3L.3_23.A1 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns,repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1 is comprised of and must be constructed from the parts 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12. This part wholly contains the following features (positions offset from first base of sequence): kind and name offset notes loxP_site loxpsym_delyeast103_25(chrIII)3000..3001 (3000..3033) gene YCL073C (413..2260) Protein of unconfirmed function%3B displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins%3B coding sequence 98% identical to that of YKR106W loxP_site loxPsym_YCL063W (8632..8665) gene YCL069W (3672..5048) Permease of basic amino acids in the vacuolar membrane ARS ARS320 (5534..6341) Autonomously Replicating Sequence on Chromosome III loxP_site loxpsym_delyeast_chr3_3_17(chrIII)5500..9500 (5500..5533) reverse_primer YCL063W_tagr1v1 (8223..8250) loxP_site loxpsym_delyeast103_24(chrIII)1..6100 (1..34) mutation_affecting_coding_sequence YCL069W_re_remove_AlwNI (4680..4691) removal of AlwNI forward_primer YCL064C_tagf1v1 (5973..6000) loxP_site loxPsym_YCL069W (5052..5085) gene YCL063W (7357..8628) Protein involved in vacuole inheritance%3B acts as a vacuole-specific receptor for myosin Myo2p forward_primer YCL063W_tagf1v1 (7971..7998) reverse_primer YCL064C_tagr1v1 (6216..6243) ARS ARS301 (5146..5401) Inactive replication origin associated with the silent mating type locus HML%2C where it functions as a transcriptional silencer gene YCL064C (5865..6947) Catabolic L-serine (L-threonine) deaminase%2C catalyzes the degradation of both L-serine and L-threonine%3B required to use serine or threonine as the sole nitrogen source%2C transcriptionally induced by serine and threonine Sequence (corresponding to coordinates 1..8879 in synthetic chromosome yeast_chr3_3_23)
Constructed using USER assembly method described in RFC38
3L.3_23.A1.01 is 744 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.01 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.01 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL073C (413..+2260) Protein of unconfirmed function%3B displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins%3B coding sequence 98% identical to that of YKR106W loxP_site loxpsym_delyeast103_24(chrIII)1..6100 (1..34) Sequence (the first 744 bases correspond to coordinates 1..744 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.02 is 731 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.02 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.02 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL073C (-320..+1527) Protein of unconfirmed function%3B displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins%3B coding sequence 98% identical to that of YKR106W Sequence (the first 731 bases correspond to coordinates 734..1464 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.03 is 779 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.03 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.03 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL073C (-1042..+805) Protein of unconfirmed function%3B displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins%3B coding sequence 98% identical to that of YKR106W Sequence (the first 779 bases correspond to coordinates 1456..2234 in synthetic chromosome yeast_chr3_3_23)
Constructed using overlap extension PCR proto descibed in RFC38
3L.3_23.A1.04 is 757 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.04 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.04 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL073C (-1814..33) Protein of unconfirmed function%3B displays a topology characteristic of the Major Facilitators Superfamily of membrane proteins%3B coding sequence 98% identical to that of YKR106W Sequence (the first 757 bases correspond to coordinates 2228..2984 in synthetic chromosome yeast_chr3_3_23)
Constructed using overlap extension PCR protocol described in RFC38
3L.3_23.A1.05 is 751 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.05 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.05 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes loxP_site loxpsym_delyeast103_25(chrIII)3000..3001 (27..60) gene YCL069W (699..+2075) Permease of basic amino acids in the vacuolar membrane Sequence (the first 751 bases correspond to coordinates 2974..3724 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.06 is 754 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.06 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.06 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL069W (-43..+1333) Permease of basic amino acids in the vacuolar membrane Sequence (the first 754 bases correspond to coordinates 3716..4469 in synthetic chromosome yeast_chr3_3_23):
3L.3_23.A1.07 is 689 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.07 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.07 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL069W (-788..588) Permease of basic amino acids in the vacuolar membrane mutation_affecting_coding_sequence YCL069W_re_remove_AlwNI (220..231) removal of AlwNI loxP_site loxPsym_YCL069W (592..625) ARS ARS301 (686..+941) Inactive replication origin associated with the silent mating type locus HML%2C where it functions as a transcriptional silencer Sequence (the first 689 bases correspond to coordinates 4461..5149 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.08 is 748 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.08 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.08 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.09, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes ARS ARS320 (394..+1201) Autonomously Replicating Sequence on Chromosome III loxP_site loxpsym_delyeast_chr3_3_17(chrIII)5500..9500 (360..393) ARS ARS301 (6..261) Inactive replication origin associated with the silent mating type locus HML%2C where it functions as a transcriptional silencer gene YCL064C (725..+1807) Catabolic L-serine (L-threonine) deaminase%2C catalyzes the degradation of both L-serine and L-threonine%3B required to use serine or threonine as the sole nitrogen source%2C transcriptionally induced by serine and threonine Sequence (the first 748 bases correspond to coordinates 5141..5888 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.09 is 744 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.09 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.09 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.10, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes ARS ARS320 (-345..462) Autonomously Replicating Sequence on Chromosome III forward_primer YCL064C_tagf1v1 (94..121) reverse_primer YCL064C_tagr1v1 (337..364) gene YCL064C (-14..+1068) Catabolic L-serine (L-threonine) deaminase%2C catalyzes the degradation of both L-serine and L-threonine%3B required to use serine or threonine as the sole nitrogen source%2C transcriptionally induced by serine and threonine Sequence (the first 744 bases correspond to coordinates 5880..6623 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.10 is 832 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.10 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.10 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.11, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL063W (743..+2014) Protein involved in vacuole inheritance%3B acts as a vacuole-specific receptor for myosin Myo2p gene YCL064C (-749..333) Catabolic L-serine (L-threonine) deaminase%2C catalyzes the degradation of both L-serine and L-threonine%3B required to use serine or threonine as the sole nitrogen source%2C transcriptionally induced by serine and threonine Sequence (the first 832 bases correspond to coordinates 6615..7446 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.11 is 656 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.11 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.11 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, and 3L.3_23.A1.12.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes gene YCL063W (-80..+1191) Protein involved in vacuole inheritance%3B acts as a vacuole-specific receptor for myosin Myo2p forward_primer YCL063W_tagf1v1 (534..561) Sequence (the first 656 bases correspond to coordinates 7438..8093 in synthetic chromosome yeast_chr3_3_23)
3L.3_23.A1.12 is 795 bases long and is cloned into the pGem-T vector. 3L.3_23.A1.12 was designed as a piece of synthetic chromosome 3 with the goal of minimizing and stabilizing that chromosome and to that end has had any tRNAs, introns, repeat regions, and transposons that were present in the wildtype chromosome removed. In addition a very few gene sequences were slightly recoded to add or remove restriction enzyme recognition sites to facilitate assembly; most gene sequences were slightly recoded to introduce unique primers for diagnostic PCR amplification, and some gene sequences were slightly recoded to address the distribution of stop codon usage. 3L.3_23.A1.12 is a constituent of 3L.3_23.A1 (along with 3L.3_23.A1.01, 3L.3_23.A1.02, 3L.3_23.A1.03, 3L.3_23.A1.04, 3L.3_23.A1.05, 3L.3_23.A1.06, 3L.3_23.A1.07, 3L.3_23.A1.08, 3L.3_23.A1.09, 3L.3_23.A1.10, and 3L.3_23.A1.11.) This part contains at least part of the following features (positions offset from first base of sequence): kind and name offset notes loxP_site loxPsym_YCL063W (548..581) reverse_primer YCL063W_tagr1v1 (139..166) gene YCL063W (-727..544) Protein involved in vacuole inheritance%3B acts as a vacuole-specific receptor for myosin Myo2p Sequence (the first 795 bases correspond to coordinates 8085..8879 in synthetic chromosome yeast_chr3_3_23)
Conversion of the iGEM parts registry to SBOL2.1