Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26133
Trapped Gene
Ncoa5 (ENSMUSG00000039804)
Vector Insertion
Chr 2: 164838663 - 164848645
Public Clones (sanger)
Private Clones OST135409 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000712365 (Chr2:164848646..164848712 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TAAGGCAGCGGAAAGAAGAA Chr2:164848686..164848705 60.09 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000712365 (Chr2:164848646..164848712 -)
Downstram Exon
ENSMUSE00000709565 (Chr2:164838336..164838662 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TAAGGCAGCGGAAAGAAGAA Chr2:164848686..164848705 60.09 45 GATCACGAAAGTCCCGAAAA Chr2:164838402..164838421 60.05 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000488296 Chr2:164860183..164860279 No primer for this exon
upstream ENSMUSE00000719097 Chr2:164860183..164860288 No primer for this exon
upstream ENSMUSE00000721865 Chr2:164860183..164860317 No primer for this exon
upstream ENSMUSE00000487387 Chr2:164848646..164848712 TAAGGCAGCGGAAAGAAGAA Chr2:164848686..164848705 60.09 45
upstream ENSMUSE00000712365 Chr2:164848646..164848712 TAAGGCAGCGGAAAGAAGAA Chr2:164848686..164848705 60.09 45

*** Putative Vector Insertion (Chr 2: 164838663 - 164848645) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000240490 Chr2:164838336..164838662 GATCACGAAAGTCCCGAAAA Chr2:164838402..164838421 60.05 45
downstream ENSMUSE00000709565 Chr2:164838336..164838662 GATCACGAAAGTCCCGAAAA Chr2:164838402..164838421 60.05 45
downstream ENSMUSE00000240478 Chr2:164835951..164836087 TTCCTCCGGCAATAGTCATC Chr2:164836012..164836031 60.04 50
downstream ENSMUSE00000240471 Chr2:164834823..164834949 TCGCTGGATCTCCTCAAAAT Chr2:164834860..164834879 59.77 45
downstream ENSMUSE00000721446 Chr2:164834823..164834949 TCGCTGGATCTCCTCAAAAT Chr2:164834860..164834879 59.77 45
downstream ENSMUSE00000240463 Chr2:164829597..164829796 GAGGAAGATCAGGTCCACGA Chr2:164829708..164829727 60.2 55
downstream ENSMUSE00000711856 Chr2:164829589..164829796 GAGGAAGATCAGGTCCACGA Chr2:164829708..164829727 60.2 55
downstream ENSMUSE00000240453 Chr2:164828139..164828459 TCTCCTCGGCAGTGAGGTAT Chr2:164828189..164828208 59.83 55
downstream ENSMUSE00000720930 Chr2:164828139..164828459 TCTCCTCGGCAGTGAGGTAT Chr2:164828189..164828208 59.83 55
downstream ENSMUSE00000715773 Chr2:164828116..164828459 TCTCCTCGGCAGTGAGGTAT Chr2:164828189..164828208 59.83 55
downstream ENSMUSE00000639203 Chr2:164825868..164827671 AGAAATCACGGACCACCAAG Chr2:164826299..164826318 59.97 50
downstream ENSMUSE00000708689 Chr2:164825863..164827671 AGAAATCACGGACCACCAAG Chr2:164826299..164826318 59.97 50
downstream ENSMUSE00000714900 Chr2:164825860..164827671 AGAAATCACGGACCACCAAG Chr2:164826299..164826318 59.97 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GATGCATTTGAAGGGACGAC Chr2:164839659..164839679 60.47 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GATGCATTTGAAGGGACGAC Chr2:164839659..164839679 60.47 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AACTAATCGCCTTGCAGCAC Chr2:164839645..164839665 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 ATTTGAAGGGACCGTGACTG Chr2:164839654..164839674 59.97 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000039804