Table 2. Newly annotated non-coding RNAs of S. carnosus TM300.
| Locus ID | Gene name | Position | Upstream* | Orientation | Downstream* | RPKM† |
|---|---|---|---|---|---|---|
| SCAs001 | jacL-1 | 9628..9890 | SCA_0010 | < | SCA_0011 | 329.72 |
| SCAs002 | jacL-2 | 16355..16590 | SCAs079 | < | SCA_0015 | 489.92 |
| SCAs003 | jacL-3 | 68516..68644 | fcbC | > | SCA_0067 | 1331.56 |
| SCAs004 | jacL-4 | 114686..114974 | SCA_0114 | > | SCA_0115 | 1318.64 |
| SCAs005 | jacL-5 | 144461..144729 | SCA_0141 | > | SCAs006 | 212.44 |
| SCAs006 | jacL-6 | 144466..144711 | SCAs005 | < | SCA_0142 | 4.05 |
| SCAs007 | jacL-7 | 195809..196025 | gltX | > | cysE | 736.45 |
| SCAs008 | jacL-8 | 239896..240240 | proP | < | thiD | 1253.87 |
| SCAs009 | jacL-9 | 248359..248731 | SCA_0240 | > | SCA_0241 | 26355.27 |
| SCAs010 | jacL-10 | 286557..286798 | tagA | > | thrS | 6.86 |
| SCAs011 | jacL-11 | 302807..302992 | SCA_0293 | < | SCA_0294 | 7754.21 |
| SCAs012 | jacL-12 | 349042..349212 | norA | > | SCA_0342 | 443 |
| SCAs013 | jacL-13 | 370812..371006 | SCA_0365 | > | SCA_0366 | 386.77 |
| SCAs014 | jacL-14 | 386729..386902 | SCA_0377 | > | SCAs090 | 324.61 |
| SCAs015 | jacL-15 | 409625..409751 | SCA_0399 | > | SCA_0400 | 7319.89 |
| SCAs016 | jacL-16 | 435453..435577 | SCA_0420 | > | SCA_0421 | 459.83 |
| SCAs017 | jacL-17 | 439576..439686 | gapA | > | pgk | 12059.66 |
| SCAs018 | jacL-18 | 449553..449930 | smpB | > | NEW_REGION_507 | 40323.14 |
| SCAs019 | jacL-19 | 465254..465398 | SCA_0454 | > | SCA_0455 | 6846.57 |
| SCAs020 | jacL-20 | 475448..475663 | int | > | SCA_0464 | 189.2 |
| SCAs021 | jacL-21 | 478847..479060 | SCA_0469 | < | SCA_0470 | 172.33 |
| SCAs022 | jacL-22 | 519236..519323 | glpQ | > | SCA_0522 | 211.43 |
| SCAs023 | jacL-23 | 704781..704974 | SCA_0700 | < | SCA_0701 | 438.43 |
| SCAs024 | jacL-24 | 736699..736810 | SCA_0733 | < | SCA_0734 | 3740.74 |
| SCAs025 | jacL-25 | 754215..755140 | SCA_0752 | > | SCA_0753 | 236.45 |
| SCAs026 | jacL-26 | 809208..809442 | rluD | > | pyrR | 10723.79 |
| SCAs027 | jacL-27 | 954424..954574 | mutS | > | mutL | 28.6 |
| SCAs028 | jacL-28 | 1026107..1026242 | SCA_1009 | < | tyrA | 2460.09 |
| SCAs029 | jacL-29 | 1028624..1028907 | SCA_1011 | > | trpE | 926.55 |
| SCAs030 | jacL-30 | 1055393..1055592 | SCA_1036 | > | lysC | 3098.2 |
| SCAs031 | jacL-31 | 1080768..1080936 | SCA_1060 | > | SCA_1061 | 139.58 |
| SCAs032 | jacL-32 | 1098995..1099432 | SCA_1079 | < | SCA_1080 | 1725.71 |
| SCAs033 | jacL-33 | 1103951..1104094 | pbp2 | < | SCA_1085 | 230.73 |
| SCAs034 | jacL-34 | 1136220..1136427 | SCA_1116 | < | srrB | 1380.1 |
| SCAs035 | jacL-35 | 1239320..1239485 | alaS | < | SCA_1231 | 28.02 |
| SCAs036 | jacL-36 | 1249565..1249804 | SCA_1240 | < | aspS | 5994.28 |
| SCAs037 | jacL-37 | 1252944..1253215 | hisS | < | SCA_1243 | 2385.58 |
| SCAs038 | jacL-38 | 1294117..1294234 | infC | < | lysP | 23251.64 |
| SCAs039 | jacL-39 | 1339350..1339494 | SCA_1325 | > | rpsD | 1271.7 |
| SCAs040 | jacL-40 | 1354036..1354126 | fhs | < | acsA | 200.81 |
| SCAs041 | jacL-41 | 1373449..1373678 | SCA_1356 | < | dat | 1246.65 |
| SCAs042 | jacL-42 | 1383627..1383700 | leuS' | > | SCA_1366 | 9195.15 |
| SCAs043 | jacL-43 | 1393914..1394102 | ribD | < | SCA_1376 | 1063.54 |
| SCAs044 | jacL-44 | 1406587..1406766 | metK | < | pckA | 2198.37 |
| SCAs045 | jacL-45 | 273470..273659 | sarA | < | SCA_0267 | 34.97 |
| SCAs046 | jacL-46 | 1546771..1546977 | SCA_1526 | < | SCA_1527 | 500.78 |
| SCAs047 | jacL-47 | 1562210..1562443 | SCA_1544 | > | agrB | 985.38 |
| SCAs048 | jacL-48 | 1585607..1585749 | ilvA | < | 23S rRNA D | 2012.07 |
| SCAs049 | jacL-49 | 1664220..1664368 | SCA_1648 | > | SCA_1649 | 196.23 |
| SCAs050 | jacL-50 | 1824275..1824411 | SCA_1822 | < | SCA_1823 | 637.82 |
| SCAs051 | jacL-51 | 1917867..1918006 | SCA_1912 | < | SCA_1913 | 832.99 |
| SCAs052 | jacL-52 | 1929303..1929527 | SCA_1921 | < | SCA_1922 | 84.17 |
| SCAs053 | jacL-53 | 1941508..1941755 | opuCA | < | SCA_1935 | 515.79 |
| SCAs054 | jacL-54 | 2031863..2032724 | SCA_2018 | > | SCA_2019 | 7319.06 |
| SCAs055 | jacL-55 | 2088262..2088525 | SCA_2075 | > | SCA_2076 | 761.4 |
| SCAs056 | jacL-56 | 2199217..2199338 | SCA_2172 | < | SCA_2173 | 1628.55 |
| SCAs057 | jacL-57 | 2224729..2224907 | SCA_2191 | < | SCA_2192 | 848.25 |
| SCAs058 | jacL-58 | 2266552..2266687 | SCA_2211 | > | SCAs059 | 4277.68 |
| SCAs059 | jacL-59 | 2266688..2266868 | SCAs058 | < | SCAs060 | 2180.71 |
| SCAs060 | jacL-60 | 2267000..2267107 | SCAs059 | > | SCAs061 | 1239.77 |
| SCAs061 | jacL-61 | 2267108..2267271 | SCAs060 | < | tatA | 1847.62 |
| SCAs062 | jacL-62 | 2294415..2294594 | SCA_2236 | < | SCA_2237 | 265.8 |
| SCAs063 | jacL-63 | 2303997..2304203 | SCA_2247 | > | SCAs064 | 1295.28 |
| SCAs064 | jacL-64 | 2304288..2304494 | SCAs063 | > | SCA_2248 | 166.93 |
| SCAs065 | jacL-65 | 2312205..2312796 | SCA_2253 | < | SCAs066 | 2442.46 |
| SCAs066 | jacL-66 | 2313086..2313451 | SCAs065 | > | SCA_2254 | 2055.21 |
| SCAs067 | jacL-67 | 2322081..2322191 | acsA | > | putP | 1655.25 |
| SCAs068 | jacL-68 | 2375256..2375403 | SCA_2309 | > | SCAs069 | 60.61 |
| SCAs069 | jacL-69 | 2375475..2375602 | SCAs068 | > | SCAs070 | 3569.06 |
| SCAs070 | jacL-70 | 2375660..2375782 | SCAs069 | < | opuD | 27.01 |
| SCAs071 | jacL-71 | 387163..387583 | SCAs014 | > | nrdI | 153.1 |
| SCAs072 | jacL-72 | 2550964..2551426 | SCA_2464 | > | serS | 45.21 |
| SCAs073 | jacL-73 | 1295825..1296074 | SCA_1288 | < | thrS | 1306.39 |
| SCAs074 | jacL-74 | 1732302..1732452 | SCA_1707 | < | rplQ | 4134.38 |
| SCAs075 | jacL-75 | 756990..757182 | SCA_0755 | > | pheS | 165.26 |
| SCAs076 | jacL-76 | 1639798..1639959 | rpmE | < | rho | 514.78 |
| SCAs077 | jacL-77 | 2552910..2553191 | serS | < | hutH | 153.16 |
| SCAs078 | jacL-78 | 1574476..1574699 | SCA_1558 | > | ilvD | 467.22 |
| SCAs079 | jacL-79 | 16200..16350 | metC | < | SCAs002 | 699.7 |
| SCAs080 | jacL-80 | 203095..203214 | rplA | > | rplJ | 2129.15 |
| SCAs081 | jacL-81 | 1298095..1298341 | thrS | < | dnaI | 793.63 |
| SCAs082 | jacL-82 | 1728725..1728877 | rplM | < | truA | 297.5 |
| SCAs083 | jacL-83 | 1200679..1200816 | SCA_1186 | > | glyS | 334.65 |
| SCAs084 | jacL-84 | 1674226..1674513 | glmS | < | mtlA | 57.68 |
| SCAs085 | jacL-85 | 365862..366036 | SCA_0360 | < | SCA_0361 | 32.28 |
| SCAs086 | jacL-86 | 1648746..1648822 | pyrG | < | SCA_1631 | 207.11 |
| SCAs087 | jacL-87 | 1278047..1278317 | valS | < | tag | 202.29 |
| SCAs088 | jacL-88 | 605369..605416 | pepF | > | SCA_0600 | 699.1 |
| SCAs089 | jacL-89 | 1811579..1811734 | SCA_1806 | < | SCA_1807 | 10.65 |
*Gene.
†RPKM, reads per kilobase material per million reads.