This is the trio of genes in M13K07 responsible for Genome Amplification
Though the genes exist in nature in M13K07, they do not yet exist in this separate form.
This is the trio of genes in M13K07 responsible for Genome Amplification. In an effort to achieve more comprehensive abstractions, genes can be grouped into families depending upon their function.
This abstraction is useful for analysis of complex functions, but there are still interactions at the base pair level that need to be resolved before it can be implemented.
This is gene II of M13K07 (Promoter, RBS, and ORF)
Though the gene and its regulatory sequences exist in nature in M13K07, they do not yet exist in this separate form.
When designing a phage, it is much more practical and effective to think of DNA in functional units than strings of regulartory and coding regions. This part combines the transcriptional and translational regions with the ORF to form a functional (where function is defined as the output of the gene).
When removed from it's place in the genome that has been determined by evolution, we can't be sure the change will be tolerated. There may be cross-talk between copied and separated elements with significant homology. Because we have removed and maintained entire portions of genes in the formation of separate genomic entities, there is also the possibility of expression of these 'partial' genes. I will address this by placing transciptional terminators and hair pins bewteen genes.
This is gene X of M13K07 (Promoter, RBS, and ORF)
When designing a phage, it is much more practical and effective to think of DNA in functional units than strings of regulatory and coding regions. This part combines the transcriptional and translational regions with the ORF to form a functional (where function is defined as the output of the gene).
When removed from its place in the genome that has been determined by evolution, we can't be sure the change will be tolerated. There may be cross-talk between copied and separated elements with significant homology. Because we have removed and maintained entire portions of genes in the formation of separate genomic entities, there is also the possibility of expression of these 'partial' genes. I will address this by placing transcriptional terminators and hair pins between genes.
This is gene V of M13K07 (Promoter, RBS, and ORF)
Double terminator consisting of BBa_B0010 and BBa_B0012
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban.
This gene is part of the bacteriophage M13 genome. It encodes a protein that is important for phage DNA replication, initiating ssDNA synthesis of the (+) strand by nicking the RF near the M13 replication origin. p10 is encoded within gII thanks to a translation re-initiation event.
need to unstuff gX from within coding sequence. RBS for downstream gV overlaps the gII stop codon.
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene II message (BBa_M13002). The part aligns with base pairs 8252-8267 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene X message (BBa_M13010). The part aligns with base pairs 480-495 in M13K07 genome. It was identified as the RBS for gene II message by Wezenbeek et al in Gene (1980) 11: 129-148
This part is from the bacteriophage M13 genome. It directs transcription of M13 gene II (BBa_M13502, BBa_M13002). Promoter identified in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
This part is from the bacteriophage M13 genome, bp 381-428 in M13K07. It directs transcription of M13 gene X (BBa_M13510, BBa_M13010). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
This gene is part of the bacteriophage M13 genome. It encodes a protein that is important for phage maturation. The protein remains in the host cytoplasm to interact with the product of gI and the OM pore (product of gIV) through which the phage ssDNA is threaded as the phage matures. GeneX protein is identical to the C-terminal portion of the gIprotein since gXprotien is normally encoded through an internal initiation of translation from the gI transcript.
This gene is part of the bacteriophage M13 genome. It encodes a single stranded DNA binding protein that is important for phage maturation.
RBS for gene V overlaps stop codon for upstream phage genes II and X.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene V message (BBa_M13005). The part aligns with base pairs 827-842 in M13K07 genome. It was identified as the RBS for the gene V message by Wezenbeek et al in Gene (1980) 11: 129-148
This part is from the bacteriophage M13 genome, bp 786-835 in M13K07. It directs transcription of M13 gene V (BBa_M13505, BBa_M13005). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
Derived from the TE terminator of T7 bacteriophage between Genes 1.3 and 1.4 <genbank>V01146</genbank>.
Transcription terminator for the E.coli RNA polymerase.
Suggested by Sri Kosuri and Drew Endy as a high efficiency terminator. The 5' end cutoff was placed immediately after the TAA stop codon and the 3' end cutoff was placed just prior to the RBS of Gene 1.4 (before AAGGAG). Use anywhere transcription should be stopped when the gene of interest is upstream of this terminator.
Transcriptional terminator consisting of a 64 bp stem-loop.
Conversion of the iGEM parts registry to SBOL2.1