Nucleoid RNAs
*in blue-annotated small RNAs (sRNAs)
*in red-annotated intergenic repetitive elements
Coordinates Annotation
______
Minus Strand
1630638-1632474 ydfK, pinQ
1049958-1052050 cspG, ymcE, gnsA entire including ***PAIR4a repeats in intergenic region between cspG and ymcE
3886350-3889554 tnaCAB
1406998-1407330 intergenic ydaN and dbpA, fnrS small RNA
939670-945210 dmsA, dmsB, dmsC and ***TERM15 upstream of dmsA
1655646-1663698 ynfDEFG, dmsD, N-terminal clcB ***REPT124 between ynfD and E and REPt125 between dmsD and clcB
2493438-2494826 b2378 (lpxP)
2350534-2354930 glpABC
2823758-2828026 srlAEBD, gutM, srlR and begining of gutQ
2848662-2854258 hypABCDE and fhlA
2347398-2350550 intergenic inaA and glpQ containing yfH pseudogene,
entire glpQ, glpT
1311910-1313402 ompW
4403910-4407570 end of purA, nsrR, rnr, beginning of rlmB
1639782-1640706 cspF entire ***including intergenic cspF and ydfT containing *** TERM25
2454253-2459021 sixA, fadJ, fadI and yfcZ
2735062-2735794 yfiA and pheL
4244710-4248514 entire malK, lamB, malM
4103742-4104442 entire cpxP
772859-774018 cydB, ybgT, ybgE, N-terminal ybgC
986238-987042 intergenic ompF and asnS, region of transcription units (OmpR, CRP, CpxR, IHF, Lrp)
2588697-2589064 ypfM
3891798-3893618 yieEF
2011710- 2017661 fliFGHIJK
1130222-1141922 flgBCDEFGHIJKL entire
19742-20634 intragenic region between nhaR and yaaY (complimentary to region of insA-1 and B-1 on the opposite strand)
2414654-2416770 C-terminal pta and entire yfcC
20001766-2005954 fliD, fliS, fliT and amyA
1644342- 1645242 flxA
728230-730034 ybfA
970766-972738 ycbJ
289806-290667 intergenic ykgS anmd yagJ, complementary to insB and insA on opposite strand
2940798- 2941570 intergenic ygdI and csdA and N-terminal of csdA
2018494-2022786 fliMNOPQR and rcsA
1257886-1258410 ychH
2802702-2806482 proV, prow, proX and ygaX including ***REP193
1935438-1937426 entire pykA and ***REPt137
1997404-2001726 fliYZAC
3086206-3087667 galP
815958-816 225 intergenic moaA 5’UTR
4327094-4328162 yjcZ
2228558-2229610 yohJ, yohK
3851342-3851730 strong peak intergenic tisB and emrD ***REP279
2763886-2765538 yfjN (rnlA) and yfjO (rnlB)
1609886-1610162 N-terminal yneG
770371-772858 cydA
1805694-1806722 entire yniA
3299430-3301538 yhbU and V
2812750-2813442 sraD sRNA and N-terminal gshA
2039294-2040186 ***REP142 and entire yodA downstream
1831302-1831626 beginning of ydjX
892318- 893074 ybjN, entire
1744526- 1745162 valV, valW, ydhR
2261790-2263426 setB
2371027-2377457 pmrD, menECBHD
2924238- 2925738 ygdH
1900518-1903498 manXYZ and yobD
1940574-1942298 znuC, znuB
2231678-2234490 yeiS, yeiT and yeiA
3352134-3358738 Lrp and Fnr binding sites, gltB and gltD
1168110-1168642 ycfR
582734-583754 appY entire
1014142-1015258 ymbA and rmf, entire
1268414-1270018 intergenic strong continuos signal, parts complementary to ldrABC on the opposite strand ***LDR REPEATS
1545350-1550034 fdnGHI
1184918-1186442 pepT
2922230-2922562 csrB sRNA
829950-831509 entire rhlE
823758-824714 entire ybhQ
404942-408090 yaiI, aroL, yaiA, aroM, yaiE and ykiA
793926-797178 entire ybhT, modA, modB, modC
831509-831869 intergenic rhlE and ybiA ***RIP75
832030-835634 dinG, ybiB, ybiC
889046-889970 ybjM
932443-936074 ftsK
936150-936738 intergenic ftsK and lolA ***REP85
989734-992610 pepN entire
1031142-1036778 hyaA, B, C, D, E and F
1037595-1041178 appC, appB, appA
1064718-1066106 entire agp
1489718- 1492682 ydcA, trg
1288102-1290578 rssA, rssB
1480814-1483138 hrpA N-terminal part
1298502-1305586 oppABCDF
1145054-1145642 intergenic rluC and ycef ***REP101
1921022-1921426 ryeA,B sRNA
2183854-2184866 yohM
2467118-2468338 yfdI
2474334-2474594 entire torI
2481598- 2485906 evgA and evgS
2535262-2536386 yfeK and yfeS
2555294-2556178 Complementary to N-terminal of eutB on opposite strand
2736150-2737082 pheA and downstram intergenic containing ***REPt190
2739742-2740530 yfiR
2748750-2751898 yfjB, recN and b2617 (bamE)
2753918-2754162 ssrA
3219430-3220634 entire ebgR
3256294-3263794 complementary to tdcGFEDCB on the opposite strand
3401374-3403218 yhdH and also yrdF’ abd yrdE’ pseudogenes
3483902-3484106 intergenic prkB and crp***REPt246
3718166-3718690 C-terminal cspA and intergenic cspA and insJ ***mokA’ 3865582-3866418 yidQ entire
3965606-3965986 intergenic rho and b3784
3980790-3982149 Entire aslB
3993438-3996026 yigA, xerC, yigB
4005678-4002500 rhtC
4006251-4066740 intergenic rhtC and rhtB ***REP289
4328262-4328538 Intergenic yjcZ and prop ***TF sites CRP and Fis
4328539-4330266 proP including downstream intergenic with basS which have***REP326
4344774-4345010 complementary to the small fragment in the middle of fumB on the opposite strand 2.1
4377414-4380354 complementary to frdCBA on the opposite strand
4395014-4397394 C-terminal amiB and entire mutL
4460798-4463610 Intergenic nrdD and treC TF bindning sites FNR, long fragment complementary treC and treB on the opposite strand
4525990-4526834 Intergenic sgcA and Q, ryjB sRNA and fragment complementary to sgcQ on the opposite strand
4543030-4543834 N-terminal fimD
4589638-4592242 entire tsr and fragment complementary to N-terminal part of yjiZ on the opposite strand
4609126-4609362 intergenic prfC and osmY, TF binding sites IHF, Lrp and CRP
4638502-4638978 Intergenic yjjY and yjtD, TF binding site FNR
Plus Strand
1638023-1639847 ydfR, essQ, cspB and ***TERM24 and 25 repeats
1430834-1433696 uspF
3256031-3265139 tdcGFEDCBA
1635745-1636901 gnsB, ynfN, cpsI and ***PAIR4b repeats
2170462-2175292 gatDCBAZY
4375949-4380475 entire ampC, frdD, frdC, frdB, frdA
2713239-2714607 yfiD
3097585-3098936 ansB
3137065-3144466 Intergenic yghU and hybG ***REP221, hybGFEDCBAO
4457129-4464246 nrdG and nrdD, treC, treB including intergenic ***IRU
18 and REP338
1050213-1050468 cspH, sold-shock protein homologue
652952-655249 complementary to citB on opposite strand, intergenic region between citB and dcuC containing ***REPt56 and entire dcuC
1959655-1975718 flhEAB, cheZYBR, tap, tar, cheWA, motBA, flhC
1746670-1752742 ydhTUXWVY
3043182-3048843 yqfF, gcvPHT
948953-954044 pflA, pflB and focA including intergenic focA and ycaO containing TF binding sites CRP, FNR, IHF, ArcA, FNR
851492-852328 ybiP and ***rybA sRNA
1119724-1120680 yceP and dinI
1956174-1956820 intergenic torY and cutC and C-terminal cutC
1019341-1020210 intergenic opaA and sulA containing ***TERM16 and
whole sulA
2705133-2708133 rseC, rseB, rseA and rpoE
787259-791351 galMKTE
1395621-1396789 uspE entire
1664399-1665366 ynfK
1487646-1488813 gapC_1 and gapC_2 including ***REPt116
887061-887349 fragment complementary to ybjK on the opposite strand and ***rybB sRNA
986270-986857 Intergenic ompF and asnS* TF binding sites OmpR, CRP, CpxR, Lrp, IHF
6370-8102 entire yaaJ
50594-53566 apaH, apaG, ksgA and pdxA
63317-65798 polB
136450-136958 yacC
183730-185174 yaeH and yaeI
239666-240246 yafV
244530-246558 yafK, yafQ and dinJ
254002-254278 intergenic prfH and pepD *** REPt20
264770-265334 ykfB and beginning of yafY
296242-296446 intergenic intF and yagP ***ptWF’ *** nc1
479618-480129 tomB and downstream intergenic tomB and acrB
484837-485358 intergenic acrA and acrR containing ***TF binding sites PhoP, MarA and SoxS
555703-556007 Intergenic ybcI and folD, there should be a small ribosome-associated protein ybcJ
640614-641136 uspG
698384-698710 Intergenic asnB and nagD containing ***RIP61
682199-683682 C-terminal hscC, rihA
812269-812616 intergenic bioD and uvrB ***DARS1
828318-832188 ybiA
836708-837392 Intergenic ybiJ and ybiC ***REP77 and entire ybiJ
847566-848185 Intergenic glnH dps including TF binfing sites IHF and NtrC and dps
927044-930219 cydC and cydD
1014598-1015195 Fragment complementary to rmf on opposite strand and intergenic rmf and fabA
1025567-1026186 mgsA
1066110-1067002 yccJ and wrbA
1113071-1114782 msyB, mdtG and intergenic mdtG and lpxL including***REPt98
1128028-1129391 flgN and flgM
1189610-1189839 Intergenic phoP and purB***REPt106
1212445-1214785 ycgEF
1239102-1241345 entire cvrA
1242814-1243786 ycgR
1259917-1260167 intergenic ychM and prsA ***TERM20
1285885-1286363 part of tpr and the region of ***tRNA repeats rTV1(TLRs)
1294351-1296276 C-terminal adhE
1310253-1310579 intergenic yciA and yciB
1314399-1321182 entire trpABCDEL
1328136-1328586 yciN
1355035-1355507 intergenic sapA and ymjA ***REP110
1358035-1359002 N-terminal puuA
1417836-1418265 racR
1426362-1426824 N-terminal insH-5
1489932-1490258 hokB, mokB and fragment complementary to sokB on the opposite strand
1553796-1554132 sra
1607586-1608759 uxaB
1630838-1631664 Intergenic ydfJ and ydfK including 5’UTR
1658340-1662975 complementary to ynfE, ynF ynfG, ynfH and dmsD on the opposite strand
1670514-1671834 mdtI and mdtJ
1734063-1735643 ydhP and ***ynhF
1762725-1763350 ydiH and ydiI *** and rydB sRNA
1789366-1790252 ydiV
1797242-1797459 pheM and intergenic pheM rplT
1816549-1819789 chbR, chbA, chbC and chbB
1821781-1823041 ydjR
1862672-1863677 yeaE
1875319-1875618 yoaF
1925036-1928591 ptrB, yebE, yebF, yebG
1931072-1932783 edd
1985772-1986103 intergenic yecJ and yecR***sRNA isrB
2078431-2079413 sbmC
2099304-2099846 wbbL_2 pseudogene
2100985-2106994 wbbL_1, wbbKJIH, glf and rfbX
2246566-2247705 yeiE
2281982-2282154 intergenic yejK and yejL
2289493-2301631 ccmHGFEDCBA and napCBHGADF
2309389-2309764 intergenic ompF and yojL
2387849-2389365 nuoN
2389491-2390960 nuoM
2391219-2400090 nuoLKJIHGFE
2407059-2409478 yfbS and intergenic yfbS aand yfbR with ***REPt168 2410711-2411371 yfbV
2425450-2426000 argT
2447172-2447430 small fragment C-terminal yfcO
2541495-2542703 intergenic cysP and b2426 (ucpA) ***RSA4 repeats and entire ucpA
2557197-2558439 complementary to infZ on the opposite strand
2580792-2583603 nudK and aegA
2595606-2595950 intergenic purC and bamC***REPt181
2637622-2637817 small fragment in hisS
2644142-2650267 pbpC, yfhM
2660147-2660370 Intergenic iscR and trmJ***REP184
2715168-2715563 intergenic ung and yfiF***REPt189
2723731-2724092 intergenic kgtP and rrfG
2734613-2737103 complementary to yfiO, yfiA, pheL and pheA on the opposite strand
2759141-2763537 yfjK, yfj and PDR-A repeats
2816686-2817059 intergenic serV and csrA
2820041-2820797 recX
2833636-2836292 hypF and hydN including intergenic ***REPt196
(Flh regulon)
2840545-2848502 hycIHGFEDCBA FhlA regulon)
2848948-2852114 complementary to hypABCDE on the opposite strand
2907656-2907879 intergenic pyrG and mazG
2922166-2922601 csrB sRNA
2940478-2940684 intergenic gcvA and ygdI, ecogene: annotated as gcvB
2948979-2949849 recD
3002231-3003868 ygeV
3010869-3013141 yqeB and C
3040475-3041236 ygqA
3297285-3299300 yhbPST
3316257-3316429 metY and intergenic with ArgR, FIS, Crp
3367054-3371645 yhcH, nanKETA
3429809-3430839 yrdD, smg, smf
3483164-3483685 yhfA and ***REPt246 in itergenic with prkB
3545718-3546004 intergenic malQ and gntT ***REP254
3546010-3550555 malQ and malP entire
3561780-3573063 yzgL, glgPACXB, asd
3581391-3582164 complementary to insA-6 and insB-6 on the opp strand
3597934-3598679 rpoH
3598690-3599085 intergenic rpoH and ftsX *TF binding sites DnaA, CRP, CytA
3654072-3654650 hdeB and hdeA
3675211-3677278 yhjG and yhjH
3706854-3708629 eptB
3739197-3739563 ysaA
3886423-3888198 Fragment complementary to entire tnaA on the opposite strand
3920671-3921037 intergenic atpI and gidB ***REP15
3923636-3923917 intergenic gidA and mioC ***oriC
3938382-3939544 yieP and intergenic with rrsC *TF binding site Fis
3960821-3962120 gpp
4108404-4108838 intergenic cdh and tpiA ***REPt303
4113543-4116228 intergenic glpX and K***REPt304, glpK and glpF
4152720-4153086 Intergenic argE and argC *TF binding site ArgR
4187574-4187924 intergenic yjaZ and thiH***sroH sRNA
4227247-4228226 pepE and intergenic with yjbB ***REP312
4295103-4297467 entire fdhF
4323826-4324408 intergenic yjdM and yjdN ***REP325
4354426-4358118 cadA, cadB
4363331-4366451 dcuA and aspA
4404050-4405116 fragment complementary to nsrR and part of rnr on the opposite strand
4414310-4414784 intergenic yjfO and yjfN and entire yjfO
4497897-4498546 yjgX_2
4516480-4517243 complementary to inA-7, insB-7_1 and insB-7_2 on the opposite strand
4562715-4563936 yjiM
4578346-4579468 hsdS
4581077-4584500 hsdR and intergenic hsdR and hsdM containing ***IRU19
4586133-4589339 yjiAXY
4638368-4638820 two intergenic peaks arcA and yjtD, annotation in Ecogene: yjjY and TF binding sites FNR