Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14772
Trapped Gene
Pip5k1a (ENSMUSG00000028126)
Vector Insertion
Chr 3: 94900964 - 94910702
Public Clones (ggtc) PST15132-NL (escells) PST11211-NR (escells) IST12065H10 (tigm)
Private Clones OST426918 (lexicon) OST336333 (lexicon) OST187383 (lexicon) OST107166 (lexicon)
OST71904 (lexicon) OST59844 (lexicon) OST42174 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000637777 (Chr3:94910298..94910701 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000637777 (Chr3:94910298..94910701 -)
Downstram Exon
ENSMUSE00000672452 (Chr3:94900965..94901240 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60 GAGCAGGATCCATCTGAAGC Chr3:94901189..94901208 59.92 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000637777 Chr3:94910298..94910701 CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60
upstream ENSMUSE00000672453 Chr3:94910298..94910745 CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60
upstream ENSMUSE00000672462 Chr3:94910298..94910778 CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60
upstream ENSMUSE00000672473 Chr3:94910298..94910797 CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60
upstream ENSMUSE00000717182 Chr3:94910298..94910797 CTAGGAAGGTGCGAGACTGC Chr3:94910555..94910574 60.16 60
upstream ENSMUSE00000672452 Chr3:94900965..94901240 AAAGACGCTTCGGACAAGTG Chr3:94901127..94901146 60.43 50

*** Putative Vector Insertion (Chr 3: 94900964 - 94910702) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000566359 Chr3:94886713..94886750 No primer for this exon
downstream ENSMUSE00000672459 Chr3:94886713..94886744 CTGTGGCTCTCTTGATTCCA Chr3:94886699..94886718 58.96 50
downstream ENSMUSE00000672468 Chr3:94886713..94886747 No primer for this exon
downstream ENSMUSE00000672457 Chr3:94882412..94882438 No primer for this exon
downstream ENSMUSE00000255143 Chr3:94882024..94882104 AATCAACACTTCGATGGCCTA Chr3:94882028..94882048 59.58 42.86
downstream ENSMUSE00000566368 Chr3:94877915..94878045 GAGGACATCACGCTCTGGTT Chr3:94877934..94877953 60.27 55
downstream ENSMUSE00000566367 Chr3:94876325..94876442 CAGGCGCATAGGTCTTGAAT Chr3:94876356..94876375 60.24 50
downstream ENSMUSE00000176504 Chr3:94875812..94875964 GGGAACCACTAGCTCCAGAA Chr3:94875885..94875904 59.28 55
downstream ENSMUSE00000672467 Chr3:94874815..94874933 GACTGACCGAGGCAAGAGAT Chr3:94874795..94874814 59.41 55
downstream ENSMUSE00000672455 Chr3:94874748..94874869 GACTGACCGAGGCAAGAGAT Chr3:94874795..94874814 59.41 55
downstream ENSMUSE00000498372 Chr3:94874634..94874933 GACTGACCGAGGCAAGAGAT Chr3:94874795..94874814 59.41 55
downstream ENSMUSE00000176506 Chr3:94871983..94872188 CTGTGGAATAGAGCGCCTTC Chr3:94872019..94872038 59.98 55
downstream ENSMUSE00000176502 Chr3:94871304..94871387 TAAAGCAGGAGCCTTTCTCC Chr3:94871315..94871334 58.67 50
downstream ENSMUSE00000176499 Chr3:94869734..94869782 GCTTTCCAAGAGTGCTCCAA Chr3:94869728..94869747 60.52 50
downstream ENSMUSE00000176508 Chr3:94869343..94869427 GGAACCGCTCAGCATAGAAG Chr3:94869360..94869379 59.98 55
downstream ENSMUSE00000672466 Chr3:94869343..94869365 No primer for this exon
downstream ENSMUSE00000176497 Chr3:94868253..94868396 CTGATCGCCGAGAGAAAGAC Chr3:94868318..94868337 60.1 55
downstream ENSMUSE00000176495 Chr3:94867577..94867706 TCCAAAGGTGGAGTCTGAGG Chr3:94867636..94867655 60.23 55
downstream ENSMUSE00000176500 Chr3:94864406..94864451 TGGGTGAACTCTGACTCTGC Chr3:94864385..94864404 58.97 55
downstream ENSMUSE00000672469 Chr3:94862494..94864007 AGACAGTTACGTGGGGGTTG Chr3:94862773..94862792 59.88 55
downstream ENSMUSE00000672458 Chr3:94862491..94864007 AGACAGTTACGTGGGGGTTG Chr3:94862773..94862792 59.88 55
downstream ENSMUSE00000672460 Chr3:94862467..94864007 AGACAGTTACGTGGGGGTTG Chr3:94862773..94862792 59.88 55
downstream ENSMUSE00000672463 Chr3:94862452..94864007 AGACAGTTACGTGGGGGTTG Chr3:94862773..94862792 59.88 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGTGGACTCCTGGGTTGAT Chr3:94910664..94910684 60.36 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTATCCGAGACGTGACTGG Chr3:94907642..94907662 58.83 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 GTGCTCACGCTCCTCCTAGA Chr3:94910299..94910319 60.7 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 GTGCTCACGCTCCTCCTAGA Chr3:94910299..94910319 60.7 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028126