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)

8 rows where transcript_id = 28932422

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Suggested facets: dinucleotide_pair, score, phase, in_cds

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
161301556 GT-AG 0 0.0014249659680407 105 rna-XM_006368150.2 28932422 2 10012712 10012816 Populus trichocarpa 3694 GAG|GTACTTTGAT...ATTTTCTTAATG/GATTTTCTTAAT...GTCAG|GGT 0 1 77.337
161301557 GT-AG 0 9.75599054869177e-05 944 rna-XM_006368150.2 28932422 3 10012898 10013841 Populus trichocarpa 3694 CAG|GTAATTTCTT...TTTCTTTTAGTT/ATTTCTTTTAGT...CACAG|ATC 0 1 79.298
161301558 GT-AG 0 1.000000099473604e-05 884 rna-XM_006368150.2 28932422 4 10013995 10014878 Populus trichocarpa 3694 TTG|GTGAGCTTCC...TGTTCCATACTT/ACTTGTCTCATT...TTCAG|ACC 0 1 83.002
161301559 GT-AG 0 1.000000099473604e-05 96 rna-XM_006368150.2 28932422 5 10015043 10015138 Populus trichocarpa 3694 CAG|GTAAGATCTC...TGTTGTTTAATC/TTTAATCTAACC...TCTAG|GCA 2 1 86.973
161301560 GT-AG 0 0.000245098555445 154 rna-XM_006368150.2 28932422 6 10015287 10015440 Populus trichocarpa 3694 AAG|GTAACTGTGA...TAATGTTTAACA/TAATGTTTAACA...TGCAG|GTA 0 1 90.557
161301561 GC-AG 0 1.000000099473604e-05 224 rna-XM_006368150.2 28932422 7 10015564 10015787 Populus trichocarpa 3694 AAG|GCAAGTAACA...AGCTTCTTCACT/TCTTCACTTATT...GGCAG|GTT 0 1 93.535
161301562 GT-AG 0 0.0001413227799911 298 rna-XM_006368150.2 28932422 8 10015876 10016173 Populus trichocarpa 3694 TAG|GTATGTATGA...TGTCTCTTTGTT/TTGTTATTCACA...TGCAG|GAG 1 1 95.666
161317264 GT-AG 0 0.0018906516356215 1048 rna-XM_006368150.2 28932422 1 10008538 10009585 Populus trichocarpa 3694 CTG|GTACTTCTTA...TAGTTCTTATTA/GTAGTTCTTATT...TTCAG|GTT   0 4.334

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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]);