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 = 23121153

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Suggested facets: dinucleotide_pair, score, phase

id ▼ dinucleotide_pair is_minor score length transcript_id ordinal_index start end taxonomy_id scored_motifs phase in_cds relative_position
125746614 GT-AG 0 1.000000099473604e-05 4340 rna-XM_010243159.1 23121153 1 6158477 6162816 Nelumbo nucifera 4432 AAG|GTAATAGTTG...GAAATTTTATCT/GATTGATTTATT...CACAG|GAC 1 1 29.46
125746615 GT-AG 0 4.313399786040848e-05 15763 rna-XM_010243159.1 23121153 2 6162937 6178699 Nelumbo nucifera 4432 AAG|GTAAGCTTAC...CTAATATTAATT/TATTAATTCATT...ATCAG|GTA 1 1 35.198
125746616 GT-AG 0 0.0002191323968626 148 rna-XM_010243159.1 23121153 3 6178795 6178942 Nelumbo nucifera 4432 ACG|GTATGATATC...TTTTCTTTGCTT/TCTTTGCTTACT...TACAG|GTT 0 1 39.742
125746617 GC-AG 0 1.000000099473604e-05 2719 rna-XM_010243159.1 23121153 4 6179061 6181779 Nelumbo nucifera 4432 AAG|GCAAGTCCAT...TTGGCTTTAATT/CTTTAATTCACA...AACAG|GAC 1 1 45.385
125746618 GC-AG 0 1.0813757071212191e-05 96 rna-XM_010243159.1 23121153 5 6181900 6181995 Nelumbo nucifera 4432 AAG|GCATGTATTA...TTTTCCCTAAAA/ACATGAATCATT...TGCAG|ATT 1 1 51.124
125746619 GT-AG 0 1.000000099473604e-05 83 rna-XM_010243159.1 23121153 6 6182109 6182191 Nelumbo nucifera 4432 GAG|GTTAGAGTCT...GTGGCTTTTACT/GTGGCTTTTACT...TCTAG|GGT 0 1 56.528
125746620 GT-AG 0 1.000000099473604e-05 1902 rna-XM_010243159.1 23121153 7 6182347 6184248 Nelumbo nucifera 4432 AGG|GTAAGAACTA...ATTTTCTGATCT/AATTTTCTGATC...TACAG|AAC 2 1 63.941

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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]);