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 = 12720310

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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
67622951 GC-AG 0 1.000000099473604e-05 733 rna-XM_009897987.1 12720310 1 1700951 1701683 Dryobates pubescens 118200 CTC|GCGCAGCTGG...AGAACCATGATA/GCTAGTTTGAGA...CTGAG|ATG 2 1 12.963
67622952 GT-AG 0 0.0151776740263132 776 rna-XM_009897987.1 12720310 2 1701743 1702518 Dryobates pubescens 118200 AAG|GTATTTTTTA...TCAGTGTTAACT/ATGTTACTAATG...CCTAG|GTC 1 1 19.39
67622953 GT-AG 0 1.000000099473604e-05 1093 rna-XM_009897987.1 12720310 3 1702682 1703774 Dryobates pubescens 118200 TGA|GTAAGTTGAA...GTATGCTTTTAT/GAAGATATGACT...TGCAG|GGA 2 1 37.146
67622954 GT-AG 0 1.000000099473604e-05 213 rna-XM_009897987.1 12720310 4 1703853 1704065 Dryobates pubescens 118200 GAG|GTGAGTCTGC...CAAGTTTTGAAT/TTTGAATTTATT...CTTAG|GTA 2 1 45.643
67622955 GT-AG 0 2.5653142740591692e-05 755 rna-XM_009897987.1 12720310 5 1704155 1704909 Dryobates pubescens 118200 GAG|GTAACAAAGT...AGATTTTTAATA/TTGTTACTAAAT...AATAG|GAA 1 1 55.338
67622956 GT-AG 0 0.000622085442213 206 rna-XM_009897987.1 12720310 6 1705041 1705246 Dryobates pubescens 118200 GCT|GTAAGTTCTG...ACCATTTTAATT/ACCATTTTAATT...TATAG|GCA 0 1 69.608
67622957 GT-AG 0 1.000000099473604e-05 458 rna-XM_009897987.1 12720310 7 1705371 1705828 Dryobates pubescens 118200 AAG|GTGAGTGGTT...TGTTCCATATGT/TTCTGTCTGAAG...TTCAG|TTG 1 1 83.115

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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]);