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
