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

20,644 rows where taxonomy_id = 3988

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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
31111395 Ricinus communis 3988 rna-XM_002540482.2 gene-LOC8279252 NW_003019478.1 - 21 666 508 1.968503937007874 0.0 1 0
31111396 Ricinus communis 3988 rna-XM_002540467.2 gene-LOC8279237 NW_003019409.1 - 7 688 582 1.718213058419244 0.0 1 0
31111398 Ricinus communis 3988 rna-XM_002540245.3 gene-LOC8266584 NW_003017707.1 - 5 845 639 3.129890453834116 0.0 2 0
31111402 Ricinus communis 3988 rna-XM_002539998.3 gene-LOC8281514 NW_003015399.1 - 190 889 483 4.140786749482402 0.0 2 0
31111403 Ricinus communis 3988 rna-XM_002539963.3 gene-LOC8281479 NW_003015011.1 - 16 468 279 7.168458781362007 0.0 2 0
31111404 Ricinus communis 3988 rna-XM_002539899.2 gene-LOC8286929 NW_003014378.1 - 9 774 386 5.181347150259067 0.0 3 0
31111407 Ricinus communis 3988 rna-XM_025160121.1 gene-LOC8282779 NW_003013466.1 + 47 927 354 5.649717514124294 0.0 2 0
31111409 Ricinus communis 3988 rna-XM_002539780.2 gene-LOC8282770 NW_003013402.1 - 217 755 271 7.380073800738007 0.0 2 0
31111411 Ricinus communis 3988 rna-XM_002539770.2 gene-LOC8283787 NW_003013334.1 - 9 918 809 2.472187886279357 0.0 2 0
31111412 Ricinus communis 3988 rna-XM_015728904.2 gene-LOC107262678 NW_003012950.1 - 6 628 507 1.9723865877712032 0.0 1 0
31111413 Ricinus communis 3988 rna-XM_002539732.2 gene-LOC8283748 NW_003012942.1 - 8 966 720 2.7777777777777777 0.0 2 0
31111415 Ricinus communis 3988 rna-XM_002539715.2 gene-LOC8283731 NW_003012800.1 + 210 967 540 3.703703703703704 0.0 2 0
31111416 Ricinus communis 3988 rna-XM_002539678.2 gene-LOC8282667 NW_003012315.1 - 84 675 474 2.109704641350211 0.0 1 0
31111417 Ricinus communis 3988 rna-XM_025160117.1 gene-LOC8282640 NW_003012051.1 - 520 875 270 3.703703703703704 0.0 1 0
31111420 Ricinus communis 3988 rna-XM_002539455.3 gene-LOC8279744 NW_003010092.1 - 5 1012 708 2.824858757062147 0.0 2 0
31111421 Ricinus communis 3988 rna-XM_015728898.2 gene-LOC8279737 NW_003010037.1 + 369 744 279 3.584229390681004 0.0 1 0
31111423 Ricinus communis 3988 rna-XM_002539417.2 gene-LOC8279705 NW_003009814.1 - 51 982 846 1.182033096926714 0.0 1 0
31111424 Ricinus communis 3988 rna-XM_002539304.3 gene-LOC8261409 NW_003008913.1 + 149 1033 555 1.8018018018018016 0.0 1 0
31111425 Ricinus communis 3988 rna-XM_015728892.1 gene-LOC107262672 NW_003008546.1 + 158 1041 609 1.6420361247947457 0.0 1 0
31111427 Ricinus communis 3988 rna-XM_025160111.1 gene-LOC112537642 NW_003008054.1 - 436 1059 378 5.291005291005291 0.0 2 0
31111428 Ricinus communis 3988 rna-XM_002539185.2 gene-LOC8287783 NW_003007995.1 - 34 973 789 1.2674271229404308 0.0 1 0
31111429 Ricinus communis 3988 rna-XM_025160110.1 gene-LOC112537630 NW_003007869.1 + 224 927 384 2.6041666666666665 0.0 1 0
31111430 Ricinus communis 3988 rna-XM_002539090.3 gene-LOC8268524 NW_003007614.1 + 5 929 570 3.5087719298245617 0.0 2 0
31111431 Ricinus communis 3988 rna-XM_015728884.1 gene-LOC8268511 NW_003007533.1 - 93 611 439 2.277904328018223 0.0 1 0
31111432 Ricinus communis 3988 rna-XM_002539014.2 gene-LOC8286217 NW_003007173.1 + 5 513 345 2.898550724637681 0.0 1 0
31111433 Ricinus communis 3988 rna-XM_002538962.3 gene-LOC8286165 NW_003006858.1 + 105 1022 708 2.824858757062147 0.0 2 0
31111434 Ricinus communis 3988 rna-XM_015728878.1 gene-LOC8286142 NW_003006789.1 + 66 728 597 1.6750418760469012 0.0 1 0
31111435 Ricinus communis 3988 rna-XM_002538934.3 gene-LOC8285976 NW_003006767.1 + 249 707 312 3.205128205128205 0.0 1 0
31111436 Ricinus communis 3988 rna-XM_025160106.1 gene-LOC112537574 NW_003006589.1 - 172 1112 339 5.899705014749262 0.0 2 0
31111437 Ricinus communis 3988 rna-XM_002538897.2 gene-LOC8285939 NW_003006563.1 + 86 868 573 3.4904013961605584 0.0 2 0
31111438 Ricinus communis 3988 rna-XM_002538871.3 gene-LOC8285913 NW_003006450.1 + 4 904 393 5.089058524173028 0.0 2 0
31111440 Ricinus communis 3988 rna-XM_015728874.2 gene-LOC107262662 NW_003006362.1 + 48 463 303 3.3003300330033003 0.0 1 0
31111441 Ricinus communis 3988 rna-XM_002538714.3 gene-LOC8273296 NW_003005877.1 + 89 1142 798 2.506265664160401 0.0 2 0
31111442 Ricinus communis 3988 rna-XM_002538701.2 gene-LOC8279388 NW_003005830.1 - 73 1001 339 2.949852507374631 0.0 1 0
31111444 Ricinus communis 3988 rna-XM_002538639.3 gene-LOC8279326 NW_003005507.1 - 19 801 513 3.898635477582846 0.0 2 0
31111446 Ricinus communis 3988 rna-XM_002538610.3 gene-LOC8268995 NW_003005396.1 - 120 1045 462 6.493506493506494 0.0 3 0
31111447 Ricinus communis 3988 rna-XM_002538591.2 gene-LOC8268976 NW_003005274.1 + 452 1166 381 7.874015748031496 0.0 3 0
31111448 Ricinus communis 3988 rna-XM_002538532.2 gene-LOC8269937 NW_003005103.1 + 6 947 861 1.1614401858304295 0.0 1 0
31111449 Ricinus communis 3988 rna-XM_025160103.1 gene-LOC8269908 NW_003004990.1 - 12 789 275 7.272727272727272 0.0 2 0
31111450 Ricinus communis 3988 rna-XM_015728854.1 gene-LOC8289906 NW_003004858.1 + 96 1154 669 1.4947683109118086 0.0 1 0
31111451 Ricinus communis 3988 rna-XM_002538449.2 gene-LOC8289895 NW_003004816.1 + 542 1045 504 0.0 0.0 1 0
31111452 Ricinus communis 3988 rna-XM_015728852.1 gene-LOC107262651 NW_003004704.1 - 5 1089 969 1.031991744066047 0.0 1 0
31111453 Ricinus communis 3988 rna-XM_015728846.1 gene-LOC107262646 NW_003004316.1 - 393 1124 414 2.415458937198068 0.0 1 0
31111454 Ricinus communis 3988 rna-XM_015728842.1 gene-LOC107262644 NW_003004143.1 + 61 797 674 1.483679525222552 0.0 1 0
31111455 Ricinus communis 3988 rna-XM_002538272.2 gene-LOC8276261 NW_003004086.1 - 117 1222 1026 0.9746588693957114 0.0 1 0
31111456 Ricinus communis 3988 rna-XM_025160098.1 gene-LOC8276252 NW_003004067.1 + 259 1230 832 1.201923076923077 0.0 1 0
31111457 Ricinus communis 3988 rna-XM_015728839.1 gene-LOC107262641 NW_003003851.1 - 259 1171 702 1.4245014245014245 0.0 1 0
31111459 Ricinus communis 3988 rna-XM_002538109.2 gene-LOC8272689 NW_003003465.1 + 59 1194 919 1.088139281828074 0.0 1 0
31111462 Ricinus communis 3988 rna-XM_002538066.3 gene-LOC8279458 NW_003003297.1 + 272 1241 915 2.185792349726776 0.0 2 0
31111463 Ricinus communis 3988 rna-XM_015728834.1 gene-LOC107262636 NW_003002929.1 - 34 1227 746 1.3404825737265416 0.0 1 0
31111464 Ricinus communis 3988 rna-XM_025160093.1 gene-LOC112537447 NW_003002620.1 + 442 1222 335 5.970149253731344 0.0 2 0
31111466 Ricinus communis 3988 rna-XM_015728830.1 gene-LOC8263988 NW_003002565.1 - 6 1155 579 1.7271157167530224 0.0 1 0
31111467 Ricinus communis 3988 rna-NM_001323710.1 gene-LOC8263958 NW_003002494.1 - 692 1332 529 1.890359168241966 0.0 1 0
31111468 Ricinus communis 3988 rna-XM_002537774.2 gene-LOC8263925 NW_003002396.1 - 281 739 279 3.584229390681004 0.0 1 0
31111469 Ricinus communis 3988 rna-XM_002537747.2 gene-LOC8263818 NW_003002330.1 - 74 1190 633 6.3191153238546605 0.0 4 0
31111470 Ricinus communis 3988 rna-XM_015728823.1 gene-LOC107262629 NW_003002233.1 - 520 1207 573 1.7452006980802792 0.0 1 0
31111472 Ricinus communis 3988 rna-XM_002537705.2 gene-LOC8263774 NW_003002195.1 - 6 567 348 2.8735632183908044 0.0 1 0
31111473 Ricinus communis 3988 rna-XM_025160088.1 gene-LOC8273981 NW_003002163.1 - 329 1278 342 8.771929824561402 0.0 3 0
31111474 Ricinus communis 3988 rna-XM_015728819.1 gene-LOC107262624 NW_003002011.1 + 87 1351 857 1.1668611435239205 0.0 1 0
31111475 Ricinus communis 3988 rna-XM_002537631.2 gene-LOC8273924 NW_003002006.1 - 61 1179 920 1.0869565217391304 0.0 1 0
31111476 Ricinus communis 3988 rna-XM_002537530.3 gene-LOC8281138 NW_003001727.1 + 778 1261 276 7.246376811594203 0.0 3 0
31111477 Ricinus communis 3988 rna-XM_002537460.3 gene-LOC8272024 NW_003001570.1 - 96 1290 477 2.0964360587002098 0.0 1 0
31111478 Ricinus communis 3988 rna-XM_025160084.1 gene-LOC112537423 NW_003001487.1 - 96 800 555 1.8018018018018016 0.0 1 0
31111480 Ricinus communis 3988 rna-XM_015728812.1 gene-LOC107262620 NW_003001392.1 + 319 1236 630 1.5873015873015872 0.0 1 0
31111481 Ricinus communis 3988 rna-XM_002537282.2 gene-LOC8269451 NW_003001121.1 + 123 675 299 3.3444816053511706 0.0 1 0
31111482 Ricinus communis 3988 rna-XM_015728807.1 gene-LOC107262618 NW_003001113.1 - 199 1296 1014 0.9861932938856016 0.0 1 0
31111486 Ricinus communis 3988 rna-XM_002537103.3 gene-LOC8274015 NW_003000710.1 - 50 1320 699 8.583690987124463 0.0 6 0
31111487 Ricinus communis 3988 rna-XM_015728797.1 gene-LOC8274011 NW_003000691.1 - 68 962 670 2.985074626865672 0.0 2 0
31111488 Ricinus communis 3988 rna-XM_002537072.2 gene-LOC8260544 NW_003000627.1 - 18 1440 358 2.793296089385475 0.0 1 0
31111489 Ricinus communis 3988 rna-XM_002537025.3 gene-LOC8260497 NW_003000517.1 + 20 880 570 5.263157894736842 0.0 3 0
31111490 Ricinus communis 3988 rna-XM_015728792.2 gene-LOC8260485 NW_003000484.1 - 27 1312 504 11.904761904761903 0.0 6 0
31111491 Ricinus communis 3988 rna-XM_002536982.2 gene-LOC8270169 NW_003000384.1 + 15 1045 465 4.301075268817204 0.0 2 0
31111492 Ricinus communis 3988 rna-XM_002536977.3 gene-LOC8270164 NW_003000373.1 - 11 586 486 2.05761316872428 0.0 1 0
31111494 Ricinus communis 3988 rna-XM_002536955.3 gene-LOC8270142 NW_003000316.1 - 6 1197 597 10.050251256281408 0.0 7 0
31111495 Ricinus communis 3988 rna-XM_025160079.1 gene-LOC8270136 NW_003000307.1 - 30 1027 498 2.008032128514056 0.0 1 0
31111496 Ricinus communis 3988 rna-XM_002536932.3 gene-LOC8270119 NW_003000268.1 + 375 1466 555 1.8018018018018016 0.0 1 0
31111497 Ricinus communis 3988 rna-XM_002536894.2 gene-LOC8259651 NW_003000194.1 + 400 1510 1007 0.9930486593843098 0.0 1 0
31111498 Ricinus communis 3988 rna-XM_015728781.1 gene-LOC8276788 NW_003000026.1 + 4 1534 513 9.746588693957117 0.0 5 0
31111499 Ricinus communis 3988 rna-XM_002536808.2 gene-LOC8276768 NW_002999989.1 - 7 1298 474 2.109704641350211 0.0 1 0
31111500 Ricinus communis 3988 rna-XM_015728778.1 gene-LOC107262602 NW_002999902.1 + 168 873 606 1.6501650165016502 0.0 1 0
31111501 Ricinus communis 3988 rna-XM_015728776.2 gene-LOC8280045 NW_002999842.1 - 275 920 270 11.11111111111111 0.0 4 0
31111502 Ricinus communis 3988 rna-XM_002536741.3 gene-LOC8280044 NW_002999833.1 - 36 640 232 4.310344827586206 0.0 1 0
31111505 Ricinus communis 3988 rna-XM_002536616.2 gene-LOC8272829 NW_002999559.1 + 83 1095 951 1.0515247108307044 0.0 1 0
31111506 Ricinus communis 3988 rna-XM_002536602.2 gene-LOC8279310 NW_002999540.1 - 5 697 507 1.9723865877712032 0.0 1 0
31111508 Ricinus communis 3988 rna-XM_015728764.1 gene-LOC107262592 NW_002999386.1 - 773 1473 537 1.86219739292365 0.0 1 0
31111509 Ricinus communis 3988 rna-XM_002536440.3 gene-LOC8287364 NW_002999148.1 - 178 1428 552 5.434782608695652 0.0 3 0
31111510 Ricinus communis 3988 rna-XM_002536427.3 gene-LOC8287351 NW_002999124.1 - 30 851 348 2.8735632183908044 0.0 1 0
31111511 Ricinus communis 3988 rna-XM_002536408.3 gene-LOC8287332 NW_002999078.1 + 291 1660 938 1.0660980810234542 0.0 1 0
31111512 Ricinus communis 3988 rna-XM_025160070.1 gene-LOC112537315 NW_002998803.1 - 33 768 664 7.530120481927711 0.0 5 0
31111516 Ricinus communis 3988 rna-XM_002536216.2 gene-LOC8266082 NW_002998641.1 + 489 1711 1153 0.8673026886383347 0.0 1 0
31111517 Ricinus communis 3988 rna-XM_002536198.3 gene-LOC8261273 NW_002998612.1 - 910 1485 360 2.7777777777777777 0.0 1 0
31111518 Ricinus communis 3988 rna-XM_002536185.3 gene-LOC8261260 NW_002998576.1 + 88 741 390 2.5641025641025643 0.0 1 0
31111519 Ricinus communis 3988 rna-XM_002536166.3 gene-LOC8261241 NW_002998507.1 + 238 1513 459 4.357298474945535 0.0 2 0
31111520 Ricinus communis 3988 rna-XM_015728739.2 gene-LOC8261211 NW_002998416.1 + 143 1643 507 7.889546351084813 0.0 4 0
31111521 Ricinus communis 3988 rna-XM_015728736.1 gene-LOC8283530 NW_002998352.1 + 20 1610 687 2.911208151382824 0.0 2 0
31111522 Ricinus communis 3988 rna-XM_002536078.3 gene-LOC8283500 NW_002998282.1 - 712 1763 837 1.194743130227001 0.0 1 0
31111524 Ricinus communis 3988 rna-XM_002536063.2 gene-LOC8283484 NW_002998235.1 - 41 1688 1415 0.7067137809187278 0.0 1 0
31111525 Ricinus communis 3988 rna-XM_015728735.1 gene-LOC107262575 NW_002998231.1 - 216 1726 1179 2.544529262086514 0.0 3 0
31111526 Ricinus communis 3988 rna-XM_002536052.2 gene-LOC8264453 NW_002998191.1 + 349 1674 942 2.123142250530785 0.0 2 0
31111527 Ricinus communis 3988 rna-XM_015728733.1 gene-LOC8264441 NW_002998140.1 + 316 1860 1440 0.6944444444444444 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]);