transcripts

Data license: ODbL · Data source: Larue & Roy, 2023

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

35,702,876 rows

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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
1 Abrus precatorius 3816 rna-XM_027475060.1 gene-LOC113846407 NW_020874290.1 + 4533741 4538479 3381 0.8873114463176576 0.0 4 0
2 Abrus precatorius 3816 rna-XM_027475355.1 gene-LOC113846730 NW_020874290.1 + 62961 68325 2898 1.0351966873706004 0.0 3 0
3 Abrus precatorius 3816 rna-XM_027475485.1 gene-LOC113846797 NW_020874290.1 + 167551 172916 2898 1.0351966873706004 0.0 3 0
4 Abrus precatorius 3816 rna-XM_027475613.1 gene-LOC113846864 NW_020874290.1 - 122536 127901 2898 1.0351966873706004 0.0 3 0
5 Abrus precatorius 3816 rna-XM_027483297.1 gene-LOC113852897 NW_020874290.1 + 2316209 2321575 2898 1.0351966873706004 0.0 3 0
6 Abrus precatorius 3816 rna-XM_027483679.1 gene-LOC113853178 NW_020874290.1 + 715572 720936 2898 1.0351966873706004 0.0 3 0
7 Abrus precatorius 3816 rna-XM_027483689.1 gene-LOC113853188 NW_020874290.1 - 767587 772952 2898 1.0351966873706004 0.0 3 0
8 Abrus precatorius 3816 rna-XM_027487127.1 gene-LOC113855453 NW_020874290.1 + 389044 394409 2898 1.0351966873706004 0.0 3 0
9 Abrus precatorius 3816 rna-XM_027486317.1 gene-LOC113854934 NW_020874290.1 - 435590 439743 2727 1.1001100110011 0.0 3 0
10 Abrus precatorius 3816 rna-XM_027486559.1 gene-LOC113855067 NW_020874290.1 - 553437 557590 2727 1.1001100110011 0.0 3 0
11 Abrus precatorius 3816 rna-XM_027486674.1 gene-LOC113855136 NW_020874290.1 - 254243 258396 2727 1.1001100110011 0.0 3 0
12 Abrus precatorius 3816 rna-XM_027513350.1 gene-LOC113874965 NW_020874290.1 + 2017696 2021849 2727 1.1001100110011 0.0 3 0
13 Abrus precatorius 3816 rna-XM_027482807.1 gene-LOC113852507 NW_020874290.1 - 4316110 4321660 2313 3.026372676178124 0.0 7 0
14 Abrus precatorius 3816 rna-XM_027482198.1 gene-LOC113851671 NW_020874290.1 + 2298301 2303593 2247 1.7801513128615931 0.0 4 0
15 Abrus precatorius 3816 rna-XM_027500329.1 gene-LOC113865607 NW_020874290.1 + 4540070 4544063 2202 2.270663033605813 0.0 5 0
16 Abrus precatorius 3816 rna-XM_027478500.1 gene-LOC113848706 NW_020874290.1 + 2724282 2743344 2184 5.952380952380952 0.0 13 0
17 Abrus precatorius 3816 rna-XM_027482550.1 gene-LOC113852315 NW_020874290.1 + 4639984 4642989 1869 2.675227394328518 0.0 5 0
18 Abrus precatorius 3816 rna-XM_027512680.1 gene-LOC113874372 NW_020874290.1 + 4127406 4136727 1623 6.161429451632778 0.0 11 0
19 Abrus precatorius 3816 rna-XM_027481780.1 gene-LOC113850980 NW_020874290.1 + 2745098 2750935 1467 4.08997955010225 0.0 6 0
20 Abrus precatorius 3816 rna-XM_027482245.1 gene-LOC113851977 NW_020874290.1 + 2699384 2700850 1311 0.7627765064836003 0.0 1 0
21 Abrus precatorius 3816 rna-XM_027483350.1 gene-LOC113852944 NW_020874290.1 - 2336476 2339692 1308 1.529051987767584 0.0 2 0
22 Abrus precatorius 3816 rna-XM_027483365.1 gene-LOC113852946 NW_020874290.1 - 2325464 2328681 1308 1.529051987767584 0.0 2 0
23 Abrus precatorius 3816 rna-XM_027476602.1 gene-LOC113847446 NW_020874290.1 - 68548 70042 1296 1.5432098765432098 0.0 3 0
24 Abrus precatorius 3816 rna-XM_027476728.1 gene-LOC113847521 NW_020874290.1 + 21430 22924 1296 1.5432098765432098 0.0 2 0
25 Abrus precatorius 3816 rna-XM_027476963.1 gene-LOC113847686 NW_020874290.1 - 173138 174632 1296 1.5432098765432098 0.0 2 0
26 Abrus precatorius 3816 rna-XM_027483374.1 gene-LOC113852952 NW_020874290.1 - 2343704 2345198 1296 1.5432098765432098 0.0 2 0
27 Abrus precatorius 3816 rna-XM_027490109.1 gene-LOC113857838 NW_020874290.1 - 199332 200826 1296 1.5432098765432098 0.0 2 0
28 Abrus precatorius 3816 rna-XM_027505535.1 gene-LOC113869255 NW_020874290.1 - 4628658 4632727 1251 12.78976818545164 0.0 17 0
29 Abrus precatorius 3816 rna-XM_027482257.1 gene-LOC113851994 NW_020874290.1 - 2827608 2828964 1245 0.8032128514056225 0.0 1 0
30 Abrus precatorius 3816 rna-XM_027483011.1 gene-LOC113852671 NW_020874290.1 + 1878411 1880732 1182 3.3840947546531304 0.0 4 0
31 Abrus precatorius 3816 rna-XM_027482819.1 gene-LOC113852515 NW_020874290.1 - 2862574 2864092 1170 2.5641025641025643 0.0 3 0
32 Abrus precatorius 3816 rna-XM_027482831.1 gene-LOC113852525 NW_020874290.1 - 2946117 2947635 1170 2.5641025641025643 0.0 3 0
33 Abrus precatorius 3816 rna-XM_027482228.1 gene-LOC113851957 NW_020874290.1 - 2660608 2666227 1125 1.777777777777778 0.0 2 0
34 Abrus precatorius 3816 rna-XM_027474323.1 gene-LOC113846245 NW_020874290.1 - 619925 623801 1059 6.610009442870632 0.0 7 0
35 Abrus precatorius 3816 rna-XM_027492279.1 gene-LOC113859243 NW_020874290.1 + 4603588 4609775 1026 0.9746588693957114 0.0 1 0
36 Abrus precatorius 3816 rna-XM_027482397.1 gene-LOC113852148 NW_020874290.1 + 3953355 3955386 996 3.0120481927710845 0.0 3 0
37 Abrus precatorius 3816 rna-XM_027477198.1 gene-LOC113847860 NW_020874290.1 - 71566 74184 933 2.143622722400857 0.0 2 0
38 Abrus precatorius 3816 rna-XM_027477316.1 gene-LOC113847944 NW_020874290.1 + 116674 119291 927 2.157497303128371 0.0 2 0
39 Abrus precatorius 3816 rna-XM_027477434.1 gene-LOC113848035 NW_020874290.1 - 176158 178776 927 2.157497303128371 0.0 2 0
40 Abrus precatorius 3816 rna-XM_027477552.1 gene-LOC113848124 NW_020874290.1 + 17283 19902 927 2.157497303128371 0.0 2 0
41 Abrus precatorius 3816 rna-XM_027483460.1 gene-LOC113853026 NW_020874290.1 - 2346726 2349344 927 2.157497303128371 0.0 2 0
42 Abrus precatorius 3816 rna-XM_027483717.1 gene-LOC113853217 NW_020874290.1 + 761724 764343 927 2.157497303128371 0.0 2 0
43 Abrus precatorius 3816 rna-XM_027483729.1 gene-LOC113853225 NW_020874290.1 - 724181 726800 927 2.157497303128371 0.0 2 0
44 Abrus precatorius 3816 rna-XM_027492318.1 gene-LOC113859558 NW_020874290.1 - 397654 400274 927 2.157497303128371 0.0 2 0
45 Abrus precatorius 3816 rna-XM_027492380.1 gene-LOC113859638 NW_020874290.1 - 202352 204970 927 2.157497303128371 0.0 2 0
46 Abrus precatorius 3816 rna-XM_027492459.1 gene-LOC113859739 NW_020874290.1 + 369365 371984 927 2.157497303128371 0.0 2 0
47 Abrus precatorius 3816 rna-XM_027483108.1 gene-LOC113852744 NW_020874290.1 - 1778233 1779698 870 4.597701149425287 0.0 4 0
48 Abrus precatorius 3816 rna-XM_027493792.1 gene-LOC113861140 NW_020874290.1 - 349388 350853 870 4.597701149425287 0.0 4 0
49 Abrus precatorius 3816 rna-XM_027493910.1 gene-LOC113861206 NW_020874290.1 - 270807 272272 870 4.597701149425287 0.0 4 0
50 Abrus precatorius 3816 rna-XM_027494027.1 gene-LOC113861276 NW_020874290.1 + 418785 420250 870 4.597701149425287 0.0 4 0
51 Abrus precatorius 3816 rna-XM_027494147.1 gene-LOC113861345 NW_020874290.1 - 493836 495301 870 4.597701149425287 0.0 4 0
52 Abrus precatorius 3816 rna-XM_027494262.1 gene-LOC113861422 NW_020874290.1 + 223479 224944 870 4.597701149425287 0.0 4 0
53 Abrus precatorius 3816 rna-XM_027494382.1 gene-LOC113861496 NW_020874290.1 + 316021 317486 870 4.597701149425287 0.0 4 0
54 Abrus precatorius 3816 rna-XM_027497799.1 gene-LOC113863977 NW_020874290.1 - 2045962 2047427 870 4.597701149425287 0.0 4 0
55 Abrus precatorius 3816 rna-XM_027510382.1 gene-LOC113872635 NW_020874290.1 - 1567305 1568770 870 4.597701149425287 0.0 4 0
56 Abrus precatorius 3816 rna-XM_027510510.1 gene-LOC113872708 NW_020874290.1 + 1561146 1562611 870 4.597701149425287 0.0 4 0
57 Abrus precatorius 3816 rna-XM_027496451.1 gene-LOC113863034 NW_020874290.1 + 477471 478497 864 2.314814814814815 0.0 2 0
58 Abrus precatorius 3816 rna-XM_027496577.1 gene-LOC113863109 NW_020874290.1 - 332823 333849 864 2.314814814814815 0.0 2 0
59 Abrus precatorius 3816 rna-XM_027482380.1 gene-LOC113852129 NW_020874290.1 - 3886271 3890719 849 2.3557126030624262 0.0 2 0
60 Abrus precatorius 3816 rna-XM_027473561.1 gene-LOC113845863 NW_020874290.1 + 2022293 2023250 843 1.1862396204033216 0.0 1 0
61 Abrus precatorius 3816 rna-XM_027483472.1 gene-LOC113853030 NW_020874290.1 + 2232678 2233635 843 1.1862396204033216 0.0 1 0
62 Abrus precatorius 3816 rna-XM_027483483.1 gene-LOC113853038 NW_020874290.1 + 2253491 2254448 843 1.1862396204033216 0.0 1 0
63 Abrus precatorius 3816 rna-XM_027492616.1 gene-LOC113859934 NW_020874290.1 + 478941 479898 843 1.1862396204033216 0.0 1 0
64 Abrus precatorius 3816 rna-XM_027492699.1 gene-LOC113860040 NW_020874290.1 - 434189 435146 843 1.1862396204033216 0.0 1 0
65 Abrus precatorius 3816 rna-XM_027492813.1 gene-LOC113860123 NW_020874290.1 - 252843 253800 843 1.1862396204033216 0.0 1 0
66 Abrus precatorius 3816 rna-XM_027492918.1 gene-LOC113860200 NW_020874290.1 - 455380 456337 843 1.1862396204033216 0.0 1 0
67 Abrus precatorius 3816 rna-XM_027492984.1 gene-LOC113860278 NW_020874290.1 - 331422 332379 843 1.1862396204033216 0.0 1 0
68 Abrus precatorius 3816 rna-XM_027492985.1 gene-LOC113860444 NW_020874290.1 - 552036 552993 843 1.1862396204033216 0.0 1 0
69 Abrus precatorius 3816 rna-XM_027507119.1 gene-LOC113870336 NW_020874290.1 - 2149207 2150164 843 1.1862396204033216 0.0 1 0
70 Abrus precatorius 3816 rna-XM_027508380.1 gene-LOC113871135 NW_020874290.1 - 2164902 2165859 843 1.1862396204033216 0.0 1 0
71 Abrus precatorius 3816 rna-XM_027482407.1 gene-LOC113852159 NW_020874290.1 + 3969192 3980573 837 2.389486260454002 0.0 2 0
72 Abrus precatorius 3816 rna-XM_027482710.1 gene-LOC113852436 NW_020874290.1 + 935700 936980 819 1.221001221001221 0.0 1 0
73 Abrus precatorius 3816 rna-XM_027493146.1 gene-LOC113860652 NW_020874290.1 + 652468 653748 819 1.221001221001221 0.0 1 0
74 Abrus precatorius 3816 rna-XM_027493252.1 gene-LOC113860720 NW_020874290.1 + 523969 525249 819 1.221001221001221 0.0 1 0
75 Abrus precatorius 3816 rna-XM_027509641.1 gene-LOC113872221 NW_020874290.1 - 1504516 1505795 819 1.221001221001221 0.0 1 0
76 Abrus precatorius 3816 rna-XM_027509884.1 gene-LOC113872351 NW_020874290.1 - 1472620 1473900 819 1.221001221001221 0.0 1 0
77 Abrus precatorius 3816 rna-XM_027510006.1 gene-LOC113872423 NW_020874290.1 - 1617790 1619070 819 1.221001221001221 0.0 1 0
78 Abrus precatorius 3816 rna-XM_027512970.1 gene-LOC113874722 NW_020874290.1 - 2769040 2775142 813 4.920049200492005 0.0 4 0
79 Abrus precatorius 3816 rna-XM_027482234.1 gene-LOC113851963 NW_020874290.1 - 2672483 2674519 783 3.8314176245210727 0.0 3 0
80 Abrus precatorius 3816 rna-XM_027482356.1 gene-LOC113852101 NW_020874290.1 + 3604972 3606105 771 3.891050583657588 0.0 3 0
81 Abrus precatorius 3816 rna-XM_027481403.1 gene-LOC113850851 NW_020874290.1 + 1755547 1756897 756 5.291005291005291 0.0 4 0
82 Abrus precatorius 3816 rna-XM_027482505.1 gene-LOC113852266 NW_020874290.1 - 4375680 4376747 669 2.989536621823617 0.0 2 0
83 Abrus precatorius 3816 rna-XM_027506809.1 gene-LOC113870186 NW_020874290.1 - 4545866 4547064 657 1.5220700152207 0.0 1 0
84 Abrus precatorius 3816 rna-XM_027504929.1 gene-LOC113868903 NW_020874290.1 + 1229774 1230811 573 1.7452006980802792 0.0 1 0
85 Abrus precatorius 3816 rna-XM_027482322.1 gene-LOC113852062 NW_020874290.1 + 2936569 2937456 537 5.58659217877095 0.0 3 0
86 Abrus precatorius 3816 rna-XM_027490153.1 gene-LOC113857653 NW_020874290.1 - 4572447 4574813 435 2.2988505747126435 0.0 1 0
87 Abrus precatorius 3816 rna-XM_027482487.1 gene-LOC113852246 NW_020874290.1 + 4282827 4284484 327 3.058103975535168 0.0 1 0
88 Abrus precatorius 3816 rna-XM_027482273.1 gene-LOC113852012 NW_020874290.1 - 2892498 2892884 324 3.08641975308642 0.0 1 0
188 Abrus precatorius 3816 rna-XM_027486907.1 gene-LOC113855315 NW_020874291.1 - 6171238 6179832 5856 1.1953551912568303 0.0 7 0
189 Abrus precatorius 3816 rna-XM_027487354.1 gene-LOC113855722 NW_020874291.1 - 998206 1024777 5265 5.5080721747388415 0.0 30 0
190 Abrus precatorius 3816 rna-XM_027487607.1 gene-LOC113855976 NW_020874291.1 + 1249974 1267673 5133 4.675628287551139 0.0 24 0
191 Abrus precatorius 3816 rna-XM_027490919.1 gene-LOC113858327 NW_020874291.1 + 476410 484259 4848 1.8564356435643563 0.0 9 0
192 Abrus precatorius 3816 rna-XM_027489363.1 gene-LOC113857448 NW_020874291.1 - 558262 575972 4548 0.8795074758135445 0.0 4 0
193 Abrus precatorius 3816 rna-XM_027489376.1 gene-LOC113857454 NW_020874291.1 - 591114 597269 4059 0.7390983000739099 0.0 3 0
194 Abrus precatorius 3816 rna-XM_027486048.1 gene-LOC113854808 NW_020874291.1 - 3715649 3739623 3705 5.398110661268555 0.0 20 0
195 Abrus precatorius 3816 rna-XM_027486895.1 gene-LOC113855305 NW_020874291.1 - 6151300 6159087 3705 1.6194331983805668 0.0 7 0
196 Abrus precatorius 3816 rna-XM_027487662.1 gene-LOC113856037 NW_020874291.1 + 6205761 6253364 3573 7.276798208788134 0.0 27 0
197 Abrus precatorius 3816 rna-XM_027487917.1 gene-LOC113856194 NW_020874291.1 + 1807253 1816005 3546 0.8460236886632826 0.0 3 0
198 Abrus precatorius 3816 rna-XM_027489389.1 gene-LOC113857460 NW_020874291.1 - 609568 613699 3513 1.138627953316254 0.0 4 0
199 Abrus precatorius 3816 rna-XM_027489934.1 gene-LOC113857749 NW_020874291.1 + 1666390 1671058 3423 1.460706982179375 0.0 5 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]);