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 = 1013839

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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
5252068 GT-AG 0 0.0001363129256618 747 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 1 264229 264975 Alectura lathami 81907 TTT|GTAAGTATTT...TTTATGTTGACC/TTTATGTTGACC...GACAG|CTG 0 1 8.502
5252069 GT-AG 0 5.029848735025917e-05 5266 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 2 258768 264033 Alectura lathami 81907 TTT|GTAAGTGTCC...TTTTCCGTATAT/ATTGTACACACA...TCTAG|TTC 0 1 34.818
5252070 GT-AG 0 2.9098875305759173e-05 5866 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 3 252827 258692 Alectura lathami 81907 AAT|GTAAGTATCC...TAACCCTTTGCA/CTGGCAGTAACC...TTCAG|CTG 0 1 44.939
5252071 GT-AG 0 1.000000099473604e-05 1262 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 4 251466 252727 Alectura lathami 81907 ACG|GTGAGTCAGG...TCTTCCTTTCCT/CAAAGCGTAAAC...CCTAG|TTT 0 1 58.3
5252072 GT-AG 0 1.000000099473604e-05 2429 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 5 248857 251285 Alectura lathami 81907 CAG|GTGAGGGCAG...TGTGTCTCACTG/GTGTGTCTCACT...CCTAG|GGC 0 1 82.591
5252073 GT-AG 0 0.0001443125702087 895 rna-gnl|WGS:VXAV|ALELAT_R02224_mrna 1013839 6 247878 248772 Alectura lathami 81907 GAG|GTACTATTGT...TCCATTTTATTT/CTCCATTTTATT...CCCAG|CTG 0 1 93.927

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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]);