Composite

Part:BBa_K277134

Designed by: James DiCarlo   Group: iGEM09_Johns_Hopkins-BAG   (2009-10-21)


3L.3_23.A1

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)

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 515
    Illegal EcoRI site found at 5425
    Illegal EcoRI site found at 6946
    Illegal EcoRI site found at 7817
    Illegal XbaI site found at 4918
    Illegal PstI site found at 4177
    Illegal PstI site found at 5767
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 515
    Illegal EcoRI site found at 5425
    Illegal EcoRI site found at 6946
    Illegal EcoRI site found at 7817
    Illegal PstI site found at 4177
    Illegal PstI site found at 5767
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 515
    Illegal EcoRI site found at 5425
    Illegal EcoRI site found at 6946
    Illegal EcoRI site found at 7817
    Illegal BglII site found at 1547
    Illegal BglII site found at 6926
    Illegal BglII site found at 7583
    Illegal BamHI site found at 1964
    Illegal BamHI site found at 3712
    Illegal BamHI site found at 6479
    Illegal XhoI site found at 4076
    Illegal XhoI site found at 5693
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 515
    Illegal EcoRI site found at 5425
    Illegal EcoRI site found at 6946
    Illegal EcoRI site found at 7817
    Illegal XbaI site found at 4918
    Illegal PstI site found at 4177
    Illegal PstI site found at 5767
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 515
    Illegal EcoRI site found at 5425
    Illegal EcoRI site found at 6946
    Illegal EcoRI site found at 7817
    Illegal XbaI site found at 4918
    Illegal PstI site found at 4177
    Illegal PstI site found at 5767
    Illegal NgoMIV site found at 5804
    Illegal AgeI site found at 4428
    Illegal AgeI site found at 6788
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 550
    Illegal BsaI.rc site found at 924
    Illegal BsaI.rc site found at 971


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