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 = 26383222

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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
146243725 GT-AG 0 5.2909576703101246e-05 520 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 1 4700324 4700843 Parasponia andersonii 3476 GAG|GTTCGCTAAA...TCTGTTTTAATT/TTTGATCTCATT...TGTAG|ATT 0 1 6.718
146243726 GT-AG 0 0.0169181754504913 108 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 2 4701054 4701161 Parasponia andersonii 3476 AGT|GTAAGCTTAT...TATGTCTTATCC/GTATGTCTTATC...GGTAG|ATT 0 1 13.436
146243727 GT-AG 0 0.064679969930617 144 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 3 4701416 4701559 Parasponia andersonii 3476 AGA|GTACGCATTT...TTTTTTTTGATA/CATTTTTTAATT...CACAG|TTG 2 1 21.561
146243728 GT-AG 0 8.504089488083512e-05 399 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 4 4701831 4702229 Parasponia andersonii 3476 GAG|GTTTTTTCAC...AATATATTAATT/AATATATTAATT...TGCAG|AAT 0 1 30.23
146243729 GT-AG 0 1.2723217433049005e-05 141 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 5 4704137 4704277 Parasponia andersonii 3476 CAG|GTACATAATT...GTTGTTTTGCTG/CATGTACTCAGT...TTCAG|TGC 2 1 91.235
146243730 GT-AG 0 0.0001521309141983 621 rna-gnl|WGS:JXTB|PanWU01x14_003790.1 26383222 6 4704510 4705130 Parasponia andersonii 3476 CGG|GTAATCTAGG...TTCATTTTATTT/TCATTTTTCATT...TGCAG|TCC 0 1 98.656

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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]);