transcripts

Data license: ODbL · Data source: Larue & Roy, 2023 · About: Minor Intron Database (WtMTA)

id
INTEGER (primary key), unique identifier for each transcript
taxonomy_id
INTEGER (foreign key referencing genomes(taxonomy_id)), NCBI taxonomy identifier for species
transcript_id
TEXT, annotated identifier for the transcript
gene_id
TEXT, annotated identifier for the associated gene
chromosome
TEXT, chromosome (or contig) where the transcript is located
strand
TEXT, DNA strand of the transcript (+ or -)
start
INTEGER, start position of the transcript in the genome (1-based, inclusive)
end
INTEGER, end position of the transcript in the genome (1-based, inclusive)
coding_length
INTEGER, length of the coding sequence in base pairs
introns_per_kbp_cds
REAL, number of introns per kilobase coding sequence
proportion_minor_introns
REAL, proportion of minor introns in the transcript
n_introns
INTEGER, total number of introns in the transcript
n_minor_introns
INTEGER, number of minor introns in the transcript

18,126 rows where taxonomy_id = 3649

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Suggested facets: strand, n_minor_introns

id ▼ taxonomy_id transcript_id gene_id chromosome strand start end coding_length introns_per_kbp_cds proportion_minor_introns n_introns n_minor_introns
6846755 Carica papaya 3649 rna-XM_022034873.1 gene-LOC110806311 NW_019011179.1 - 5 1364 819 3.663003663003663 0.0 3 0
6846756 Carica papaya 3649 rna-XM_022046209.1 gene-LOC110814818 NW_019011182.1 + 249 1104 411 9.732360097323602 0.0 4 0
6846758 Carica papaya 3649 rna-XM_022032219.1 gene-LOC110806876 NW_019011192.1 - 3281 5282 1089 5.5096418732782375 0.0 6 0
6846759 Carica papaya 3649 rna-XM_022033347.1 gene-LOC110807744 NW_019011194.1 - 1456 3166 990 1.0101010101010102 0.0 2 0
6846760 Carica papaya 3649 rna-XM_022034493.1 gene-LOC110808585 NW_019011196.1 + 6 15230 1134 6.172839506172839 0.0 7 0
6846761 Carica papaya 3649 rna-XM_022035607.1 gene-LOC110809417 NW_019011197.1 - 10706 13941 1194 0.8375209380234506 0.0 1 0
6846762 Carica papaya 3649 rna-XM_022036755.1 gene-LOC110810273 NW_019011197.1 - 8449 9595 813 4.920049200492005 0.0 4 0
6846763 Carica papaya 3649 rna-XM_022037894.1 gene-LOC110811125 NW_019011197.1 - 3906 7913 588 6.802721088435374 0.0 4 0
6846766 Carica papaya 3649 rna-XM_022052915.1 gene-LOC110822426 NW_019011200.1 - 13461 17152 2283 0.4380201489268506 0.0 1 0
6846767 Carica papaya 3649 rna-XM_022044300.1 gene-LOC110815939 NW_019011200.1 - 20264 26800 1866 9.64630225080386 0.0 18 0
6846768 Carica papaya 3649 rna-XM_022048797.1 gene-LOC110819282 NW_019011200.1 + 7060 9598 1257 7.159904534606206 0.0 11 0
6846769 Carica papaya 3649 rna-XM_022050666.1 gene-LOC110820710 NW_019011200.1 - 10177 12217 909 7.700770077007701 0.0 7 0
6846770 Carica papaya 3649 rna-XM_022054030.1 gene-LOC110823307 NW_019011200.1 - 30313 31624 723 1.3831258644536653 0.0 1 0
6846771 Carica papaya 3649 rna-XM_022051818.1 gene-LOC110821566 NW_019011200.1 + 5 3058 3051 0.6555227794165848 0.0 4 0
6846772 Carica papaya 3649 rna-XM_022046210.1 gene-LOC110817325 NW_019011200.1 - 39216 40052 837 0.0 0.0 1 0
6846773 Carica papaya 3649 rna-XM_022055108.1 gene-LOC110824210 NW_019011202.1 + 273 1285 720 1.3888888888888888 0.0 1 0
6846774 Carica papaya 3649 rna-XM_022056016.1 gene-LOC110825246 NW_019011210.1 + 14 2479 1401 4.996431120628123 0.0 7 0
6846777 Carica papaya 3649 rna-XM_022056743.1 gene-LOC110826111 NW_019011217.1 + 1910 6091 855 3.5087719298245617 0.0 3 0
6846778 Carica papaya 3649 rna-XM_022056846.1 gene-LOC110826209 NW_019011219.1 + 5273 8035 1161 2.5839793281653747 0.0 3 0
6846780 Carica papaya 3649 rna-XM_022031159.1 gene-LOC110806312 NW_019011223.1 - 12053 16683 1800 1.1111111111111112 0.0 2 0
6846781 Carica papaya 3649 rna-XM_022031270.1 gene-LOC110806398 NW_019011224.1 - 5406 7080 1575 0.6349206349206349 0.0 1 0
6846782 Carica papaya 3649 rna-XM_022031594.1 gene-LOC110806642 NW_019011224.1 - 20 3263 807 1.2391573729863692 0.0 1 0
6846783 Carica papaya 3649 rna-XM_022031490.1 gene-LOC110806556 NW_019011224.1 - 3809 4700 618 4.854368932038835 0.0 3 0
6846784 Carica papaya 3649 rna-XM_022031700.1 gene-LOC110806739 NW_019011230.1 + 56 979 636 4.716981132075471 0.0 3 0
6846785 Carica papaya 3649 rna-XM_022031813.1 gene-LOC110806824 NW_019011242.1 - 6 1828 1191 1.6792611251049538 0.0 2 0
6846786 Carica papaya 3649 rna-XM_022031932.1 gene-LOC110806905 NW_019011254.1 + 846 2702 618 8.090614886731391 0.0 5 0
6846787 Carica papaya 3649 rna-XM_022032150.1 gene-LOC110807089 NW_019011258.1 + 7 633 627 0.0 0.0 1 0
6846788 Carica papaya 3649 rna-XM_022032257.1 gene-LOC110807182 NW_019011260.1 + 5 2496 882 3.401360544217687 0.0 3 0
6846790 Carica papaya 3649 rna-XM_022032446.1 gene-LOC110807307 NW_019011262.1 - 2242 6619 849 8.244994110718492 0.0 7 0
6846791 Carica papaya 3649 rna-XM_022032552.1 gene-LOC110807389 NW_019011265.1 - 481 3339 963 9.345794392523365 0.0 10 0
6846792 Carica papaya 3649 rna-XM_022032662.1 gene-LOC110807487 NW_019011266.1 - 2972 5987 633 4.739336492890995 0.0 4 0
6846794 Carica papaya 3649 rna-XM_022033164.1 gene-LOC110807849 NW_019011269.1 - 10716 14247 1449 2.7605244996549345 0.0 4 0
6846795 Carica papaya 3649 rna-XM_022032923.1 gene-LOC110807694 NW_019011269.1 + 1172 2337 996 1.004016064257028 0.0 1 0
6846796 Carica papaya 3649 rna-XM_022033048.1 gene-LOC110807771 NW_019011269.1 - 16320 17821 383 7.832898172323759 0.0 3 0
6846797 Carica papaya 3649 rna-XM_022033503.1 gene-LOC110808102 NW_019011271.1 + 5063 9471 3078 0.649772579597141 0.0 2 0
6846798 Carica papaya 3649 rna-XM_022033624.1 gene-LOC110808187 NW_019011275.1 + 13 989 405 9.876543209876544 0.0 4 0
6846800 Carica papaya 3649 rna-XM_022034007.1 gene-LOC110808467 NW_019011288.1 + 23 4022 1269 8.668242710795903 0.0 11 0
6846801 Carica papaya 3649 rna-XM_022034233.1 gene-LOC110808645 NW_019011289.1 + 1243 3083 768 1.3020833333333333 0.0 2 0
6846802 Carica papaya 3649 rna-XM_022034118.1 gene-LOC110808554 NW_019011289.1 + 3166 4094 651 1.5360983102918586 0.0 1 0
6846803 Carica papaya 3649 rna-XM_022034351.1 gene-LOC110808726 NW_019011292.1 - 1532 2190 348 8.620689655172413 0.0 3 0
6846804 Carica papaya 3649 rna-XM_022034569.1 gene-LOC110808899 NW_019011297.1 - 7761 10528 1896 2.109704641350211 0.0 4 0
6846805 Carica papaya 3649 rna-XM_022034456.1 gene-LOC110808811 NW_019011297.1 + 5346 7293 978 5.112474437627812 0.0 6 0
6846806 Carica papaya 3649 rna-XM_022034760.1 gene-LOC110809020 NW_019011297.1 + 10527 11394 444 2.2522522522522523 0.0 1 0
6846807 Carica papaya 3649 rna-XM_022035059.1 gene-LOC110809256 NW_019011299.1 + 858 5658 4359 0.6882312456985547 0.0 3 0
6846809 Carica papaya 3649 rna-XM_022035240.1 gene-LOC110809389 NW_019011300.1 - 8019 13117 1065 5.633802816901409 0.0 6 0
6846810 Carica papaya 3649 rna-XM_022035357.1 gene-LOC110809466 NW_019011301.1 + 1713 4021 1089 1.8365472910927456 0.0 2 0
6846811 Carica papaya 3649 rna-XM_022035466.1 gene-LOC110809560 NW_019011301.1 - 8806 10557 495 4.040404040404041 0.0 3 0
6846813 Carica papaya 3649 rna-XM_022035723.1 gene-LOC110809765 NW_019011302.1 - 6267 14538 2796 3.57653791130186 0.0 10 0
6846814 Carica papaya 3649 rna-XM_022036756.1 gene-LOC110810533 NW_019011304.1 - 34249 34607 216 4.62962962962963 0.0 1 0
6846818 Carica papaya 3649 rna-XM_022036953.1 gene-LOC110810678 NW_019011315.1 + 395 1176 616 1.6233766233766236 0.0 1 0
6846819 Carica papaya 3649 rna-XM_022037069.1 gene-LOC110810753 NW_019011326.1 + 180 867 282 7.092198581560283 0.0 2 0
6846821 Carica papaya 3649 rna-XM_022037402.1 gene-LOC110811013 NW_019011335.1 - 450 1582 495 8.080808080808081 0.0 5 0
6846822 Carica papaya 3649 rna-XM_022037517.1 gene-LOC110811098 NW_019011336.1 + 127 2986 1455 4.123711340206186 0.0 6 0
6846823 Carica papaya 3649 rna-XM_022037704.1 gene-LOC110811245 NW_019011338.1 + 596 4203 1482 3.373819163292848 0.0 5 0
6846824 Carica papaya 3649 rna-XM_022037821.1 gene-LOC110811323 NW_019011339.1 - 5536 7675 1035 1.932367149758454 0.0 2 0
6846825 Carica papaya 3649 rna-XM_022038039.1 gene-LOC110811485 NW_019011343.1 + 6213 9376 594 11.784511784511784 0.0 7 0
6846826 Carica papaya 3649 rna-XM_022038153.1 gene-LOC110811578 NW_019011343.1 - 5018 5962 384 5.208333333333333 0.0 2 0
6846827 Carica papaya 3649 rna-XM_022038522.1 gene-LOC110811875 NW_019011367.1 - 15 1628 1614 0.0 0.0 1 0
6846828 Carica papaya 3649 rna-XM_022038626.1 gene-LOC110811960 NW_019011372.1 - 316 2641 1419 0.7047216349541932 0.0 1 0
6846829 Carica papaya 3649 rna-XM_022038747.1 gene-LOC110812046 NW_019011373.1 + 372 1726 273 10.989010989010987 0.0 3 0
6846830 Carica papaya 3649 rna-XM_022038858.1 gene-LOC110812136 NW_019011375.1 - 326 3598 875 5.714285714285714 0.0 5 0
6846831 Carica papaya 3649 rna-XM_022038974.1 gene-LOC110812218 NW_019011376.1 + 4062 4883 579 1.7271157167530224 0.0 1 0
6846832 Carica papaya 3649 rna-XM_022039203.1 gene-LOC110812396 NW_019011378.1 - 4 2207 825 10.90909090909091 0.0 9 0
6846833 Carica papaya 3649 rna-XM_022039422.1 gene-LOC110812574 NW_019011381.1 - 86 961 426 11.737089201877934 0.0 5 0
6846834 Carica papaya 3649 rna-XM_022039523.1 gene-LOC110812666 NW_019011384.1 + 4813 24654 774 14.21188630490956 0.0 11 0
6846835 Carica papaya 3649 rna-XM_022039819.1 gene-LOC110812891 NW_019011395.1 + 785 2190 702 2.849002849002849 0.0 2 0
6846836 Carica papaya 3649 rna-XM_022039948.1 gene-LOC110812950 NW_019011398.1 - 22 672 292 6.849315068493151 0.0 2 0
6846837 Carica papaya 3649 rna-XM_022040279.1 gene-LOC110813209 NW_019011403.1 - 1612 3710 1266 2.3696682464454977 0.0 3 0
6846838 Carica papaya 3649 rna-XM_022040517.1 gene-LOC110813382 NW_019011436.1 + 717 2774 990 1.0101010101010102 0.0 1 0
6846839 Carica papaya 3649 rna-XM_022040642.1 gene-LOC110813458 NW_019011442.1 - 256 1290 957 1.0449320794148382 0.0 1 0
6846840 Carica papaya 3649 rna-XM_022040872.1 gene-LOC110813622 NW_019011444.1 + 157 6842 792 10.101010101010102 0.0 8 0
6846841 Carica papaya 3649 rna-XM_022040761.1 gene-LOC110813538 NW_019011444.1 + 8494 10069 744 4.032258064516129 0.0 4 0
6846842 Carica papaya 3649 rna-XM_022041099.1 gene-LOC110813802 NW_019011446.1 - 7284 10919 3396 0.2944640753828033 0.0 1 0
6846843 Carica papaya 3649 rna-XM_022041266.1 gene-LOC110813940 NW_019011446.1 - 1405 4037 504 5.952380952380952 0.0 3 0
6846844 Carica papaya 3649 rna-XM_022040988.1 gene-LOC110813707 NW_019011446.1 + 4469 6761 222 4.504504504504505 0.0 1 0
6846848 Carica papaya 3649 rna-XM_022041880.1 gene-LOC110814391 NW_019011469.1 + 981 1830 553 5.424954792043399 0.0 3 0
6846849 Carica papaya 3649 rna-XM_022042104.1 gene-LOC110814570 NW_019011472.1 + 1856 2358 363 5.5096418732782375 0.0 2 0
6846851 Carica papaya 3649 rna-XM_022042289.1 gene-LOC110814701 NW_019011479.1 - 331 3159 996 12.048192771084338 0.0 13 0
6846852 Carica papaya 3649 rna-XM_022042398.1 gene-LOC110814786 NW_019011480.1 + 1067 10144 2310 2.5974025974025974 0.0 6 0
6846853 Carica papaya 3649 rna-XM_022042502.1 gene-LOC110814883 NW_019011482.1 - 11969 15945 2514 1.988862370723946 0.0 6 0
6846854 Carica papaya 3649 rna-XM_022042617.1 gene-LOC110814977 NW_019011482.1 - 3001 4349 1092 3.663003663003663 0.0 4 0
6846855 Carica papaya 3649 rna-XM_022042737.1 gene-LOC110815053 NW_019011483.1 + 9862 12790 1455 1.3745704467353952 0.0 2 0
6846856 Carica papaya 3649 rna-XM_022042920.1 gene-LOC110815205 NW_019011483.1 + 3330 5642 861 2.3228803716608595 0.0 2 0
6846858 Carica papaya 3649 rna-XM_022043121.1 gene-LOC110815325 NW_019011484.1 + 10643 22802 1668 4.196642685851319 0.0 7 0
6846859 Carica papaya 3649 rna-XM_022043236.1 gene-LOC110815406 NW_019011484.1 + 5356 8837 1554 3.861003861003861 0.0 6 0
6846861 Carica papaya 3649 rna-XM_022043917.1 gene-LOC110815905 NW_019011485.1 - 11722 12810 975 1.0256410256410255 0.0 1 0
6846862 Carica papaya 3649 rna-XM_022043498.1 gene-LOC110815492 NW_019011485.1 + 8623 10985 726 2.7548209366391188 0.0 3 0
6846863 Carica papaya 3649 rna-XM_022044262.1 gene-LOC110816162 NW_019011486.1 - 34 811 561 1.7825311942959 0.0 1 0
6846864 Carica papaya 3649 rna-XM_022044379.1 gene-LOC110816232 NW_019011488.1 - 5 877 873 0.0 0.0 1 0
6846865 Carica papaya 3649 rna-XM_022044491.1 gene-LOC110816309 NW_019011498.1 + 5480 6234 408 7.352941176470588 0.0 3 0
6846866 Carica papaya 3649 rna-XM_022044605.1 gene-LOC110816398 NW_019011498.1 + 39 1226 351 11.396011396011396 0.0 4 0
6846867 Carica papaya 3649 rna-XM_022044727.1 gene-LOC110816476 NW_019011505.1 - 65 2982 798 7.518796992481203 0.0 6 0
6846868 Carica papaya 3649 rna-XM_022044959.1 gene-LOC110816645 NW_019011520.1 - 16 1690 648 9.25925925925926 0.0 6 0
6846869 Carica papaya 3649 rna-XM_022045072.1 gene-LOC110816726 NW_019011525.1 + 2808 3248 273 3.663003663003663 0.0 2 0
6846871 Carica papaya 3649 rna-XM_022045294.1 gene-LOC110816906 NW_019011540.1 + 123 1294 671 7.451564828614009 0.0 5 0
6846873 Carica papaya 3649 rna-XM_022045705.1 gene-LOC110817221 NW_019011572.1 + 163 3017 1081 4.6253469010175765 0.0 5 0
6846874 Carica papaya 3649 rna-XM_022045818.1 gene-LOC110817304 NW_019011577.1 - 1426 3158 369 5.420054200542006 0.0 2 0
6846875 Carica papaya 3649 rna-XM_022046133.1 gene-LOC110817465 NW_019011597.1 - 179 1028 381 5.2493438320209975 0.0 2 0
6846876 Carica papaya 3649 rna-XM_022046249.1 gene-LOC110817599 NW_019011598.1 - 4 6328 339 2.949852507374631 0.0 2 0
6846878 Carica papaya 3649 rna-XM_022046550.1 gene-LOC110817809 NW_019011611.1 - 983 1458 255 3.92156862745098 0.0 1 0

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CREATE TABLE "transcripts" (
"id" INTEGER,
  "taxonomy_id" INTEGER,
  "transcript_id" TEXT,
  "gene_id" TEXT,
  "chromosome" TEXT,
  "strand" TEXT,
  "start" INTEGER,
  "end" INTEGER,
  "coding_length" INTEGER,
  "introns_per_kbp_cds" REAL,
  "proportion_minor_introns" REAL,
  "n_introns" INTEGER,
  "n_minor_introns" INTEGER
  ,PRIMARY KEY ([id]),
   FOREIGN KEY([taxonomy_id]) REFERENCES [genomes]([taxonomy_id])
);
CREATE INDEX [idx_transcripts_taxonomy_id]
    ON [transcripts] ([taxonomy_id]);
CREATE INDEX [idx_transcripts_gene_id]
    ON [transcripts] ([gene_id]);
CREATE INDEX [idx_transcripts_chromosome]
    ON [transcripts] ([chromosome]);