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 = 32656412

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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
182390158 GT-AG 0 1.000000099473604e-05 2843 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 1 26499 29341 Serilophus lunatus 239386 ACG|GTGGGTGTCC...CCTCTCCTGCCT/GAGGGTCACACC...CACAG|CCG 1 1 13.558
182390159 GT-AG 0 1.000000099473604e-05 90 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 2 29514 29603 Serilophus lunatus 239386 GCC|GTGAGTGGCC...CTGCCCTTCCCA/GCCCTTCCCAGG...CCCAG|GCT 2 1 31.091
182390160 GT-AG 0 1.000000099473604e-05 172 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 3 29804 29975 Serilophus lunatus 239386 AAA|GTGAGTGTGG...GTGTCCCCATCC/GGTGTCCCCATC...TGCAG|ACC 1 1 51.478
182390161 GT-AG 0 1.000000099473604e-05 82 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 4 30090 30171 Serilophus lunatus 239386 CAG|GTAGAGCCCC...GTCTCCTTTGTG/CGGGGGCTCATC...CTTAG|GGG 1 1 63.099
182390162 GT-AG 0 1.000000099473604e-05 523 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 5 30279 30801 Serilophus lunatus 239386 CCG|GTGAGTGAGG...GGGGTCTCACCC/GGGGGTCTCACC...CCCAG|TGG 0 1 74.006
182390163 GT-AG 0 1.000000099473604e-05 1489 rna-gnl|WGS:VXBA|SERLUN_R08704_mrna 32656412 6 30945 32433 Serilophus lunatus 239386 GGC|GTGAGTGTCC...CGGGCCGTGTCC/TGGGGGGTCAGG...CACAG|GTG 2 1 88.583

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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]);