Summary (enrichment more than 3-fold)
Yüklə 31,8 Kb.
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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
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
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
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
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 Yüklə 31,8 Kb. Dostları ilə paylaş:
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