Gene
Name:	rodZ
Synonym(s):	ECK2512, EG10015, b2516, yfgA
Genome position(nucleotides):	2641831 <-- 2642844 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.54
External database links:

ASAP:	ABE-0008283
ECHOBASE:	EB0015
OU-MICROARRAY:	b2516
PortEco:	rodZ
STRING:	511145.b2516
COLOMBOS:	rodZ

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2809 (cluster)	2641405	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641404 to 2641405, where the highest frequency is at position 2639427. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[8]
promoter	ispGp1	2641880	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: -0.33. P-value: 4.644e-6 Read more >	[ICWHO]	[9]
promoter	TSS_2810	2641922	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_2811 (cluster)	2641929	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641928 to 2641929, where the highest frequency is at position 2639951. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[8]
promoter	TSS_2812	2641933	reverse	nd	[RS-EPT-CBR]	[8]
promoter	ispGp4	2641950	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.09. P-value: 2.761e-6 Read more >	[ICWHO]	[9]
promoter	ispGp5	2641954	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 6.606. P-value: 2.005e-6 Read more >	[ICWHO]	[9]
promoter	TSS_2813 (cluster)	2641985	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641984 to 2641985, where the highest frequency is at position 2640007. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[8]
promoter	TSS_2814 (cluster)	2641990	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2641989 to 2641990, where the highest frequency is at position 2640012. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[8]
promoter	TSS_2815	2641997	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_2816	2642045	reverse	nd	[RS-EPT-CBR]	[8]
promoter	rodZp1	2642932	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.284. P-value: 9.142e-5 Read more >	[ICWHO]	[9]
promoter	rodZp2	2642934	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.548. P-value: 4.330e-6 Read more >	[ICWHO]	[9]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Alyahya SA., Alexander R., Costa T., Henriques AO., Emonet T., Jacobs-Wagner C., 2009, RodZ, a component of the bacterial core morphogenic apparatus., Proc Natl Acad Sci U S A 106(4):1239-44
[2] Bendezu FO., Hale CA., Bernhardt TG., de Boer PA., 2009, RodZ (YfgA) is required for proper assembly of the MreB actin cytoskeleton and cell shape in E. coli., EMBO J 28(3):193-204
[3] Ikebe R., Kuwabara Y., Chikada T., Niki H., Shiomi D., 2018, The periplasmic disordered domain of RodZ promotes its self-interaction in Escherichia coli., Genes Cells 23(4):307-317
[4] Jacques PE., Rodrigue S., Gaudreau L., Goulet J., Brzezinski R., 2006, Detection of prokaryotic promoters from the genomic distribution of hexanucleotide pairs., BMC Bioinformatics 7:423
[5] Niba ET., Li G., Aoki K., Kitakawa M., 2010, Characterization of rodZ mutants: RodZ is not absolutely required for the cell shape and motility., FEMS Microbiol Lett 309(1):35-42
[6] Porter T., Frederick D., Johnson E., Jones PG., 2016, A requirement for cell elongation protein RodZ and cell division proteins FtsN and DedD to maintain the small rod morphology of Escherichia coli at growth temperatures near 8°C., J Gen Appl Microbiol 62(4):189-98
[7] Shiomi D., Sakai M., Niki H., 2008, Determination of bacterial rod shape by a novel cytoskeletal membrane protein., EMBO J 27(23):3081-91
[8] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[9] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78