# Copies and Copyright-Notice # # RegulonDB is free for academic/noncommercial use # # User is not entitled to change or erase data sets of the RegulonDB # database or to eliminate copyright notices from RegulonDB. Furthermore, # User is not entitled to expand RegulonDB or to integrate RegulonDB partly # or as a whole into other databank systems, without prior written consent # from CCG-UNAM. # # Please check the license at http://regulondb.ccg.unam.mx/menu/download/full_version/terms_and_conditions.jsp # # Citation # # Tierrafría, V. H. et al. (2022). RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12, # Microb Genom. 2022 May;8(5). doi: 10.1099/mgen.0.000833. PMID: 35584008. https://doi.org/10.1099/mgen.0.000833 # # # Contact # # Person: RegulonDB Team # Web Page: http://regulondb.ccg.unam.mx/menu/about_regulondb/contact_us/index.jsp # (regulondb@ccg.unam.mx) # # # Release: 11.2 Date: 05/22/2023 # Genome version: U00096.3, Refseq version: NC_000913.3; GI:556503834 # ___________________________________________________________________________ # Created: 06/12/2023 13:38:31 # Columns: # (1) Gene identifier assigned by RegulonDB # (2) Gene name # (3) Blattner number (bnumber) of the gene # (4) Gene left end position in the genome # (5) Gene right end position in the genome # (6) DNA strand where the gene is coded # (7) Product name of the gene # (8) Evidence that supports the existence of the gene # (9) PMIDs list # (10) Evidence confidence level (Confirmed, Strong, Weak) # (11) All bnumber related to gene # (12) Other database's id related to gene ECK120002653 sokC b4413 16952 17010 forward small regulatory RNA antitoxin SokC [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence],[EXP-IMP|W|Inferred from mutant phenotype] 10361310,1943701, Weak b4413 ECK120002641 sroA b4762 75516 75608 reverse small RNA SroA 12376536,28071751,28520932, b4762 ECK120002667 sgrS b4577 77367 77593 forward small regulatory RNA SgrS [EXP|W|Inferred from experiment],[EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 15522088,15650111,23873911,25582129,28119418,28289085,29137641,30287822,30700509,32291821,33425989, Weak b4577 ECK125302576 ftsO b4810 92485 92658 forward small regulatory RNA FtsO [EXP-IMP|W|Inferred from mutant phenotype] 33460557, Weak b4810 ECK120002606 tff b4414 189712 189847 forward putative small RNA T44 [COMP|W|Inferred by computational analysis] 11553332, Weak b4414 ECK125302575 ispZ b4809 194784 194844 forward small regulatory RNA IspZ [EXP-IMP|W|Inferred from mutant phenotype] 33460557, Weak b4809 ECK125135291 eyeA b4690 272580 272654 forward CP4-6 prophage; small RNA EyeA b4690 ECK125146691 nc1 297137 297304 reverse small noncoding RNA involved in nucleoid organization [EXP-IMP|W|Inferred from mutant phenotype] 22942248, Weak ECK120002574 sraA 458728 458784 reverse small RNA SraA 11448770,11553332, ECK120002469 ffs b0455 476448 476561 forward signal recognition particle 4.5S RNA 11904184,12702815,1331806,15611297,7525539,8073757,8772186,95791, b0455 ECK120002642 chiX b4585 507204 507287 forward small regulatory RNA ChiX [EXP-IMP|W|Inferred from mutant phenotype] 19400782,19426207,30287822,33748186, Weak b4585 ECK125303723 allZ b4831 533629 533863 forward small RNA AllZ b4831 ECK125289860 ipeX 574367 574515 reverse small RNA IpeX 16385048, ECK125328227 sokE b4835 607733 607792 reverse small RNA SokE b4835 ECK120002643 sroC b4763 686681 686843 reverse small regulatory RNA SroC [EXP-IMP|W|Inferred from mutant phenotype] 25916829,26469694,29992897,34093460, Weak b4763 ECK125302574 chiZ b4808 708236 708333 forward small regulatory RNA ChiZ [EXP-IMP|W|Inferred from mutant phenotype] 33460557, Weak b4808 ECK125276535 sdhX b4764 765050 765150 forward small regulatory RNA SdhX [EXP-IMP|W|Inferred from mutant phenotype] 18467773,30541135,30591570, Weak b4764 ECK125303724 zbiJ b4814 837435 837531 reverse small regulatory RNA ZbiJ [EXP-IDA|W|Inferred from direct assay] 33622723,34093460, Weak b4814 ECK120002592 rybA b4416 852725 853064 reverse small RNA RybA [EXP-IMP|W|Inferred from mutant phenotype] 11445539,22336764,26076491, Weak b4416 ECK120002591 rybB b4417 887979 888057 reverse small regulatory RNA RybB [EXP-IEP|W|Inferred from expression pattern],[EXP-IMP|W|Inferred from mutant phenotype] 11445539,17007876,17416652,21768388,22439016,25001303,25030700,25582129,26484242,26992034,30287822, Weak b4417 ECK125303710 flgO b4826 1140986 1141063 forward small RNA FlgO b4826 ECK120002575 sraB b4418 1146589 1146757 forward small RNA SraB 11448770,12202758, b4418 ECK125303707 bhsB b4832 1169303 1169402 forward small RNA BhsB b4832 ECK120002608 C0293 b4806 1196711 1196782 forward e14 prophage; small regulatory RNA C0293 [EXP-IMP|W|Inferred from mutant phenotype] 32061118, Weak b4806 ECK120002656 rdlA b4420 1269323 1269389 forward putative antisense regulatory RNA RdlA [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence] 12123448, Weak b4420 ECK120002658 rdlB b4422 1269858 1269923 forward putative antisense regulatory RNA RdlB [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence],[EXP-IMP|W|Inferred from mutant phenotype] 12123448,26469694, Weak b4422 ECK120002660 rdlC b4424 1270393 1270460 forward putative antisense regulatory RNA RdlC [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence],[EXP-IMP|W|Inferred from mutant phenotype] 12123448,26469694, Weak b4424 ECK125303716 narS b4813 1279337 1279520 forward putative small regulatory RNA NarS [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence] 31863581, Weak b4813 ECK120002661 rttR b4425 1287066 1287236 reverse small RNA RttR b4425 ECK120002610 mcaS b4426 1405658 1405751 reverse small regulatory RNA McaS [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 22250746,22289118,22414234,30287822,30799856,34067197, Weak b4426 ECK125095415 fnrS b4699 1409129 1409250 forward small regulatory RNA FnrS [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 20070527,20075074, Weak b4699 ECK125165375 ralA b4714 1413556 1413734 forward Rac prophage; small regulatory RNA antitoxin RalA [EXP-IMP|W|Inferred from mutant phenotype] 24748661, Weak b4714 ECK125303713 kilS b4833 1418405 1418502 reverse Rac prophage; small RNA KilS b4833 ECK120002612 micC b4427 1437121 1437231 forward small regulatory RNA MicC [EXP-IEP|W|Inferred from expression pattern],[EXP-IGI|W|Inferred from genetic interaction] 12069726,15466019,17264113,20068355, Weak b4427 ECK120030076 rydC b4597 1491442 1491506 reverse small regulatory RNA RydC [EXP-IMP|W|Inferred from mutant phenotype] 15618228,30700509,31308070, Weak b4597 ECK120002663 sokB b4429 1492119 1492175 forward putative small regulatory RNA antitoxin SokB [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence] 10361310,16751270,17065468, Weak b4429 ECK125095180 mgrR b4698 1622817 1622914 reverse small regulatory RNA MgrR [EXP-IMP|W|Inferred from mutant phenotype] 19889087, Weak b4698 ECK120002557 dicF b1574 1649382 1649434 forward Qin prophage; small regulatory RNA DicF [EXP-IMP|W|Inferred from mutant phenotype],[EXP-IGI|W|Inferred from genetic interaction] 1552861,18388495,27822514,8763959, Weak b1574 ECK120002588 rydB b4430 1764713 1764780 reverse small regulatory RNA RydB [EXP-IMP|W|Inferred from mutant phenotype] 11445539,12069726,21546360, Weak b4430 ECK120002576 rprA b4431 1770372 1770477 forward small regulatory RNA RprA [EXP-IDA|W|Inferred from direct assay],[EXP-IEP|W|Inferred from expression pattern],[EXP-IMP|W|Inferred from mutant phenotype] 11251852,11448770,12410838,17264113,18826256,20455949,26264774,28479746,29294085,29905843,30287822,30562360,30802490,31186337,31552789, Weak b4431 ECK120002577 ryeA b4432 1923066 1923337 forward small antisense RNA RyeA 11448770,12069726,12762038,28314872,31270363, b4432 ECK120002594 sdsR b4433 1923104 1923207 reverse small regulatory RNA SdsR [EXP-IMP|W|Inferred from mutant phenotype] 11553332,18467773,25724987,26469694,32087965, Weak b4433 ECK125165376 micL b4717 1958441 1958520 reverse small regulatory RNA MicL-S [EXP-IMP|W|Inferred from mutant phenotype],[EXP-IGI|W|Inferred from genetic interaction] 14622403,24722986,25030700,28373273, Weak b4717 ECK125303725 motR b4828 1977208 1977302 reverse small RNA MotR b4828 ECK125229289 3'ETS-leuZ b4759 1991748 1991814 reverse small regulatory RNA 3'ETS [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 25891076,30061117, Weak b4759 ECK125135297 sdsN b4719 1996921 1997057 forward small regulatory RNA SdsN [EXP-IMP|W|Inferred from mutant phenotype] 27166377, Weak b4719 ECK125303717 fliX b4827 2001912 2002106 reverse small RNA FliX b4827 ECK120003633 dsrA b1954 2025223 2025313 reverse small regulatory RNA DsrA [EXP-IMP|W|Inferred from mutant phenotype] 12069726,25262352,25582129,30287822,32845055, Weak b1954 ECK120029424 rseX b4603 2033649 2033739 forward small regulatory RNA RseX [EXP-IDA|W|Inferred from direct assay] 16513633,25724987,30287822,34327153, Weak b4603 ECK120002616 isrC b4435 2071317 2071511 forward CP4-44 prophage; small RNA IsrC b4435 ECK120002595 sibA b4436 2153311 2153454 forward small RNA SibA b4436 ECK120002596 sibB b4437 2153646 2153781 forward small RNA SibB [EXP-IMP|W|Inferred from mutant phenotype] 18710431, Weak b4437 ECK120002589 cyaR b4438 2167114 2167200 forward small regulatory RNA CyaR [EXP-IMP|W|Inferred from mutant phenotype] 18619465,18978044,20627350,30287822, Weak b4438 ECK125289861 orzP 2204402 2204484 forward small RNA OrzP ECK120002505 micF b4439 2313084 2313176 forward small regulatory RNA MicF [EXP|W|Inferred from experiment],[EXP-IDA|W|Inferred from direct assay] 12069726,17009960,17264113,2193928,2478539,25246476,26774489,30287822,32157864,9478198, Weak b4439 ECK125229288 ryeG 2470472 2470665 reverse small RNA RyeG [EXP-IMP|W|Inferred from mutant phenotype] 20683441,26469694, Weak ECK120002645 sroE b4761 2640595 2640686 reverse small RNA SroE 11553332, b4761 ECK125302578 timR b4811 2653356 2653455 reverse putative small regulatory RNA TimR [COMP-HINF-FN-FROM-SEQ|W|Human inference of function from sequence] 33172998, Weak b4811 ECK120002590 ryfA b4440 2653855 2654158 forward small regulatory RNA RyfA [EXP-IMP|W|Inferred from mutant phenotype] 10673004,26469694, Weak b4440 ECK120002620 glmY b4441 2691157 2691340 reverse small regulatory RNA GlmY [EXP-IMP|W|Inferred from mutant phenotype] 17854828,19734312,22355164,22661574,26531825,28977623,30040820, Weak b4441 ECK120030082 ohsC b4608 2700520 2700598 forward small regulatory RNA OhsC [EXP-IMP|W|Inferred from mutant phenotype] 18710431, Weak b4608 ECK120030083 ryfD b4609 2734153 2734295 reverse small regulatory RNA RyfD [EXP-IMP|W|Inferred from mutant phenotype] 26469694, Weak b4609 ECK125289863 raiZ b4805 2737381 2737542 forward small RNA RaiZ b4805 ECK120002578 micA b4442 2814802 2814874 forward small regulatory RNA MicA [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 11448770,16204185,16313626,20976191,23594456,24163336,24244437,25030700,25046628,29467745,30287822, Weak b4442 ECK125135289 sokX b4701 2887353 2887411 forward small RNA SokX b4701 ECK120002573 csrB b4408 2924156 2924524 reverse small regulatory RNA CsrB [EXP-IDA|W|Inferred from direct assay] 11310739,11535784,11741870,16822857,17026754,17064377,18080813,20118252,24512078,24708042,28796489,30589862,9211896, Weak b4408 ECK120002579 gcvB b4443 2942696 2942901 forward small regulatory RNA GcvB [EXP-IEP|W|Inferred from expression pattern],[EXP-IMP|W|Inferred from mutant phenotype],[EXP-IGI|W|Inferred from genetic interaction] 10972807,11448770,12069726,17264113,18312576,19118351,19221499,22020646,23316042,24391513,25358737,27588604,29905843,30447071,31553492,33169170,34065855, Weak b4443 ECK120002580 omrA b4444 2976102 2976189 reverse small regulatory RNA OmrA [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 11448770,11553332,16359331,18953042,20407422,22040174,32133913, Weak b4444 ECK120002593 omrB b4445 2976304 2976385 reverse small regulatory RNA OmrB [EXP-IMP|W|Inferred from mutant phenotype] 16359331,18953042, Weak b4445 ECK120002541 ssrS b2911 3055983 3056165 forward 6S RNA [EXP-IDA|W|Inferred from direct assay] 10892648,1098044,29686109,4570237,4929322,6231216, Weak b2911 ECK120002597 sibC b4446 3056851 3056991 forward small regulatory RNA antitoxin SibC [EXP-IMP|W|Inferred from mutant phenotype] 18710431,26020590, Weak b4446 ECK125135301 och5 3067187 3067344 forward small regulatory RNA Och5 [EXP-IMP|W|Inferred from mutant phenotype] 26469694, Weak ECK120002623 sibD b4447 3194721 3194865 reverse small RNA SibD [EXP-IMP|W|Inferred from mutant phenotype] 12069726,18710431,19350225, Weak b4447 ECK120030085 sibE b4611 3195097 3195240 reverse small RNA SibE [EXP-IMP|W|Inferred from mutant phenotype] 18710431, Weak b4611 ECK120002511 rnpB b3123 3270216 3270592 reverse RNase P catalytic RNA component [EXP-IDA|W|Inferred from direct assay] 6197186, Weak b3123 ECK120002582 sraG b4449 3311183 3311398 forward small regulatory RNA SraG [EXP-IMP|W|Inferred from mutant phenotype] 11448770,27495318, Weak b4449 ECK120002583 arcZ b4450 3350577 3350697 forward small regulatory RNA ArcZ [EXP-IMP|W|Inferred from mutant phenotype] 20457943,23659637,26469694,28794186,30287822, Weak b4450 ECK120002584 ryhB b4451 3580922 3581016 reverse small regulatory RNA RyhB [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 11917098,12069726,14617150,19541626,22083717,22096151,23671689,26637361,27085802,27651365,27757702,28119418,30107543,30287822,30700509,31002843,32209682,33748186, Weak b4451 ECK125158033 agrA b4712 3648063 3648144 forward small RNA AgrA 27651528, b4712 ECK125158035 agrB b4713 3648294 3648375 forward small regulatory RNA AgrB [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 23408903,27651528, Weak b4713 ECK125135001 arrS b4704 3657985 3658054 reverse small regulatory RNA ArrS [EXP-IMP|W|Inferred from mutant phenotype] 24600026, Weak b4704 ECK125242747 gadF b4718 3658992 3659082 forward small regulatory RNA GadF [EXP-IMP|W|Inferred from mutant phenotype] 27588604, Weak b4718 ECK120002624 gadY b4452 3664864 3664969 forward small regulatory RNA GadY [EXP-IDA|W|Inferred from direct assay],[EXP-IEP|W|Inferred from expression pattern] 15466020,21147125,21314918,31186337, Weak b4452 ECK120002627 rdlD b4454 3700136 3700199 forward antisense regulatory RNA RdlD [EXP-IMP|W|Inferred from mutant phenotype] 12123448,15718303,32518184, Weak b4454 ECK125303721 xylZ b4834 3729386 3729545 reverse small RNA XylZ b4834 ECK125240975 rirA b4760 3808166 3808238 reverse small regulatory RNA RirA [EXP-IMP|W|Inferred from mutant phenotype],[EXP-IPI|W|Inferred from physical interaction] 27629414, Weak b4760 ECK125303709 uhpU b4829 3845730 3845995 reverse small RNA UhpU b4829 ECK120015142 istR b4616 3853118 3853257 reverse small regulatory RNA IstR-1 [EXP|W|Inferred from experiment],[EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 11448770,15620655,17499044, Weak b4616 ECK120015142 istR b4616 3853118 3853257 reverse small RNA IstR-2 [EXP|W|Inferred from experiment],[EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 11448770,15620655,17499044, Weak b4616 ECK125289862 rbsZ b4804 3937045 3937278 forward small regulatory RNA RbsZ [EXP-IMP|W|Inferred from mutant phenotype] 31761494, Weak b4804 ECK120002585 glmZ b4456 3986432 3986603 forward small regulatory RNA GlmZ [EXP-IMP|W|Inferred from mutant phenotype] 11448770,17824929,22661574,28119418,28977623,30287822,32424019, Weak b4456 ECK125145757 esrE b4707 4019978 4020229 forward small RNA EsrE b4707 ECK120002540 spf b3864 4049899 4050009 forward small regulatory RNA Spot 42 [EXP-IMP|W|Inferred from mutant phenotype],[EXP-IPI|W|Inferred from physical interaction] 12069726,12101127,1715853,18388495,23980183,26045496,30287822,6183253, Weak b3864 ECK120002586 csrC b4457 4051036 4051281 forward small regulatory RNA CsrC [EXP-IDA|W|Inferred from direct assay],[EXP-IMP|W|Inferred from mutant phenotype] 12694612,15916613,17064377,19619561,24708042,28732463,30589862, Weak b4457 ECK125230238 cpxQ b4716 4106330 4106387 forward small regulatory RNA CpxQ [EXP-IMP|W|Inferred from mutant phenotype],[EXP-IGI|W|Inferred from genetic interaction] 27048800, Weak b4716 ECK120002558 oxyS b4458 4158278 4158394 reverse small regulatory RNA OxyS [EXP-IMP|W|Inferred from mutant phenotype] 16030151,16597239,18467773,19119855,21106118,21205841,23011127,24169950,25582129,25724987,25798870,25873159,26960359,27095210,28119418,30340824,7986015,9230301, Weak b4458 ECK120002647 sroH b4691 4190327 4190487 reverse small RNA SroH b4691 ECK125303715 aceK-int b4830 4218879 4218963 forward small RNA AceK-int b4830 ECK125302577 malH b4807 4242531 4242633 reverse small regulatory RNA MalH [EXP-IMP|W|Inferred from mutant phenotype] 32356726,33043783, Weak b4807 ECK125256957 pspH b4758 4263139 4263249 forward small regulatory RNA PspH [EXP-IMP|W|Inferred from mutant phenotype] 25266388,27588604, Weak b4758 ECK120002587 ryjA b4459 4277926 4278066 reverse small RNA RyjA 11448770, b4459 ECK125256963 naRNA6 4325805 4325881 reverse naRNA6 26307168, ECK125256972 naRNA5 4325905 4325981 reverse naRNA5 26307168, ECK125256968 naRNA4 4326005 4326081 reverse naRNA4 [EXP-IMP|W|Inferred from mutant phenotype] 26307168, Weak ECK125256964 naRNA3 4326105 4326181 reverse naRNA3 26307168, ECK125256959 naRNA2 4326205 4326281 reverse naRNA2 26307168, ECK125256969 naRNA1 4326305 4326381 reverse naRNA1 26307168, ECK125303719 aspX b4825 4366839 4366951 reverse small regulatory RNA AspX [EXP-IMP|W|Inferred from mutant phenotype] 34210798, Weak b4825 ECK125135311 4441225 4441330 reverse small RNA ECK120030092 ryjB b4624 4527977 4528066 forward small RNA RyjB [EXP-IMP|W|Inferred from mutant phenotype] 31744883,34967409, Weak b4624 ECK120030093 symR b4625 4579835 4579911 forward small regulatory RNA antitoxin SymR [EXP-IMP|W|Inferred from mutant phenotype] 17462020, Weak b4625