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 = 38690324

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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
213933157 GT-AG 0 0.1664910008437588 212 rna-XM_016044816.2 38690324 1 35626021 35626232 Ziziphus jujuba 326968 AAG|GTATGCTCTT...GTCTTCTTGATA/GTCTTCTTGATA...AACAG|GAA 0 1 52.737
213933158 GT-AG 0 6.817052231407752e-05 113 rna-XM_016044816.2 38690324 2 35625821 35625933 Ziziphus jujuba 326968 TTG|GTAAGCAATT...TTTTTTTTAATG/TTTTTTTTAATG...ATTAG|GTC 0 1 54.673
213933159 GT-AG 0 0.0005096115790734 83 rna-XM_016044816.2 38690324 3 35625096 35625178 Ziziphus jujuba 326968 AGA|GTAAGTTTTT...GAGGCTTTGAAA/TTTGGTCTGATG...TTCAG|GCT 0 1 68.959
213933160 GT-AG 0 1.000000099473604e-05 341 rna-XM_016044816.2 38690324 4 35624590 35624930 Ziziphus jujuba 326968 GAG|GTATAACACT...TAATTTTGATAT/TGGATTCTCACA...TGCAG|CAA 0 1 72.63
213933161 GT-AG 0 1.000000099473604e-05 129 rna-XM_016044816.2 38690324 5 35624166 35624294 Ziziphus jujuba 326968 CAG|GTAAGTAATT...TTTATTTTATTT/ATTTTTTTCAAT...TAAAG|GCA 1 1 79.194
213933162 GT-AG 0 1.000000099473604e-05 116 rna-XM_016044816.2 38690324 6 35623835 35623950 Ziziphus jujuba 326968 CAG|GTACTTTCAT...AGTTCATTTGTA/TAAATAATGATA...TATAG|GTC 0 1 83.979
213933163 GT-AG 0 1.000000099473604e-05 79 rna-XM_016044816.2 38690324 7 35623450 35623528 Ziziphus jujuba 326968 GAG|GTGGGTGGTC...TATGCTTTATAA/ATATGCTTTATA...TTTAG|GCC 0 1 90.788
213933164 GT-AG 0 1.000000099473604e-05 106 rna-XM_016044816.2 38690324 8 35623280 35623385 Ziziphus jujuba 326968 CAG|GTTTGTGTCT...TCTGTTTTGTCC/CTGATATTCACA...TACAG|TCA 1 1 92.212
213933165 GT-AG 0 4.883113251243806e-05 99 rna-XM_016044816.2 38690324 9 35622941 35623039 Ziziphus jujuba 326968 ATG|GTATGACCGG...TTGGTCTTGATG/AATTTTCTCATT...TCCAG|GGC 1 1 97.552

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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]);