Gene
Name:	cspH
Synonym(s):	ECK0979, G6510, b0989, cspK
Genome position(nucleotides):	1050963 <-- 1051175 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	46.95
External database links:

ASAP:	ABE-0003341
ECHOBASE:	EB4029
ECOLIHUB:	cspH
OU-MICROARRAY:	b0989
STRING:	511145.b0989
COLOMBOS:	cspH

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_1309 (cluster)	1050701	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1050700 to 1050701, where the highest frequency is at position 1049924. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[4]
promoter	cspHp8	1051205	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.735. P-value: 4.725e-5 Read more >	[ICWHO]	[5]
promoter	cspHp10	1051278	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.943. P-value: 8.190e-5 Read more >	[ICWHO]	[5]
promoter	cspHp12	1051284	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.249. P-value: 4.773e-5 Read more >	[ICWHO]	[5]
promoter	cspHp14	1051304	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.566. P-value: 4.690e-6 Read more >	[ICWHO]	[5]
promoter	cspGp	1051305	forward	nd	[AIPP], [RS-EPT-CBR]	[4], [6]
promoter	cspHp15	1051307	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 7.075. P-value: 2.232e-5 Read more >	[ICWHO]	[5]
promoter	cspHp9	1051330	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.843. P-value: 5.381e-5 Read more >	[ICWHO]	[5]
promoter	cspHp13	1051373	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.72. P-value: 2.300e-5 Read more >	[ICWHO]	[5]

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

Reference(s)
[1] Higuchi K., Yabuki T., Ito M., Kigawa T., 2020, Cold shock proteins improve E. coli cell-free synthesis in terms of soluble yields of aggregation-prone proteins., Biotechnol Bioeng 117(6):1628-1639
[2] Kram KE., Henderson AL., Finkel SE., 2020, Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival., mSystems 5(4)
[3] Nahku R., Peebo K., Valgepea K., Barrick JE., Adamberg K., Vilu R., 2011, Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture., Microbiology 157(Pt 9):2604-2610
[4] 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.
[5] 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
[6] Wang N., Yamanaka K., Inouye M., 1999, CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock., J Bacteriol 181(5):1603-9

RNA cis-regulatory element

Attenuation:	Transcriptional