Tools
The ORFeome Collaboration has the following tools available for public use:
- Order ORF clones
- Clone status search - find out if there is an ORF clone for your favorite gene
- Get library/vector information
- Plate availability query
- ORFeome Query (OQ) - SQL-type query provides information about ORF clones and libraries
- Download data via FTP
Other ORFeome Tools:
The following tools are from external
sources; the data available may extend
and/or overlap with that available from internal sources.
- MGC/ORFeome Genome Browser (UCSC)
- Search the DFCI-CCSB horfeome database (DFCI-CCSB)
- Search the FLEXGene database (HIP)
- Search the IMAGE IQ, which provides access to IMAGE clone data.
OC Collaborator Vector and Library Information
| Center | Vector | 3' End of attL1.x + seq to ATG | 3' End of ORF to attL2.x |
|---|---|---|---|
| MGC |
pENTR223.1 (SpnR) |
-G TAC AAA AAA GCA GAA GGG CCG
TCA AGG CCC ACC ATG- Y K K A E G P S R P T |
-NNN GGC CTC ATG GGC CCA GCT TTC TTG TAC- G L M G P A F L Y |
| MGC (GENEART) |
pENTR223.1 (SpnR) |
-G TAC AAA AAA GCA GAA GGG CCG
TCA AGG CCC ACC ATG- Y K K A E G P S R P T |
-TAA GGC CTC ATG GGC CCA GCT TTC TTG TAC- * G L M G P A F L Y |
| MGC (GENEART) |
pENTR223.1 (SpnR) |
-G TAC AAA AAA GCA GAA GGG CCG
TCA AGG CCC ACC ATG- Y K K A E G P S R P T |
-TCA GGC CTC ATG GGC CCA GCT TTC TTG TAC- S G L M G P A F L Y |
|
WTSI
CMO |
pENTR223 (SpnR) |
-G TAC AAA AAA GTT GGC ACC ATG- Y K K V G T |
-NNN CCA ACT TTC TTG TAC- P T F L Y |
|
DF-CCSB
CMO |
pENTR223 (SpnR) |
-G TAC AAA AAA GTT GGC ACC ATG- Y K K V G T |
-NNN TTG CCA ACT TTC TTG TAC- L P T F L Y |
|
DF-CCSB
CMO |
pENTR223 (SpnR) |
-G TAC AAA AAA GTT GGC ATG- Y K K V G |
-NNN TTG CCA ACT TTC TTG TAC- L P T F L Y |
| HIP | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TAG GAC CCA GCT TTC TTG TAC- * D P A F L Y ( closed/open with TAG suppr. ) |
| HIP | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TTG GAC CCA GCT TTC TTG TAC- L D P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TGA ATC CAC CCA GCT TTC TTG TAC- * I P P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TGG ATC CAC CCA GCT TTC TTG TAC- W I H P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-AAG CTT GAC CCA GCT TTC TTG TAC- K L D P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TGT ATT CAC CCA GCT TTC TTG TAC- C I H P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCT GGC ACC ATG- Y K K A G T |
-GGC GAC CCA GCT TTC TTG TAC- G D P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TAG CTT GAC CCA GCT TTC TTG TAC- * L D P A F L Y |
| DKFZ | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T |
-TGA ATT CAC CCA GCT TTC TTG TAC- * I P P A F L Y |
| DKFZ | pENTR201 (KnR) |
-G TAC AAA AAA GCT GGC ACC ATG- Y K K A G T |
-GGC GAC CCA GCT TTC TTG TAC- G D P A F L Y |
| DKFZ | pENTR201 (KnR) |
-G TAC AAA AAA GCT GGC ACC ACC ATG- Y K K A G T |
-TAG GGC GAC CCA GCT TTC TTG TAC- * G D P A F L Y |
| DKFZ | pENTR/D-TOPO (KnR) |
-G TAC AAA AAA GCA GGC TCC GCG
GCC GCC CCC TTC ACC ATG- Y K K A G S A A A P F T |
-AGG GGT GGG CGC GCC GAC CCA GCT TTC TTG TAC- K G G R A D P A F L Y |
| Kazusa | pENTR201 (KnR) |
-G TAC AAA AAA GCA GGC TTC GAA GGA GAT AGA ACC ATG- Y K K A G F E G D R T |
-TAA GTA GAC CCA GCT TTC TTG TAC- * V D P A F L Y -TAC GTA GAC CCA GCT TTC TTG TAC- Y V D P A F L Y |
| Invitrogen | pENTR221 (KnR) |
-G TAC AAA AAA GCA GGC ACC ATG- Y K K A G T |
-TAG AAC CCA GCT TTC TTG TAC- * T P A F L Y |
| Invitrogen | pENTR201 (KnR) |
-G TAC AAA AAA GCA GGC TTC GAA
GGA GAT AGA ACC ATG- Y K K A G F E G D R T |
-TAG GAC CCA GCT TTC TTG TAC- * D P A F L Y ( closed/open with TAG suppr. ) |
Cloning Method Overview (CMO)
Wellcome Trust Sanger InstituteORFs flanked by att sites were amplified from fully sequence verified cDNA clones in two rounds of PCR. Amplified products were separated by agarose gel electrophoresis, excised, purified and recombined into pDONR223 using BP® clonase. After full sequence verification, only clones which exactly matched the original cDNA and att sequences were accepted.
Dana Farber Cancer InstituteMGC clones were cherry-picked into a non-redundant set and 8 ul of each clone was inoculated in 1 ml LB containing either ampicillin (100 ug/ml) or chloramphenicol (34 ug/ml) depending on the MGC vector. A BP recombinational reaction contains 2 ul of 5 X BP3 buffer; 2 ul of BP clonase; 1 ul of pDONR223 (150 ng/uL); 2 ul of PCR product (2-200 ng/uL); 3 uL H2O. The 5 X BP3 buffer consists of 100 mM Tris-Cl (pH 7.5); 20 mM EDTA; 30 mM spermidine-HCL; 25% glycerol; 225 mM NaCl. LR reactions we performed as described previously with minor changes (Reboul et al. 2003, Rual et al. 2004). BP products were transformed into liquid cultures of E. coli, with antibiotic selection of spectinomycin at 50 ug/mL.