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)

7 rows where transcript_id = 16792035

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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
89436820 GT-AG 0 1.000000099473604e-05 868 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 1 8113642 8114509 Halcyon senegalensis 342381 CAG|GTGGGTGAAG...AATATTTTGTTG/TTTGTTGCTATT...TTCAG|GTG 1 1 13.66
89436821 GT-AG 0 1.000000099473604e-05 428 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 2 8114648 8115075 Halcyon senegalensis 342381 TAG|GTAATGTTTG...GACACCTGCCCA/CGGTGGCTGACA...AACAG|ACA 1 1 23.905
89436822 GT-AG 0 1.000000099473604e-05 377 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 3 8115402 8115778 Halcyon senegalensis 342381 GAG|GTCAGTCACC...GAGCTCTGAACC/GAGTTACTGACG...TGTAG|ATC 0 1 48.107
89436823 GT-AG 0 1.000000099473604e-05 173 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 4 8115959 8116131 Halcyon senegalensis 342381 CAG|GTTGGTGGGG...GTTGCTGTATTT/CTGTATTTCACT...TCCAG|CAG 0 1 61.47
89436824 GT-AG 0 1.000000099473604e-05 177 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 5 8116285 8116461 Halcyon senegalensis 342381 AAG|GTACAGGATG...GTGCTTTTGACC/GTGCTTTTGACC...AACAG|CAT 0 1 72.829
89436825 GT-AG 0 1.000000099473604e-05 122 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 6 8116588 8116709 Halcyon senegalensis 342381 CAG|GTGATAAAAC...GATACATTGTCC/CATCGTGTGACA...ACCAG|GCG 0 1 82.183
89436826 GT-AG 0 0.0023822806807824 561 rna-gnl|WGS:WBNJ|HALSEN_R05805_mrna 16792035 7 8116902 8117462 Halcyon senegalensis 342381 CTG|GTATGTCTGT...ACTTCCTTGCTT/GAATGATTAATT...TTCAG|ACC 0 1 96.437

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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]);