Where the Minor Things Are (WtMTA): (Yet Another) Minor Intron Database

The Where the Minor Things Are (WtMTA) intron database contains information about introns in > 1500 species identified by Larue & Roy, 2023 as containing minor introns, with a total of more than 250 million rows. The data includes intron information such as type classification (major or minor), phase, genomic coordinates, etc. for all annotated introns included in our analyses, as well as additional metadata about parent genes, transcripts, and genomes.

Intron classifications were generated using intronIC, and other intron-based metadata (introns per kbps coding sequence, etc.) was obtained using custom Python workflows. All substrate data was sourced from publicly-available genomic resources such as NCBI, Ensembl and JGI.

Exploring the database

Unless you are interested in the entirety of the data (see the section on running the database locally), the best place to start exploring may be via the genomes table. There, you can select a species of interest and drill down to the associated introns and/or transcripts for further filtering.

The results of any query can be downloaded in a number of plaintext formats (e.g., CSV), provided they don’t exceed 1 GB (see Advanced Export below the paginated results; select stream all rows to ensure the full dataset is returned). This should be sufficient to retrieve, for example, the complete intron/transcript set for any individual genome, or a subset of introns/transcripts across a number of different genomes.

Searching within tables

The genomes and transcripts table provide limited search functionality, allowing for queries of complete words only (i.e., no wildcards). For example, to return information about all cnidarian genomes, the genomes table should be searched for cnidaria, but not (for example) cnidar*.

Obtaining a local copy of the DB

The SQLite database file was created using sqlite-utils and Datasette.

You are free to download the entire WtMTA database file via the link at the bottom of this page. After doing so, you can recreate most of the functionality of this website on a local computer/server.

To explore a local version of this database using Datasette, first install Datasette:

python3 -m pip install datasette

Then, run Datasette with the SQLite database file:

datasette -i WtMTA.db

This command will start a local web server (the default URL will be displayed by Datasette automatically), and you can explore the database interactively using your web browser. See Datasette’s documentation for details and additional options.

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

Custom SQL query returning 101 rows (hide)

This data as json, CSV

idtaxonomy_idtranscript_idgene_idchromosomestrandstartendcoding_lengthintrons_per_kbp_cdsproportion_minor_intronsn_intronsn_minor_introns
1 3816 rna-XM_027475060.1 gene-LOC113846407 NW_020874290.1 + 4533741 4538479 3381 0.8873114463176576 0.0 4 0
2 3816 rna-XM_027475355.1 gene-LOC113846730 NW_020874290.1 + 62961 68325 2898 1.0351966873706004 0.0 3 0
3 3816 rna-XM_027475485.1 gene-LOC113846797 NW_020874290.1 + 167551 172916 2898 1.0351966873706004 0.0 3 0
4 3816 rna-XM_027475613.1 gene-LOC113846864 NW_020874290.1 - 122536 127901 2898 1.0351966873706004 0.0 3 0
5 3816 rna-XM_027483297.1 gene-LOC113852897 NW_020874290.1 + 2316209 2321575 2898 1.0351966873706004 0.0 3 0
6 3816 rna-XM_027483679.1 gene-LOC113853178 NW_020874290.1 + 715572 720936 2898 1.0351966873706004 0.0 3 0
7 3816 rna-XM_027483689.1 gene-LOC113853188 NW_020874290.1 - 767587 772952 2898 1.0351966873706004 0.0 3 0
8 3816 rna-XM_027487127.1 gene-LOC113855453 NW_020874290.1 + 389044 394409 2898 1.0351966873706004 0.0 3 0
9 3816 rna-XM_027486317.1 gene-LOC113854934 NW_020874290.1 - 435590 439743 2727 1.1001100110011 0.0 3 0
10 3816 rna-XM_027486559.1 gene-LOC113855067 NW_020874290.1 - 553437 557590 2727 1.1001100110011 0.0 3 0
11 3816 rna-XM_027486674.1 gene-LOC113855136 NW_020874290.1 - 254243 258396 2727 1.1001100110011 0.0 3 0
12 3816 rna-XM_027513350.1 gene-LOC113874965 NW_020874290.1 + 2017696 2021849 2727 1.1001100110011 0.0 3 0
13 3816 rna-XM_027482807.1 gene-LOC113852507 NW_020874290.1 - 4316110 4321660 2313 3.026372676178124 0.0 7 0
14 3816 rna-XM_027482198.1 gene-LOC113851671 NW_020874290.1 + 2298301 2303593 2247 1.7801513128615931 0.0 4 0
15 3816 rna-XM_027500329.1 gene-LOC113865607 NW_020874290.1 + 4540070 4544063 2202 2.270663033605813 0.0 5 0
16 3816 rna-XM_027478500.1 gene-LOC113848706 NW_020874290.1 + 2724282 2743344 2184 5.952380952380952 0.0 13 0
17 3816 rna-XM_027482550.1 gene-LOC113852315 NW_020874290.1 + 4639984 4642989 1869 2.675227394328518 0.0 5 0
18 3816 rna-XM_027512680.1 gene-LOC113874372 NW_020874290.1 + 4127406 4136727 1623 6.161429451632778 0.0 11 0
19 3816 rna-XM_027481780.1 gene-LOC113850980 NW_020874290.1 + 2745098 2750935 1467 4.08997955010225 0.0 6 0
20 3816 rna-XM_027482245.1 gene-LOC113851977 NW_020874290.1 + 2699384 2700850 1311 0.7627765064836003 0.0 1 0
21 3816 rna-XM_027483350.1 gene-LOC113852944 NW_020874290.1 - 2336476 2339692 1308 1.529051987767584 0.0 2 0
22 3816 rna-XM_027483365.1 gene-LOC113852946 NW_020874290.1 - 2325464 2328681 1308 1.529051987767584 0.0 2 0
23 3816 rna-XM_027476602.1 gene-LOC113847446 NW_020874290.1 - 68548 70042 1296 1.5432098765432098 0.0 3 0
24 3816 rna-XM_027476728.1 gene-LOC113847521 NW_020874290.1 + 21430 22924 1296 1.5432098765432098 0.0 2 0
25 3816 rna-XM_027476963.1 gene-LOC113847686 NW_020874290.1 - 173138 174632 1296 1.5432098765432098 0.0 2 0
26 3816 rna-XM_027483374.1 gene-LOC113852952 NW_020874290.1 - 2343704 2345198 1296 1.5432098765432098 0.0 2 0
27 3816 rna-XM_027490109.1 gene-LOC113857838 NW_020874290.1 - 199332 200826 1296 1.5432098765432098 0.0 2 0
28 3816 rna-XM_027505535.1 gene-LOC113869255 NW_020874290.1 - 4628658 4632727 1251 12.78976818545164 0.0 17 0
29 3816 rna-XM_027482257.1 gene-LOC113851994 NW_020874290.1 - 2827608 2828964 1245 0.8032128514056225 0.0 1 0
30 3816 rna-XM_027483011.1 gene-LOC113852671 NW_020874290.1 + 1878411 1880732 1182 3.3840947546531304 0.0 4 0
31 3816 rna-XM_027482819.1 gene-LOC113852515 NW_020874290.1 - 2862574 2864092 1170 2.5641025641025643 0.0 3 0
32 3816 rna-XM_027482831.1 gene-LOC113852525 NW_020874290.1 - 2946117 2947635 1170 2.5641025641025643 0.0 3 0
33 3816 rna-XM_027482228.1 gene-LOC113851957 NW_020874290.1 - 2660608 2666227 1125 1.777777777777778 0.0 2 0
34 3816 rna-XM_027474323.1 gene-LOC113846245 NW_020874290.1 - 619925 623801 1059 6.610009442870632 0.0 7 0
35 3816 rna-XM_027492279.1 gene-LOC113859243 NW_020874290.1 + 4603588 4609775 1026 0.9746588693957114 0.0 1 0
36 3816 rna-XM_027482397.1 gene-LOC113852148 NW_020874290.1 + 3953355 3955386 996 3.0120481927710845 0.0 3 0
37 3816 rna-XM_027477198.1 gene-LOC113847860 NW_020874290.1 - 71566 74184 933 2.143622722400857 0.0 2 0
38 3816 rna-XM_027477316.1 gene-LOC113847944 NW_020874290.1 + 116674 119291 927 2.157497303128371 0.0 2 0
39 3816 rna-XM_027477434.1 gene-LOC113848035 NW_020874290.1 - 176158 178776 927 2.157497303128371 0.0 2 0
40 3816 rna-XM_027477552.1 gene-LOC113848124 NW_020874290.1 + 17283 19902 927 2.157497303128371 0.0 2 0
41 3816 rna-XM_027483460.1 gene-LOC113853026 NW_020874290.1 - 2346726 2349344 927 2.157497303128371 0.0 2 0
42 3816 rna-XM_027483717.1 gene-LOC113853217 NW_020874290.1 + 761724 764343 927 2.157497303128371 0.0 2 0
43 3816 rna-XM_027483729.1 gene-LOC113853225 NW_020874290.1 - 724181 726800 927 2.157497303128371 0.0 2 0
44 3816 rna-XM_027492318.1 gene-LOC113859558 NW_020874290.1 - 397654 400274 927 2.157497303128371 0.0 2 0
45 3816 rna-XM_027492380.1 gene-LOC113859638 NW_020874290.1 - 202352 204970 927 2.157497303128371 0.0 2 0
46 3816 rna-XM_027492459.1 gene-LOC113859739 NW_020874290.1 + 369365 371984 927 2.157497303128371 0.0 2 0
47 3816 rna-XM_027483108.1 gene-LOC113852744 NW_020874290.1 - 1778233 1779698 870 4.597701149425287 0.0 4 0
48 3816 rna-XM_027493792.1 gene-LOC113861140 NW_020874290.1 - 349388 350853 870 4.597701149425287 0.0 4 0
49 3816 rna-XM_027493910.1 gene-LOC113861206 NW_020874290.1 - 270807 272272 870 4.597701149425287 0.0 4 0
50 3816 rna-XM_027494027.1 gene-LOC113861276 NW_020874290.1 + 418785 420250 870 4.597701149425287 0.0 4 0
51 3816 rna-XM_027494147.1 gene-LOC113861345 NW_020874290.1 - 493836 495301 870 4.597701149425287 0.0 4 0
52 3816 rna-XM_027494262.1 gene-LOC113861422 NW_020874290.1 + 223479 224944 870 4.597701149425287 0.0 4 0
53 3816 rna-XM_027494382.1 gene-LOC113861496 NW_020874290.1 + 316021 317486 870 4.597701149425287 0.0 4 0
54 3816 rna-XM_027497799.1 gene-LOC113863977 NW_020874290.1 - 2045962 2047427 870 4.597701149425287 0.0 4 0
55 3816 rna-XM_027510382.1 gene-LOC113872635 NW_020874290.1 - 1567305 1568770 870 4.597701149425287 0.0 4 0
56 3816 rna-XM_027510510.1 gene-LOC113872708 NW_020874290.1 + 1561146 1562611 870 4.597701149425287 0.0 4 0
57 3816 rna-XM_027496451.1 gene-LOC113863034 NW_020874290.1 + 477471 478497 864 2.314814814814815 0.0 2 0
58 3816 rna-XM_027496577.1 gene-LOC113863109 NW_020874290.1 - 332823 333849 864 2.314814814814815 0.0 2 0
59 3816 rna-XM_027482380.1 gene-LOC113852129 NW_020874290.1 - 3886271 3890719 849 2.3557126030624262 0.0 2 0
60 3816 rna-XM_027473561.1 gene-LOC113845863 NW_020874290.1 + 2022293 2023250 843 1.1862396204033216 0.0 1 0
61 3816 rna-XM_027483472.1 gene-LOC113853030 NW_020874290.1 + 2232678 2233635 843 1.1862396204033216 0.0 1 0
62 3816 rna-XM_027483483.1 gene-LOC113853038 NW_020874290.1 + 2253491 2254448 843 1.1862396204033216 0.0 1 0
63 3816 rna-XM_027492616.1 gene-LOC113859934 NW_020874290.1 + 478941 479898 843 1.1862396204033216 0.0 1 0
64 3816 rna-XM_027492699.1 gene-LOC113860040 NW_020874290.1 - 434189 435146 843 1.1862396204033216 0.0 1 0
65 3816 rna-XM_027492813.1 gene-LOC113860123 NW_020874290.1 - 252843 253800 843 1.1862396204033216 0.0 1 0
66 3816 rna-XM_027492918.1 gene-LOC113860200 NW_020874290.1 - 455380 456337 843 1.1862396204033216 0.0 1 0
67 3816 rna-XM_027492984.1 gene-LOC113860278 NW_020874290.1 - 331422 332379 843 1.1862396204033216 0.0 1 0
68 3816 rna-XM_027492985.1 gene-LOC113860444 NW_020874290.1 - 552036 552993 843 1.1862396204033216 0.0 1 0
69 3816 rna-XM_027507119.1 gene-LOC113870336 NW_020874290.1 - 2149207 2150164 843 1.1862396204033216 0.0 1 0
70 3816 rna-XM_027508380.1 gene-LOC113871135 NW_020874290.1 - 2164902 2165859 843 1.1862396204033216 0.0 1 0
71 3816 rna-XM_027482407.1 gene-LOC113852159 NW_020874290.1 + 3969192 3980573 837 2.389486260454002 0.0 2 0
72 3816 rna-XM_027482710.1 gene-LOC113852436 NW_020874290.1 + 935700 936980 819 1.221001221001221 0.0 1 0
73 3816 rna-XM_027493146.1 gene-LOC113860652 NW_020874290.1 + 652468 653748 819 1.221001221001221 0.0 1 0
74 3816 rna-XM_027493252.1 gene-LOC113860720 NW_020874290.1 + 523969 525249 819 1.221001221001221 0.0 1 0
75 3816 rna-XM_027509641.1 gene-LOC113872221 NW_020874290.1 - 1504516 1505795 819 1.221001221001221 0.0 1 0
76 3816 rna-XM_027509884.1 gene-LOC113872351 NW_020874290.1 - 1472620 1473900 819 1.221001221001221 0.0 1 0
77 3816 rna-XM_027510006.1 gene-LOC113872423 NW_020874290.1 - 1617790 1619070 819 1.221001221001221 0.0 1 0
78 3816 rna-XM_027512970.1 gene-LOC113874722 NW_020874290.1 - 2769040 2775142 813 4.920049200492005 0.0 4 0
79 3816 rna-XM_027482234.1 gene-LOC113851963 NW_020874290.1 - 2672483 2674519 783 3.8314176245210727 0.0 3 0
80 3816 rna-XM_027482356.1 gene-LOC113852101 NW_020874290.1 + 3604972 3606105 771 3.891050583657588 0.0 3 0
81 3816 rna-XM_027481403.1 gene-LOC113850851 NW_020874290.1 + 1755547 1756897 756 5.291005291005291 0.0 4 0
82 3816 rna-XM_027482505.1 gene-LOC113852266 NW_020874290.1 - 4375680 4376747 669 2.989536621823617 0.0 2 0
83 3816 rna-XM_027506809.1 gene-LOC113870186 NW_020874290.1 - 4545866 4547064 657 1.5220700152207 0.0 1 0
84 3816 rna-XM_027504929.1 gene-LOC113868903 NW_020874290.1 + 1229774 1230811 573 1.7452006980802792 0.0 1 0
85 3816 rna-XM_027482322.1 gene-LOC113852062 NW_020874290.1 + 2936569 2937456 537 5.58659217877095 0.0 3 0
86 3816 rna-XM_027490153.1 gene-LOC113857653 NW_020874290.1 - 4572447 4574813 435 2.2988505747126435 0.0 1 0
87 3816 rna-XM_027482487.1 gene-LOC113852246 NW_020874290.1 + 4282827 4284484 327 3.058103975535168 0.0 1 0
88 3816 rna-XM_027482273.1 gene-LOC113852012 NW_020874290.1 - 2892498 2892884 324 3.08641975308642 0.0 1 0
188 3816 rna-XM_027486907.1 gene-LOC113855315 NW_020874291.1 - 6171238 6179832 5856 1.1953551912568303 0.0 7 0
189 3816 rna-XM_027487354.1 gene-LOC113855722 NW_020874291.1 - 998206 1024777 5265 5.5080721747388415 0.0 30 0
190 3816 rna-XM_027487607.1 gene-LOC113855976 NW_020874291.1 + 1249974 1267673 5133 4.675628287551139 0.0 24 0
191 3816 rna-XM_027490919.1 gene-LOC113858327 NW_020874291.1 + 476410 484259 4848 1.8564356435643563 0.0 9 0
192 3816 rna-XM_027489363.1 gene-LOC113857448 NW_020874291.1 - 558262 575972 4548 0.8795074758135445 0.0 4 0
193 3816 rna-XM_027489376.1 gene-LOC113857454 NW_020874291.1 - 591114 597269 4059 0.7390983000739099 0.0 3 0
194 3816 rna-XM_027486048.1 gene-LOC113854808 NW_020874291.1 - 3715649 3739623 3705 5.398110661268555 0.0 20 0
195 3816 rna-XM_027486895.1 gene-LOC113855305 NW_020874291.1 - 6151300 6159087 3705 1.6194331983805668 0.0 7 0
196 3816 rna-XM_027487662.1 gene-LOC113856037 NW_020874291.1 + 6205761 6253364 3573 7.276798208788134 0.0 27 0
197 3816 rna-XM_027487917.1 gene-LOC113856194 NW_020874291.1 + 1807253 1816005 3546 0.8460236886632826 0.0 3 0
198 3816 rna-XM_027489389.1 gene-LOC113857460 NW_020874291.1 - 609568 613699 3513 1.138627953316254 0.0 4 0
199 3816 rna-XM_027489934.1 gene-LOC113857749 NW_020874291.1 + 1666390 1671058 3423 1.460706982179375 0.0 5 0
200 3816 rna-XM_027489025.1 gene-LOC113857218 NW_020874291.1 + 2944533 2979663 3363 9.217960154623848 0.0 31 0