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

20,795 rows where taxonomy_id = 9901

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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
4280199 Bison bison 9901 rna-XM_010842218.1 gene-LOC104987666 NW_011371433.1 - 1160 5046 804 3.7313432835820897 0.0 3 0
4280200 Bison bison 9901 rna-XM_010852999.1 gene-LOC104995474 NW_011371471.1 + 2425 5390 492 6.097560975609756 0.0 4 0
4280201 Bison bison 9901 rna-XM_010828113.1 gene-LOC105003085 NW_011371559.1 - 1929 22832 1296 6.172839506172839 0.0 8 0
4280202 Bison bison 9901 rna-XM_010833701.1 gene-FBXW5 NW_011371590.1 - 31285 33952 1698 4.122497055359246 0.0 8 0
4280203 Bison bison 9901 rna-XM_010832683.1 gene-TRAF2 NW_011371590.1 + 15443 25276 1551 5.802707930367505 0.0 9 0
4280204 Bison bison 9901 rna-XM_010836520.1 gene-LOC104985807 NW_011371616.1 + 259 631 290 3.4482758620689653 0.0 1 0
4280205 Bison bison 9901 rna-XM_010837582.1 gene-LOC104986599 NW_011371715.1 - 198 1268 258 3.875968992248062 0.0 2 0
4280207 Bison bison 9901 rna-XM_010841128.1 gene-CETN2 NW_011371797.1 + 14769 17390 492 6.097560975609756 0.0 4 0
4280208 Bison bison 9901 rna-XM_010840064.1 gene-LOC104988418 NW_011371797.1 - 1999 6171 330 3.0303030303030303 0.0 2 0
4280209 Bison bison 9901 rna-XM_010842990.1 gene-LOC104990487 NW_011371851.1 - 7446 32203 609 8.210180623973727 0.0 5 0
4280210 Bison bison 9901 rna-XM_010845119.1 gene-LOC104992031 NW_011372037.1 - 4 8939 2568 7.009345794392523 0.0 18 0
4280211 Bison bison 9901 rna-XM_010846182.1 gene-LOC104992831 NW_011372071.1 + 1108 1961 238 4.201680672268908 0.0 1 0
4280213 Bison bison 9901 id-LOC104994411 gene-LOC104994411 NW_011372187.1 - 7 546 465 2.150537634408602 0.0 1 0
4280215 Bison bison 9901 rna-XM_010850098.1 gene-CCDC120 NW_011372294.1 - 4 6209 1296 6.944444444444444 0.0 9 0
4280216 Bison bison 9901 rna-XM_010852281.1 gene-ZDHHC15 NW_011372390.1 + 887 35328 459 10.893246187363834 0.0 5 0
4280219 Bison bison 9901 rna-XM_010858945.1 gene-OTUD5 NW_011372607.1 + 4160 11680 1109 8.115419296663662 0.0 9 0
4280220 Bison bison 9901 rna-XM_010860054.1 gene-PIM2 NW_011372607.1 + 12485 20848 1014 5.9171597633136095 0.0 6 0
4280221 Bison bison 9901 rna-XM_010857213.1 gene-LOC105000825 NW_011372607.1 + 23579 25423 447 2.237136465324385 0.0 1 0
4280222 Bison bison 9901 rna-XM_010861178.1 gene-LOC105003545 NW_011372639.1 + 2611 6182 987 2.026342451874367 0.0 2 0
4280223 Bison bison 9901 rna-XM_010862207.1 gene-LOC105004301 NW_011372659.1 + 2065 33944 557 7.1813285457809695 0.0 4 0
4280224 Bison bison 9901 rna-XM_010829888.1 gene-MAFK NW_011372864.1 - 7 1168 474 2.109704641350211 0.0 1 0
4280225 Bison bison 9901 rna-XM_010831009.1 gene-LOC104981505 NW_011372865.1 + 8485 49794 1040 8.653846153846155 0.0 9 0
4280226 Bison bison 9901 rna-XM_010831999.1 gene-FAM193A NW_011372879.1 + 14000 50798 2210 4.97737556561086 0.0 12 0
4280227 Bison bison 9901 rna-XM_010832232.1 gene-LOC104982768 NW_011372881.1 + 101 860 363 5.5096418732782375 0.0 2 0
4280231 Bison bison 9901 rna-XM_010832839.1 gene-LOC104983357 NW_011373113.1 + 88 1160 656 4.573170731707317 0.0 3 0
4280233 Bison bison 9901 rna-XM_010833123.1 gene-LOC104983571 NW_011373314.1 - 2371 5336 492 6.097560975609756 0.0 4 0
4280234 Bison bison 9901 rna-XM_010833307.1 gene-ASB9 NW_011373327.1 + 24731 47986 702 8.547008547008549 0.0 6 0
4280235 Bison bison 9901 rna-XM_010833209.1 gene-ASB11 NW_011373327.1 + 3365 13889 645 6.2015503875969 0.0 4 0
4280237 Bison bison 9901 rna-XM_010833702.1 gene-LOC104984059 NW_011373416.1 - 16 3818 330 6.0606060606060606 0.0 2 0
4280238 Bison bison 9901 rna-XM_010834073.1 gene-LOC104984360 NW_011373455.1 - 6 924 561 5.347593582887701 0.0 3 0
4280239 Bison bison 9901 rna-XM_010834178.1 gene-LOC104984437 NW_011373515.1 - 15 681 455 4.395604395604396 0.0 2 0
4280240 Bison bison 9901 rna-XM_010834294.1 gene-LOC104984503 NW_011373674.1 + 587 943 357 0.0 0.0 1 0
4280241 Bison bison 9901 rna-XM_010834413.1 gene-LOC104984566 NW_011373730.1 - 17926 21183 321 6.230529595015576 0.0 2 0
4280242 Bison bison 9901 rna-XM_010834842.1 gene-LOC104984866 NW_011373965.1 - 18 518 319 6.269592476489028 0.0 2 0
4280244 Bison bison 9901 rna-XM_010835528.1 gene-LOC104985356 NW_011374644.1 + 7468 11876 1656 1.8115942028985508 0.0 3 0
4280246 Bison bison 9901 rna-XM_010836020.1 gene-LOC104985694 NW_011375746.1 + 62 611 243 4.11522633744856 0.0 1 0
4280247 Bison bison 9901 rna-XM_010836256.1 gene-LOC104985831 NW_011375910.1 - 27 1055 475 8.421052631578947 0.0 4 0
4280248 Bison bison 9901 rna-XM_010836841.1 gene-LOC104986289 NW_011376540.1 + 93 923 638 1.567398119122257 0.0 1 0
4280249 Bison bison 9901 rna-XM_010836945.1 gene-LOC104986372 NW_011376695.1 - 8356 15051 789 5.069708491761723 0.0 4 0
4280250 Bison bison 9901 rna-XM_010837116.1 gene-LOC104986495 NW_011376967.1 + 4 872 371 8.086253369272237 0.0 3 0
4280251 Bison bison 9901 rna-XM_010837236.1 gene-LOC104986573 NW_011377127.1 - 52 537 375 2.6666666666666665 0.0 1 0
4280253 Bison bison 9901 rna-XM_010837734.1 gene-LOC104986960 NW_011377733.1 + 7 504 426 2.347417840375587 0.0 1 0
4280254 Bison bison 9901 rna-XM_010838075.1 gene-TRABD NW_011378093.1 + 57 558 339 5.899705014749262 0.0 2 0
4280255 Bison bison 9901 rna-XM_010838290.1 gene-LOC104987379 NW_011378614.1 + 4325 6076 668 1.497005988023952 0.0 1 0
4280257 Bison bison 9901 rna-XM_010838636.1 gene-LOC104987584 NW_011379094.1 + 756 1749 393 5.089058524173028 0.0 2 0
4280258 Bison bison 9901 rna-XM_010838955.1 gene-LOC104987842 NW_011379171.1 + 370 1028 389 2.5706940874035986 0.0 1 0
4280259 Bison bison 9901 rna-XM_010839050.1 gene-LOC104987926 NW_011379187.1 + 153 710 360 5.555555555555555 0.0 3 0
4280260 Bison bison 9901 rna-XM_010839157.1 gene-LOC104987990 NW_011379190.1 + 111 1356 981 1.0193679918450562 0.0 1 0
4280261 Bison bison 9901 rna-XM_010839486.1 gene-LOC104988212 NW_011379407.1 + 138 698 470 2.127659574468085 0.0 1 0
4280263 Bison bison 9901 rna-XM_010839693.1 gene-LOC104988364 NW_011379452.1 + 27 573 505 1.98019801980198 0.0 1 0
4280264 Bison bison 9901 rna-XM_010839809.1 gene-LOC104988443 NW_011379479.1 - 28 644 304 6.578947368421052 0.0 3 0
4280265 Bison bison 9901 rna-XM_010840106.1 gene-LOC104988671 NW_011379547.1 + 127 3240 1359 2.207505518763797 0.0 3 0
4280266 Bison bison 9901 rna-XM_010840214.1 gene-THAP7 NW_011379704.1 - 5 925 738 1.3550135501355014 0.0 1 0
4280267 Bison bison 9901 rna-XM_010840316.1 gene-LOC104988826 NW_011379742.1 + 1528 4209 432 2.314814814814815 0.0 1 0
4280273 Bison bison 9901 rna-XM_010842339.1 gene-LOC104990307 NW_011383165.1 + 241 762 522 0.0 0.0 1 0
4280274 Bison bison 9901 rna-XM_010842581.1 gene-LOC104990459 NW_011384013.1 - 57 680 552 1.8115942028985508 0.0 1 0
4280275 Bison bison 9901 rna-XM_010843804.1 gene-LOC104991349 NW_011386922.1 - 331 2120 465 6.451612903225806 0.0 3 0
4280276 Bison bison 9901 id-LOC104991558 gene-LOC104991558 NW_011386983.1 - 72 745 415 2.409638554216868 0.0 1 0
4280277 Bison bison 9901 rna-XM_010844240.1 gene-LOC104991646 NW_011386992.1 + 374 1251 363 8.264462809917356 0.0 3 0
4280278 Bison bison 9901 rna-XM_010844438.1 gene-LOC104991795 NW_011387191.1 + 76 1021 573 5.235602094240838 0.0 3 0
4280279 Bison bison 9901 rna-XM_010844960.1 gene-LOC104992167 NW_011387395.1 + 31 550 306 3.2679738562091503 0.0 1 0
4280281 Bison bison 9901 rna-XM_010845197.1 gene-LOC104992312 NW_011387544.1 - 297 791 234 4.273504273504274 0.0 1 0
4280282 Bison bison 9901 rna-XM_010845296.1 gene-LOC104992398 NW_011387592.1 + 376 1108 402 4.975124378109452 0.0 2 0
4280284 Bison bison 9901 rna-XM_010845789.1 gene-LOC104992771 NW_011389185.1 + 6 621 477 2.0964360587002098 0.0 1 0
4280287 Bison bison 9901 rna-XM_010846145.1 gene-LOC104993027 NW_011390040.1 + 6 568 341 2.932551319648094 0.0 1 0
4280288 Bison bison 9901 rna-XM_010846584.1 gene-LOC104993328 NW_011390690.1 + 686 4948 303 6.600660066006601 0.0 2 0
4280290 Bison bison 9901 rna-XM_010847513.1 gene-FIGF NW_011392402.1 - 8698 18097 652 6.134969325153374 0.0 4 0
4280291 Bison bison 9901 rna-XM_010847607.1 gene-LOC104994110 NW_011392442.1 - 32 516 404 2.4752475247524752 0.0 1 0
4280294 Bison bison 9901 rna-XM_010848319.1 gene-LOC104994641 NW_011393732.1 - 153 560 321 6.230529595015576 0.0 2 0
4280295 Bison bison 9901 rna-XM_010848505.1 gene-LOC104994811 NW_011394796.1 - 15 453 300 3.333333333333333 0.0 1 0
4280296 Bison bison 9901 rna-XM_010848722.1 gene-LOC104994972 NW_011395116.1 + 10 454 414 2.415458937198068 0.0 1 0
4280298 Bison bison 9901 rna-XM_010849224.1 gene-DGAT1 NW_011398121.1 - 7 699 373 10.723860589812332 0.0 4 0
4280300 Bison bison 9901 rna-XM_010849979.1 gene-LOC104995891 NW_011401955.1 - 16015 26307 740 5.405405405405405 0.0 5 0
4280303 Bison bison 9901 rna-XM_010850666.1 gene-LOC104996383 NW_011404686.1 - 21 1655 925 3.243243243243243 0.0 3 0
4280304 Bison bison 9901 rna-XM_010850770.1 gene-LOC104996467 NW_011404690.1 + 7 1186 459 2.1786492374727677 0.0 1 0
4280305 Bison bison 9901 rna-XM_010850868.1 gene-LOC104996552 NW_011404704.1 - 484 1412 267 3.745318352059925 0.0 1 0
4280306 Bison bison 9901 rna-XM_010850971.1 gene-LOC104996638 NW_011404713.1 - 236 1277 531 1.8832391713747645 0.0 1 0
4280307 Bison bison 9901 rna-XM_010851090.1 gene-LOC104996708 NW_011404775.1 + 211 1212 342 2.923976608187134 0.0 1 0
4280308 Bison bison 9901 rna-XM_010851189.1 gene-LOC104996785 NW_011404793.1 - 86 1499 626 6.389776357827476 0.0 4 0
4280309 Bison bison 9901 rna-XM_010851630.1 gene-LOC104997081 NW_011404952.1 - 7 1240 753 2.6560424966799467 0.0 2 0
4280310 Bison bison 9901 rna-XM_010851759.1 gene-LOC104997131 NW_011405052.1 + 1121 1504 303 3.3003300330033003 0.0 1 0
4280311 Bison bison 9901 rna-XM_010851982.1 gene-LOC104997284 NW_011405135.1 + 34 1064 309 3.236245954692557 0.0 1 0
4280312 Bison bison 9901 rna-XM_010852095.1 gene-LOC104997357 NW_011405141.1 - 59 1069 231 4.329004329004329 0.0 1 0
4280313 Bison bison 9901 rna-XM_010852201.1 gene-LOC104997436 NW_011405160.1 + 334 963 252 3.968253968253968 0.0 1 0
4280314 Bison bison 9901 rna-XM_010852329.1 gene-LOC104997502 NW_011405367.1 - 6 937 618 3.236245954692557 0.0 2 0
4280316 Bison bison 9901 rna-XM_010852695.1 gene-LOC104997739 NW_011405984.1 - 28 501 324 3.08641975308642 0.0 1 0
4280317 Bison bison 9901 rna-XM_010852798.1 gene-LOC104997832 NW_011405993.1 - 185 727 291 3.436426116838488 0.0 1 0
4280319 Bison bison 9901 rna-XM_010852964.1 gene-LOC104997957 NW_011406419.1 - 25 4226 1156 6.055363321799308 0.0 7 0
4280320 Bison bison 9901 rna-XM_010853071.1 gene-LOC104998038 NW_011406519.1 - 199 789 260 3.8461538461538463 0.0 1 0
4280321 Bison bison 9901 rna-XM_010853170.1 gene-LOC104998118 NW_011406793.1 + 334 823 400 2.5 0.0 1 0
4280322 Bison bison 9901 rna-XM_010853484.1 gene-LOC104998339 NW_011407419.1 - 248 608 263 3.802281368821293 0.0 1 0
4280324 Bison bison 9901 rna-XM_010854747.1 gene-LOC104999207 NW_011409338.1 + 125 521 268 3.7313432835820897 0.0 1 0
4280326 Bison bison 9901 rna-XM_010855268.1 gene-LOC104999679 NW_011410424.1 + 159 9344 511 9.784735812133071 0.0 5 0
4280327 Bison bison 9901 rna-XM_010855973.1 gene-AWAT1 NW_011412352.1 + 23606 30045 734 6.811989100817439 0.0 5 0
4280331 Bison bison 9901 rna-XM_010857010.1 gene-LOC105000909 NW_011419333.1 - 4655 10396 1615 9.907120743034056 0.0 16 0
4280333 Bison bison 9901 rna-XM_010857369.1 gene-LOC105001162 NW_011423845.1 + 7 579 476 4.201680672268908 0.0 2 0
4280335 Bison bison 9901 rna-XM_010858120.1 gene-LOC105001724 NW_011431345.1 - 4358 5923 291 3.436426116838488 0.0 1 0
4280336 Bison bison 9901 rna-XM_010858244.1 gene-LOC105001791 NW_011434091.1 - 10 381 256 3.90625 0.0 1 0
4280337 Bison bison 9901 rna-XM_010858426.1 gene-LOC105001955 NW_011434520.1 - 10 557 453 2.207505518763797 0.0 1 0
4280339 Bison bison 9901 rna-XM_010859124.1 gene-LOC105002466 NW_011439233.1 + 293 1787 456 2.1929824561403506 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]);