Part:BBa_K277123

3L.3_23.D3.02

3L.3_23.D3.02 is 748 bases long and is cloned into the pGem-T vector.

3L.3_23.D3.02 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. The whole synthetic chromosome may be viewed at http://macbeth.clark.jhu.edu/cgi-bin/gbrowse 3L.3_23.D3.02 is a constituent of 3L.3_23.D3 (along with 3L.3_23.D3.01, 3L.3_23.D3.03, 3L.3_23.D3.04, 3L.3_23.D3.05, 3L.3_23.D3.06, 3L.3_23.D3.07, 3L.3_23.D3.08, 3L.3_23.D3.09, 3L.3_23.D3.10, 3L.3_23.D3.11, and 3L.3_23.D3.12.)

This part contains at least part of the following features (positions offset from first base of sequence):

kind and name offset notes

ARS ARS307 (452..+967) Autonomously Replicating Sequence on Chromosome III

gene YCL005W (-307..463) Protein of unknown function%3B null mutant shows a reduced affinity for the alcian blue dye suggesting a decreased net negative charge of the cell surface

mutation_affecting_coding_sequence YCL005W_re_remove_BlpI (392..400) removal of BlpI

reverse_primer YCL005W_tagr1v1 (52..79)

Sequence (corresponds to coordinates 89253..90000 in synthetic chromosome yeast_chr3_3_23)

Sequence and Features

Assembly Compatibility:

• 10
  INCOMPATIBLE WITH RFC[10]

  Illegal EcoRI site found at 451
  Illegal XbaI site found at 19
  
• 12
  INCOMPATIBLE WITH RFC[12]

  Illegal EcoRI site found at 451
  
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal EcoRI site found at 451
  
• 23
  INCOMPATIBLE WITH RFC[23]

  Illegal EcoRI site found at 451
  Illegal XbaI site found at 19
  
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal EcoRI site found at 451
  Illegal XbaI site found at 19
  
• 1000
  COMPATIBLE WITH RFC[1000]