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16S Viewer

16S viewer

   Click here or on the 16S viewer sreenshot to access to the interactive application   

In this 16S viewer, developed by Era7 Bioinformatics' team, you can highligth and see the variable sub-regions, and some primers used for 16S taxonomic profiling.

The positions of the variable sub-regions were taken from Yang B, Wang Y and Qian PY, BMC Bioinformatics. 2016:

Definition of sub-regions

Referring to the previous studies [11, 12], 10 markers located in conserved regions of the 16S rRNA genes were selected to divide the full-length aligned 16S rRNA sequences into nine sub-regions (Additional file 1: Table S1). Each region starts with a conserved sequence, and the remainder is a downstream variable sequence. The tenth conserved region was the termination marker and was removed from the ninth subregion. The breakpoints of each region in the aligned data are shown in Table 1. The sub-regions were sequentially marked from V1 to V9.

Primers were extracted from http://lutzonilab.org/16s-ribosomal-dna/

See more information about 16S primers in our 16S primers page.

16S reference sequence from Escherichia coli K12 MG1655

This is the sequece of reference used in our 16S viewer in fasta format:

>ENA|U00096.3:4035531..4037072:rRNA|U00096.3:4035531..4037072:rRNA.3 Escherichia coli str. K-12 substr. MG1655 16S ribosomal RNA of rrnA operon
AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAA
GTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAA
TGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCAT
AACGTCGCAAGACCAAAGAGGGGTACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATG
GGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGA
GGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGG
GGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCT
TCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATT
GACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAG
GGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCA
GATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTC
GTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACC
GGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCA
AACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCC
CTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCA
AGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAAT
TCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAG
AATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGA
AATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGC 
CGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTC
ATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCG
ACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAAC
TCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGT
TCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGT 
AGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAA
CAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA

The primers included in the 16S viewer in the 16S E. coli sequence

ENA|U00096.3:4035531..4037072:rRNA|U00096.3:4035531..4037072:rRNA.3 Escherichia coli str. K-12 substr. MG1655 16S ribosomal RNA of rrnA operon:
aaattgaaga gtttgatcat ggctcagatt gaacgctggc ggcaggccta acacatgcaa   60
gtcgaacggt aacaggaaga agcttgcttc tttgctgacg agtggcggac gggtgagtaa  120
tgtctgggaa actgcctgat ggagggggat aactactgga aacggtagct aataccgcat  180
aacgtcgcaa gaccaaagag gggtaccttc gggcctcttg ccatcggatg tgcccagatg  240
ggattagcta gtaggtgggg taacggctca cctaggcgac gatccctagc tggtctgaga  300
ggatgaccag ccacactgga actgagacac ggtccagact cctacgggag gcagcagtgg  360
ggaatattgc acaatgggcg caagcctgat gcagccatgc cgcgtgtatg aagaaggcct  420
tcgggttgta aagtactttc agcggggagg aagggagtaa agttaatacc tttgctcatt  480
gacgttaccc gcagaagaag caccggctaa ctccgtgcca gcagccgcgg taatacggag  540
ggtgcaagcg ttaatcggaa ttactgggcg taaagcgcac gcaggcggtt tgttaagtca  600
gatgtgaaat ccccgggctc aacctgggaa ctgcatctga tactggcaag cttgagtctc  660
gtagaggggg gtagaattcc aggtgtagcg gtgaaatgcg tagagatctg gaggaatacc  720
ggtggcgaag gcggccccct ggacgaagac tgacgctcag gtgcgaaagc gtggggagca  780
aacaggatta gataccctgg tagtccacgc cgtaaacgat gtcgacttgg aggttgtgcc  840
cttgaggcgt ggcttccgga gctaacgcgt taagtcgacc gcctggggag tacggccgca  900
aggttaaaac tcaaatgaat tgacgggggc ccgcacaagc ggtggagcat gtggtttaat  960
tcgatgcaac gcgaagaacc ttacctggtc ttgacatcca cggaagtttt cagagatgag 1020
aatgtgcctt cgggaaccgt gagacaggtg ctgcatggct gtcgtcagct cgtgttgtga 1080
aatgttgggt taagtcccgc aacgagcgca acccttatcc tttgttgcca gcggtccggc 1140
cgggaactca aaggagactg ccagtgataa actggaggaa ggtggggatg acgtcaagtc 1200
atcatggccc ttacgaccag ggctacacac gtgctacaat ggcgcataca aagagaagcg 1260
acctcgcgag agcaagcgga cctcataaag tgcgtcgtag tccggattgg agtctgcaac 1320
tcgactccat gaagtcggaa tcgctagtaa tcgtggatca gaatgccacg gtgaatacgt 1380
tcccgggcct tgtacacacc gcccgtcaca ccatgggagt gggttgcaaa agaagtaggt 1440
agcttaacct tcgggagggc gcttaccact ttgtgattca tgactggggt gaagtcgtaa 1500
caaggtaacc gtaggggaac ctgcggttgg atcacctcct ta                    1542

FORWARD PRIMERS:
AGAGTTTGATCCTGGCTCAG    8F
CCAGACTCCTACGGGAGGCAGC  CC[F]
CTCCTACGGGAGGCAGCAG     357F
CAACGAGCGCAACCCT        16S.1100.F16 
GGGCTACACACGYGCWAC      1237F

REVERSE PRIMERS:
CAGCMGCCGCGGTAATWC      519R
AAACTYAAAKGAATTGACGG    907R
GAATTGACGGGGGCCCGCACAAG CD[R]
TGYACACACCGCCCGTC       1391R

Variable and conserved regions in E. coli 16S sequence

In our 16S viewer we have marked the variable sub-regions. A constant region (previous in the sequence) and a variable region compose each variable sub-region. We have marked these variable and constant regions in the Escherichia coli 16S reference sequence.

The positions of the variable regions were taken from Table S2.2 of this publication: 

ENA|U00096.3:4035531..4037072:rRNA|U00096.3:4035531..4037072:rRNA.3 Escherichia coli str. K-12 substr. MG1655 16S ribosomal RNA of rrnA operon:

aaattgaaga gtttgatcat ggctcagatt gaacgctggc ggcaggccta acacatgcaa   60

gtcgaacggt aacaggaaga agcttgcttc tttgctgacg agtggcggac gggtgagtaa  120

tgtctgggaa actgcctgat ggagggggat aactactgga aacggtagct aataccgcat  180

aacgtcgcaa gaccaaagag gggtaccttc gggcctcttg ccatcggatg tgcccagatg  240

ggattagcta gtaggtgggg taacggctca cctaggcgac gatccctagc tggtctgaga  300

ggatgaccag ccacactgga actgagacac ggtccagact cctacgggag gcagcagtgg  360

ggaatattgc acaatgggcg caagcctgat gcagccatgc cgcgtgtatg aagaaggcct  420

tcgggttgta aagtactttc agcggggagg aagggagtaa agttaatacc tttgctcatt  480

gacgttaccc gcagaagaag caccggctaa ctccgtgcca gcagccgcgg taatacggag  540

ggtgcaagcg ttaatcggaa ttactgggcg taaagcgcac gcaggcggtt tgttaagtca  600

gatgtgaaat ccccgggctc aacctgggaa ctgcatctga tactggcaag cttgagtctc  660

gtagaggggg gtagaattcc aggtgtagcg gtgaaatgcg tagagatctg gaggaatacc  720

ggtggcgaag gcggccccct ggacgaagac tgacgctcag gtgcgaaagc gtggggagca  780

aacaggatta gataccctgg tagtccacgc cgtaaacgat gtcgacttgg aggttgtgcc  840

cttgaggcgt ggcttccgga gctaacgcgt taagtcgacc gcctggggag tacggccgca  900

aggttaaaac tcaaatgaat tgacgggggc ccgcacaagc ggtggagcat gtggtttaat  960

tcgatgcaac gcgaagaacc ttacctggtc ttgacatcca cggaagtttt cagagatgag 1020

aatgtgcctt cgggaaccgt gagacaggtg ctgcatggct gtcgtcagct cgtgttgtga 1080

aatgttgggt taagtcccgc aacgagcgca acccttatcc tttgttgcca gcggtccggc 1140

cgggaactca aaggagactg ccagtgataa actggaggaa ggtggggatg acgtcaagtc 1200

atcatggccc ttacgaccag ggctacacac gtgctacaat ggcgcataca aagagaagcg 1260

acctcgcgag agcaagcgga cctcataaag tgcgtcgtag tccggattgg agtctgcaac 1320

tcgactccat gaagtcggaa tcgctagtaa tcgtggatca gaatgccacg gtgaatacgt 1380

tcccgggcct tgtacacacc gcccgtcaca ccatgggagt gggttgcaaa agaagtaggt 1440

agcttaacct tcgggagggc gcttaccact ttgtgattca tgactggggt gaagtcgtaa 1500

caaggtaacc gtaggggaac ctgcggttgg atcacctcct ta                    1542

Constant regions
V1: 69 – 99
V2: 137 – 242
V3: 433 – 497
V4: 576 – 682
V5: 822 – 879
V6: 986 – 1043
V7: 1117 – 1173
V8: 1243 – 1294
V9: 1435 - 1465
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