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

20,628 rows where taxonomy_id = 72004

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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
4570470 Bos mutus 72004 rna-XM_014479648.1 gene-LOC102264424 NW_005392812.1 - 10994 35526 1250 5.6 0.0 7 0
4570471 Bos mutus 72004 rna-XM_005886627.2 gene-MSI2 NW_005392813.1 - 76250 332305 675 10.37037037037037 0.0 9 0
4570473 Bos mutus 72004 rna-XM_005886628.1 gene-WRNIP1 NW_005392815.1 + 40606 51043 1440 4.166666666666667 0.0 6 0
4570474 Bos mutus 72004 rna-XM_005886629.2 gene-SERPINB1 NW_005392815.1 - 73396 80510 1233 4.866180048661801 0.0 6 0
4570475 Bos mutus 72004 rna-XM_005886632.2 gene-LOC102267172 NW_005392815.1 - 130998 148493 1137 4.397537379067723 0.0 6 0
4570476 Bos mutus 72004 rna-XM_005886630.2 gene-LOC102266689 NW_005392815.1 - 110322 116776 1125 5.333333333333333 0.0 8 0
4570477 Bos mutus 72004 rna-XM_014478443.1 gene-LOC102268001 NW_005392816.1 - 318 144933 3649 7.399287476020828 0.0 27 0
4570480 Bos mutus 72004 rna-XM_005886639.1 gene-LOC102269946 NW_005392819.1 + 3321 10888 1679 5.955926146515783 0.0 10 0
4570482 Bos mutus 72004 rna-XM_005886640.2 gene-NUP98 NW_005392820.1 - 49435 122456 5400 5.7407407407407405 0.0 32 0
4570483 Bos mutus 72004 rna-XM_005886649.2 gene-RRM1 NW_005392820.1 + 391159 430993 2376 7.996632996632995 0.0 19 0
4570484 Bos mutus 72004 rna-XM_005886646.2 gene-STIM1 NW_005392820.1 + 183975 387461 2370 5.063291139240507 0.0 12 0
4570485 Bos mutus 72004 rna-XM_005886651.1 gene-LOC102273748 NW_005392820.1 - 9519 17646 1023 2.932551319648094 0.0 3 0
4570486 Bos mutus 72004 rna-XM_005886644.2 gene-PGAP2 NW_005392820.1 + 146664 156746 954 5.241090146750524 0.0 6 0
4570487 Bos mutus 72004 rna-XM_005886654.2 gene-CHRNA10 NW_005392820.1 - 35642 40715 918 4.357298474945535 0.0 5 0
4570488 Bos mutus 72004 rna-XM_005886652.1 gene-LOC102274037 NW_005392820.1 - 17788 30060 891 3.3670033670033668 0.0 3 0
4570489 Bos mutus 72004 rna-XM_005886653.2 gene-ART1 NW_005392820.1 + 30488 34315 765 5.228758169934641 0.0 4 0
4570491 Bos mutus 72004 rna-XM_005886657.2 gene-GADD45G NW_005392821.1 - 175308 176252 480 6.25 0.0 3 0
4570492 Bos mutus 72004 rna-XM_014476438.1 gene-SCHIP1 NW_005392822.1 - 72054 217867 1194 5.862646566164154 0.0 7 0
4570493 Bos mutus 72004 rna-XM_005886663.1 gene-LOC102277717 NW_005392823.1 - 243805 262463 1446 6.224066390041493 0.0 9 0
4570494 Bos mutus 72004 rna-XM_005886664.2 gene-MOB3B NW_005392823.1 - 41002 137172 621 1.6103059581320451 0.0 2 0
4570495 Bos mutus 72004 rna-XM_005886662.1 gene-IFNK NW_005392823.1 + 205285 205932 648 0.0 0.0 1 0
4570497 Bos mutus 72004 rna-XM_005886671.2 gene-NRCAM NW_005392826.1 + 605143 692631 3909 7.418777180864671 0.0 29 0
4570498 Bos mutus 72004 rna-XM_005886668.2 gene-PNPLA8 NW_005392826.1 + 315178 355113 2355 3.397027600849257 0.0 9 0
4570499 Bos mutus 72004 rna-XM_005911688.1 gene-LAMB4 NW_005392826.1 + 738110 781859 2094 7.163323782234958 0.0 15 0
4570500 Bos mutus 72004 rna-XM_014476836.1 gene-NME8 NW_005392826.1 - 225634 265186 1767 7.923033389926429 0.0 15 0
4570501 Bos mutus 72004 rna-XM_005886666.1 gene-SFRP4 NW_005392826.1 + 206198 216028 1041 4.803073967339097 0.0 5 0
4570502 Bos mutus 72004 rna-XM_014476817.1 gene-EPDR1 NW_005392826.1 - 162297 197308 702 4.273504273504274 0.0 3 0
4570503 Bos mutus 72004 rna-XM_005886677.2 gene-GPR141 NW_005392826.1 - 280337 281218 882 0.0 0.0 1 0
4570504 Bos mutus 72004 rna-XM_014476895.1 gene-LOC102281846 NW_005392827.1 + 47302 105681 1788 5.033557046979865 0.0 9 0
4570505 Bos mutus 72004 rna-XM_005886678.2 gene-ARAP2 NW_005392829.1 - 29741 209530 5127 6.0464209089135945 0.0 31 0
4570506 Bos mutus 72004 rna-XM_005886679.1 gene-DTHD1 NW_005392829.1 + 267262 349155 2403 3.329171868497711 0.0 8 0
4570507 Bos mutus 72004 rna-XM_005886681.2 gene-MTMR9 NW_005392830.1 + 267532 334354 1650 5.454545454545455 0.0 9 0
4570508 Bos mutus 72004 rna-XM_005886684.1 gene-BLK NW_005392830.1 + 490752 508840 1506 7.304116865869854 0.0 12 0
4570509 Bos mutus 72004 rna-XM_005886687.2 gene-FDFT1 NW_005392830.1 + 722147 747745 1254 5.582137161084529 0.0 7 0
4570510 Bos mutus 72004 rna-XM_005886680.2 gene-XKR6 NW_005392830.1 + 148640 169497 1149 0.8703220191470844 0.0 1 0
4570511 Bos mutus 72004 rna-XM_005886682.1 gene-LOC102283236 NW_005392830.1 + 366847 375990 1122 6.238859180035651 0.0 8 0
4570512 Bos mutus 72004 rna-XM_005886688.2 gene-CTSB NW_005392830.1 - 753423 760935 1008 7.936507936507936 0.0 9 0
4570513 Bos mutus 72004 rna-XM_005886686.2 gene-NEIL2 NW_005392830.1 + 703128 711102 990 3.0303030303030303 0.0 4 0
4570514 Bos mutus 72004 rna-XM_005886685.2 gene-GATA4 NW_005392830.1 + 686543 693734 711 5.625879043600563 0.0 5 0
4570515 Bos mutus 72004 rna-XM_005886683.1 gene-FAM167A NW_005392830.1 - 403722 417897 636 1.572327044025157 0.0 3 0
4570516 Bos mutus 72004 rna-XM_014476983.1 gene-DEFB134 NW_005392830.1 - 868177 870664 254 3.937007874015748 0.0 1 0
4570517 Bos mutus 72004 rna-XM_005886690.1 gene-LOC102285566 NW_005392831.1 - 471728 613498 1905 7.349081364829396 0.0 14 0
4570518 Bos mutus 72004 rna-XM_005886691.2 gene-CACHD1 NW_005392832.1 + 25555 259543 3672 7.080610021786492 0.0 26 0
4570519 Bos mutus 72004 rna-XM_005886692.2 gene-JAK1 NW_005392832.1 - 466842 525062 3477 6.614897900488927 0.0 24 0
4570520 Bos mutus 72004 rna-XM_005886693.1 gene-RAVER2 NW_005392832.1 + 357904 463467 1848 5.952380952380952 0.0 11 0
4570522 Bos mutus 72004 rna-XM_014477460.1 gene-LOC102288035 NW_005392833.1 + 3589 68342 2319 7.7619663648124195 0.0 18 0
4570523 Bos mutus 72004 rna-XM_014477531.1 gene-PLCB4 NW_005392834.1 - 603292 719545 2760 9.420289855072465 0.0344827586206896 29 1
4570524 Bos mutus 72004 rna-XM_005886694.1 gene-PAK7 NW_005392834.1 + 427629 539084 2160 3.2407407407407405 0.0 8 0
4570525 Bos mutus 72004 rna-XM_005886695.2 gene-LAMP5 NW_005392834.1 - 553579 564852 843 5.931198102016607 0.0 5 0
4570526 Bos mutus 72004 rna-XM_014477485.1 gene-LOC106700735 NW_005392834.1 - 5767 6814 252 3.968253968253968 0.0 1 0
4570527 Bos mutus 72004 rna-XM_014477756.1 gene-LOC106700771 NW_005392835.1 - 887116 888886 618 3.236245954692557 0.0 2 0
4570530 Bos mutus 72004 rna-XM_005886702.1 gene-LOC102267253 NW_005392836.1 - 561377 824015 4548 6.156552330694811 0.0 28 0
4570531 Bos mutus 72004 rna-XM_005886712.2 gene-MYO5B NW_005392837.1 - 1437209 1635739 5664 7.062146892655367 0.0 40 0
4570532 Bos mutus 72004 rna-XM_005886705.1 gene-DYM NW_005392837.1 - 673492 1048819 2010 7.462686567164179 0.0 15 0
4570533 Bos mutus 72004 rna-XM_005886703.2 gene-CTIF NW_005392837.1 + 238635 487858 1803 5.546311702717693 0.0 10 0
4570534 Bos mutus 72004 rna-XM_005886710.2 gene-LIPG NW_005392837.1 + 1157186 1187678 1503 5.9880239520958085 0.0 9 0
4570535 Bos mutus 72004 rna-XM_014478215.1 gene-ACAA2 NW_005392837.1 - 1389951 1420679 1245 7.228915662650603 0.0 9 0
4570536 Bos mutus 72004 rna-XM_014477931.1 gene-SMAD7 NW_005392837.1 - 548111 575469 975 4.102564102564102 0.0 4 0
4570537 Bos mutus 72004 rna-XM_005886706.2 gene-RPL17 NW_005392837.1 - 1099423 1103045 555 9.00900900900901 0.0 6 0
4570538 Bos mutus 72004 rna-XM_005886708.2 gene-LOC102268745 NW_005392837.1 - 1094231 1095387 231 4.329004329004329 0.0 2 0
4570541 Bos mutus 72004 rna-XM_014478250.1 gene-LOC102271291 NW_005392838.1 - 217804 237953 1416 9.180790960451978 0.0 13 0
4570542 Bos mutus 72004 rna-XM_005886713.1 gene-SH3YL1 NW_005392838.1 + 22 61010 1026 8.771929824561402 0.0 9 0
4570543 Bos mutus 72004 rna-XM_005886714.2 gene-FAM110C NW_005392838.1 + 155578 155937 360 0.0 0.0 1 0
4570544 Bos mutus 72004 rna-XM_005886728.2 gene-CLCN1 NW_005392839.1 + 300841 337359 3060 7.516339869281046 0.0 23 0
4570545 Bos mutus 72004 rna-XM_005886724.2 gene-EPHA1 NW_005392839.1 - 389303 403359 2853 5.608131791097091 0.0 16 0
4570546 Bos mutus 72004 rna-XM_005886726.2 gene-TCAF2 NW_005392839.1 - 587390 600279 2745 2.185792349726776 0.0 7 0
4570547 Bos mutus 72004 rna-XM_005886729.2 gene-ZYX NW_005392839.1 + 378313 388035 2073 5.306319343945972 0.0 11 0
4570548 Bos mutus 72004 rna-XM_005886720.2 gene-CASP2 NW_005392839.1 + 277742 293831 1359 7.358351729212656 0.0 10 0
4570549 Bos mutus 72004 rna-XM_005886723.1 gene-FAM131B NW_005392839.1 - 341781 346605 999 5.005005005005005 0.0 6 0
4570550 Bos mutus 72004 rna-XM_014478590.1 gene-GSTK1 NW_005392839.1 + 251108 255723 732 8.196721311475411 0.0 6 0
4570551 Bos mutus 72004 rna-XM_005886719.2 gene-TMEM139 NW_005392839.1 + 273878 274717 627 1.594896331738437 0.0 2 0
4570552 Bos mutus 72004 rna-XM_014478497.1 gene-LOC102276867 NW_005392839.1 - 489244 490419 537 3.7243947858473 0.0 2 0
4570553 Bos mutus 72004 rna-XM_014478824.1 gene-LOC106700918 NW_005392839.1 + 105949 112371 441 6.802721088435374 0.0 3 0
4570554 Bos mutus 72004 rna-XM_005886715.2 gene-LOC102271568 NW_005392839.1 + 80394 90581 438 6.849315068493151 0.0 3 0
4570556 Bos mutus 72004 rna-XM_005886734.2 gene-TCAF1 NW_005392840.1 - 20272 42904 2766 2.530730296456978 0.0 8 0
4570557 Bos mutus 72004 rna-XM_005886752.2 gene-LOC102283148 NW_005392840.1 - 337414 344590 1023 5.865102639296188 0.0 6 0
4570558 Bos mutus 72004 rna-XM_005886753.2 gene-NT5C1A NW_005392840.1 - 424139 431528 918 4.357298474945535 0.0 5 0
4570559 Bos mutus 72004 rna-XM_005886745.1 gene-HEYL NW_005392840.1 - 383143 388867 903 3.3222591362126246 0.0 3 0
4570560 Bos mutus 72004 rna-XM_005886751.1 gene-LOC102282585 NW_005392840.1 + 293212 294144 888 1.1261261261261262 0.0 1 0
4570561 Bos mutus 72004 rna-XM_005886746.1 gene-HPCAL4 NW_005392840.1 - 456931 459087 576 3.472222222222222 0.0 3 0
4570562 Bos mutus 72004 rna-XM_005886806.2 gene-PKD1 NW_005392841.1 + 990895 1023526 13167 4.253056884635832 0.0 56 0
4570563 Bos mutus 72004 rna-XM_005886793.2 gene-SRRM2 NW_005392841.1 + 335118 349518 8259 1.695120474633733 0.0 14 0
4570564 Bos mutus 72004 rna-XM_005886782.2 gene-TSC2 NW_005392841.1 - 1024726 1056549 5433 7.730535615681944 0.0 42 0
4570565 Bos mutus 72004 rna-XM_005886773.2 gene-ABCA3 NW_005392841.1 + 816457 847669 5127 5.851375073142188 0.0 30 0
4570566 Bos mutus 72004 rna-XM_014479972.1 gene-LOC102273949 NW_005392841.1 - 695716 783425 5034 6.3567739372268575 0.0 32 0
4570567 Bos mutus 72004 rna-XM_014480049.1 gene-CASKIN1 NW_005392841.1 + 921451 937504 2892 6.224066390041493 0.0 20 0
4570568 Bos mutus 72004 rna-XM_005911737.1 gene-LOC102275653 NW_005392841.1 + 1076747 1100704 2807 7.125044531528322 0.0 20 0
4570569 Bos mutus 72004 rna-XM_014479945.1 gene-CCNF NW_005392841.1 - 678315 695648 2508 6.379585326953748 0.0 16 0
4570570 Bos mutus 72004 rna-XM_005886777.2 gene-E4F1 NW_005392841.1 - 882165 891829 2364 6.768189509306261 0.0 16 0
4570571 Bos mutus 72004 rna-XM_005886756.2 gene-ZSCAN10 NW_005392841.1 + 108040 112266 2361 1.6941973739940703 0.0 4 0
4570572 Bos mutus 72004 rna-XM_014479649.1 gene-FLYWCH1 NW_005392841.1 - 271619 281576 2238 5.361930294906166 0.0 12 0
4570573 Bos mutus 72004 rna-XM_014480079.1 gene-TRAF7 NW_005392841.1 - 938635 948291 2157 8.80853036624942 0.0 20 0
4570574 Bos mutus 72004 rna-XM_014479894.1 gene-NTN3 NW_005392841.1 - 647529 669924 2031 5.908419497784343 0.0 12 0
4570575 Bos mutus 72004 rna-XM_005886787.1 gene-LOC102268844 NW_005392841.1 - 45456 69646 1794 7.246376811594203 0.0 13 0
4570576 Bos mutus 72004 rna-XM_014479769.1 gene-PRSS22 NW_005392841.1 - 432687 460542 1746 6.872852233676976 0.0 12 0
4570577 Bos mutus 72004 rna-XM_014480749.1 gene-TBC1D24 NW_005392841.1 - 638512 644083 1680 4.166666666666667 0.0 9 0
4570578 Bos mutus 72004 rna-XM_005886754.1 gene-ZNF205 NW_005392841.1 - 83329 90911 1653 3.0248033877797944 0.0 6 0
4570579 Bos mutus 72004 rna-XM_005886771.1 gene-PDPK1 NW_005392841.1 - 544044 578990 1593 7.532956685499058 0.0833333333333333 12 1
4570580 Bos mutus 72004 rna-XM_005886789.1 gene-MMP25 NW_005392841.1 - 144360 178734 1527 5.893909626719057 0.0 9 0
4570581 Bos mutus 72004 rna-XM_005886758.2 gene-CCDC64B NW_005392841.1 + 180175 186585 1521 5.259697567389876 0.0 9 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]);