053.2 23121150 3 6567872 6568010 Nelumbo nucifera 4432 GAA|GTAAGCTTTT...TTGTCCTTAATT/TTGTCCTTAATT...TGCAG|CTT 0 1 19.661
125746589 GT-AG 0 1.000000099473604e-05 106 rna-XM_010246053.2 23121150 4 6567301 6567406 Nelumbo nucifera 4432 TTG|GTGAGCTCTG...TGGTTTTTATTT/TTTTTATTTATC...TGCAG|AAC 0 1 41.584
125746590 GT-AG 0 0.001203752397336 104 rna-XM_010246053.2 23121150 5 6567095 6567198 Nelumbo nucifera 4432 CTG|GTAGCTGGCA...GGGCTTTTAGTA/ACTTGTCTAAAC...CGCAG|ATT 0 1 46.393
125746591 GT-AG 0 1.000000099473604e-05 92 rna-XM_010246053.2 23121150 6 6566793 6566884 Nelumbo nucifera 4432 AAG|GTGAAAAATA...TGACCCTGAAAA/CAAGTACTGACC...GATAG|GTT 0 1 56.294
125746592 GT-AG 0 3.685431691371183e-05 95 rna-XM_010246053.2 23121150 7 6566517 6566611 Nelumbo nucifera 4432 GAG|GTACAGTAAT...AAGCCTTTGATG/TCAAACTTCATG...TACAG|TGA 1 1 64.828
125746593 GT-AG 0 1.000000099473604e-05 98 rna-XM_010246053.2 23121150 8 6566153 6566250 Nelumbo nucifera 4432 CAG|GTAAAACTAA...CTGTCTTTGAAT/AATTTTGTAATC...TACAG|TGG 0 1 77.369
125746594 GT-AG 0 0.0209149039241326 141 rna-XM_010246053.2 23121150 9 6565922 6566062 Nelumbo nucifera 4432 CGG|GTATGTTTGA...TACTCCCTGATT/TACTCCCTGATT...TACAG|ACT 0 1 81.612

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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]);