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 = 26670778

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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
147887320 GT-AG 0 1.000000099473604e-05 624 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 1 14407 15030 Pedionomus torquatus 227192 AAA|GTAAGTCAAG...CCACCCCAGACT/CCCAGACTGAAG...TCTAG|TTA 1 1 15.593
147887321 GT-AG 0 1.000000099473604e-05 321 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 2 15114 15434 Pedionomus torquatus 227192 AAG|GTAAAGTAAA...TTATCTTTCTTC/ACCTATTTCAGG...CGCAG|GTG 0 1 22.196
147887322 GT-AG 0 0.0006733854013291 756 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 3 15645 16400 Pedionomus torquatus 227192 CTT|GTGACCAACA...ACAGCATTAGCA/TCGGTGGTGACC...CCAAG|GCA 0 1 38.902
147887323 GT-AG 0 1.000000099473604e-05 437 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 4 16498 16934 Pedionomus torquatus 227192 TAG|GTGAGAAAAA...CTGTTCTTGTTT/CACGGCTGCATC...TCCAG|GTG 1 1 46.619
147887324 GT-AG 0 2.1182022759500324e-05 195 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 5 17135 17329 Pedionomus torquatus 227192 CTG|GTACAAACAT...TTCCTCTTATTT/CTTCCTCTTATT...ATCAG|ATT 0 1 62.53
147887325 GT-AG 0 0.2115539766703352 92 rna-gnl|WGS:VZRU|PEDTOR_R03468_mrna 26670778 6 17459 17550 Pedionomus torquatus 227192 GAG|GTATCTCTAG...TATCTCTTTCCC/TGGTAACTGAGC...AGCAG|GTA 0 1 72.792

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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]);