# STOCKHOLM 1.0
#=GF ID naRNA4
#=GF AC RF02564
#=GF DE Nucleoid-associated noncoding RNA 4 (CssrE)
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 59.5
#=GF NC 59.4
#=GF TC 59.5
#=GF SE Argasinska J
#=GF SS Published; PMID:26307168
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF DR GO; 0036386; bacterial nucleoid DNA packaging;
#=GF DR GO; 0043590; bacterial nucleoid;
#=GF DR GO; 0005515; protein binding;
#=GF RN [1]
#=GF RM 26307168
#=GF RT A New Noncoding RNA Arranges Bacterial Chromosome Organization.
#=GF RA Qian Z, Macvanin M, Dimitriadis EK, He X, Zhurkin V, Adhya S
#=GF RL MBio. 2015; [Epub ahead of print]
#=GF RN [2]
#=GF RM 21483688
#=GF RT An integrated approach for finding overlooked genes in Shigella.
#=GF RA Peng J, Yang J, Jin Q
#=GF RL PLoS One. 2011;6:e18509.
#=GF CC In E. coli small RNA transcribed from repeated extragenic palindromic
#=GF CC element (REP325) called nucleoid-associated ncRNA 4 (nRNA4) collaborates
#=GF CC HU protein in condensing the DNA. The secondary structure but not the
#=GF CC sequence of the RNA is important in nucleoid condensation. Also identified
#=GF CC in Shigella as CssrE [2]. 
#=GF WK Nucleoid
#=GF SQ 3

AM946981.2/4233354-4233278 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAACGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
CP000819.1/4304795-4304719 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAAUGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
AP009048.1/4330759-4330683 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAACGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
#=GC SS_cons               :<<<<<<<--<<<<____>>>>-->>>>>>>:::::::::::::<<<<<<<<-<<<<<____>>>>>->>>>>>>>:
#=GC RF                    GGCCGGauAAGGCGUUUACGCCGCauCCGGCAAcGGUGCCGACUGCCuGaugCGaCGCUUGCGCGuCUuauCaGGCC
//
