Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI32271
Trapped Gene
BC033915 (ENSMUSG00000034135)
Vector Insertion
Chr 9: 45935157 - 45963461
Public Clones IST11560D4 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 8% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000251521 (Chr9:45935093..45935156 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCTAGCGGAGGGGAGATATT Chr9:45935135..45935154 59.67 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000251521 (Chr9:45935093..45935156 +)
Downstram Exon
ENSMUSE00000251500 (Chr9:45963462..45963623 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCTAGCGGAGGGGAGATATT Chr9:45935135..45935154 59.67 55 TTTGAACTTCCGTCGAGCTT Chr9:45963520..45963539 59.99 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000716228 Chr9:45820955..45821213 CGCATCGGCTACTACGAGAT Chr9:45821124..45821143 60.4 55
upstream ENSMUSE00000708962 Chr9:45821083..45821213 CGCATCGGCTACTACGAGAT Chr9:45821124..45821143 60.4 55
upstream ENSMUSE00000509505 Chr9:45821107..45821213 CGCATCGGCTACTACGAGAT Chr9:45821124..45821143 60.4 55
upstream ENSMUSE00000508466 Chr9:45931300..45931416 CCGGGAGGTTCAGATAATGA Chr9:45931359..45931378 59.89 50
upstream ENSMUSE00000251521 Chr9:45935093..45935156 GCTAGCGGAGGGGAGATATT Chr9:45935135..45935154 59.67 55

*** Putative Vector Insertion (Chr 9: 45935157 - 45963461) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000251500 Chr9:45963462..45963623 TTTGAACTTCCGTCGAGCTT Chr9:45963520..45963539 59.99 45
downstream ENSMUSE00000216314 Chr9:45985955..45986079 TGGAGTGAAGAGGTTGCTGA Chr9:45985986..45986005 59.54 50
downstream ENSMUSE00000216320 Chr9:45986515..45986638 GGACATAAAGAACGGGATGC Chr9:45986637..45986656 59.39 50
downstream ENSMUSE00000535595 Chr9:46002246..46002364 TCTCCGAGCTTCATCCACTT Chr9:46002345..46002364 59.95 50
downstream ENSMUSE00000535593 Chr9:46002903..46003013 CAGCCCCATGTCTTCCATAG Chr9:46002995..46003014 60.47 55
downstream ENSMUSE00000535592 Chr9:46003249..46003392 CGGGACGCAGAGTTTTATGT Chr9:46003339..46003358 60.13 50
downstream ENSMUSE00000473458 Chr9:46003876..46003953 GAACTTGAGGGACGCTAAGG Chr9:46003924..46003943 58.93 55
downstream ENSMUSE00000472651 Chr9:46004067..46004176 TGTGCCTCCTCATTGACAAA Chr9:46004157..46004176 60.24 45
downstream ENSMUSE00000535589 Chr9:46006230..46006383 CAACAGGTTGTGCGTGAAGT Chr9:46006344..46006363 59.79 50
downstream ENSMUSE00000535588 Chr9:46006635..46006790 GCTGTAGTGTAGGCGGCTGT Chr9:46006671..46006690 60.48 60
downstream ENSMUSE00000469567 Chr9:46010083..46010153 TCCTCATCCACAGGGGTAAC Chr9:46010117..46010136 59.78 55
downstream ENSMUSE00000468488 Chr9:46012289..46012432 TGCCTTTTGGACCTATTTGC Chr9:46012318..46012337 60.07 45
downstream ENSMUSE00000471583 Chr9:46016005..46016155 GAGATGCAGGGTGTTGGAGT Chr9:46016041..46016060 60.12 55
downstream ENSMUSE00000462543 Chr9:46016801..46016926 CTGCTGGAGGATCTGATGGT Chr9:46016920..46016939 60.22 55
downstream ENSMUSE00000465486 Chr9:46017147..46017232 GTTGGTTTTCACAGGCAACC Chr9:46017207..46017226 60.4 50
downstream ENSMUSE00000467470 Chr9:46017638..46017747 GAGACGTGATCATGGCACTG Chr9:46017747..46017766 60.28 55
downstream ENSMUSE00000466468 Chr9:46018559..46018898 CCCAGGCAGGTTAGTGCTAC Chr9:46018670..46018689 59.76 60
downstream ENSMUSE00000535584 Chr9:46019753..46020645 ACTGGTCCGAAAACAGATGG Chr9:46019829..46019848 59.97 50
downstream ENSMUSE00000710331 Chr9:46019933..46020645 TGTTGCTGCCTTTTGATGAG Chr9:46020136..46020155 59.99 45
downstream ENSMUSE00000535583 Chr9:46027509..46027672 ATAGGCATCGTCGCTGTTCT Chr9:46027675..46027694 59.87 50
downstream ENSMUSE00000535581 Chr9:46028293..46028425 CATTCCTGGCAAGGTATCCA Chr9:46028322..46028341 60.85 50
downstream ENSMUSE00000535577 Chr9:46029150..46029317 CGTAGCTGGATAGCGAGAGG Chr9:46029235..46029254 60.13 60
downstream ENSMUSE00000484973 Chr9:46030152..46032269 TAGCCACTGCCTATGTGCTG Chr9:46031406..46031425 60.03 55
downstream ENSMUSE00000713173 Chr9:46030152..46030358 CCTTGGTGCCTTGGTCATAC Chr9:46030348..46030367 60.38 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTGCTGAGCCATTTCTTGT Chr9:45947162..45947182 60.4 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTGCTGAGCCATTTCTTGT Chr9:45947162..45947182 60.4 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034135