Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI32333
Trapped Gene
Akap9 (ENSMUSG00000040407)
Vector Insertion
Chr 5: 4067923 - 4069006
Public Clones IST13206C4 (tigm) IST12071C1 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000702989 (Chr5:4067740..4067922 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACCTTACGGAGCATTGTCA Chr5:4067847..4067866 59.72 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000702989 (Chr5:4067740..4067922 +)
Downstram Exon
ENSMUSE00000299823 (Chr5:4069007..4069207 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACCTTACGGAGCATTGTCA Chr5:4067847..4067866 59.72 50 GCAAGGCATCGTTTCGTAGT Chr5:4069169..4069188 60.28 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000555151 Chr5:3928186..3928490 AGCTCTGTCCGCCTCTTTCT Chr5:3928375..3928394 60.67 55
upstream ENSMUSE00000656238 Chr5:3948681..3948896 GTGAGCTCTGCTCGGAAAGT Chr5:3948799..3948818 59.75 55
upstream ENSMUSE00000656236 Chr5:3951690..3951734 No primer for this exon
upstream ENSMUSE00000555130 Chr5:3954397..3954450 GGCTGCAATTCTGTGATGAA Chr5:3954403..3954422 59.81 45
upstream ENSMUSE00000656233 Chr5:3954792..3954962 GCAAGGAGCTCAGTCCAGTC Chr5:3954827..3954846 60.14 60
upstream ENSMUSE00000656231 Chr5:3956157..3956312 AGCGAGACGGCATCATAACT Chr5:3956185..3956204 59.87 50
upstream ENSMUSE00000656229 Chr5:3957624..3957800 ACAGCACTCTCAGCCGAACT Chr5:3957649..3957668 60.21 55
upstream ENSMUSE00000719502 Chr5:3960112..3962457 CCAAGCGAGAAAAGTTGGAG Chr5:3962009..3962028 59.99 50
upstream ENSMUSE00000721568 Chr5:3960112..3962457 CCAAGCGAGAAAAGTTGGAG Chr5:3962009..3962028 59.99 50
upstream ENSMUSE00000505652 Chr5:3968580..3968793 AACTCATGCGGATCAGGTTC Chr5:3968636..3968655 60.08 50
upstream ENSMUSE00000703022 Chr5:3968580..3968793 AACTCATGCGGATCAGGTTC Chr5:3968636..3968655 60.08 50
upstream ENSMUSE00000503624 Chr5:3970664..3970737 CGACTTCAACAGGCAGTGTC Chr5:3970693..3970712 59.47 55
upstream ENSMUSE00000703021 Chr5:3970664..3970737 CGACTTCAACAGGCAGTGTC Chr5:3970693..3970712 59.47 55
upstream ENSMUSE00000381275 Chr5:3971902..3972037 TCTCAAAATCAAAGCCCAGAA Chr5:3971989..3972009 59.81 38.1
upstream ENSMUSE00000703020 Chr5:3971902..3972037 TCTCAAAATCAAAGCCCAGAA Chr5:3971989..3972009 59.81 38.1
upstream ENSMUSE00000299575 Chr5:3972756..3972841 AGAATGCCGCAAACTCTCAG Chr5:3972799..3972818 60.54 50
upstream ENSMUSE00000703019 Chr5:3972756..3972841 AGAATGCCGCAAACTCTCAG Chr5:3972799..3972818 60.54 50
upstream ENSMUSE00000299561 Chr5:3975599..3975710 AACAAAATGCGGCAGAAGAG Chr5:3975642..3975661 60.39 45
upstream ENSMUSE00000703018 Chr5:3975599..3975710 AACAAAATGCGGCAGAAGAG Chr5:3975642..3975661 60.39 45
upstream ENSMUSE00000299549 Chr5:3976128..3976326 AACCGAAGCAAACCACAGAG Chr5:3976246..3976265 60.29 50
upstream ENSMUSE00000703017 Chr5:3976128..3976326 AACCGAAGCAAACCACAGAG Chr5:3976246..3976265 60.29 50
upstream ENSMUSE00000333130 Chr5:3981118..3981214 GGTGCCCAGAAACCAGTGTA Chr5:3981152..3981171 60.95 55
upstream ENSMUSE00000703016 Chr5:3981118..3981214 GGTGCCCAGAAACCAGTGTA Chr5:3981152..3981171 60.95 55
upstream ENSMUSE00000382496 Chr5:3992046..3992138 CGAAGTGAGGCAAGAAACAA Chr5:3992060..3992079 59.05 45
upstream ENSMUSE00000703015 Chr5:3992046..3992138 CGAAGTGAGGCAAGAAACAA Chr5:3992060..3992079 59.05 45
upstream ENSMUSE00000481796 Chr5:4001405..4001758 GAGGCAACGGACAAGAATTT Chr5:4001573..4001592 59.17 45
upstream ENSMUSE00000703014 Chr5:4001405..4001758 GAGGCAACGGACAAGAATTT Chr5:4001573..4001592 59.17 45
upstream ENSMUSE00000506559 Chr5:4003561..4003782 GTTGGAAGATATGCGGCAAG Chr5:4003623..4003642 60.61 50
upstream ENSMUSE00000703013 Chr5:4003561..4003782 GTTGGAAGATATGCGGCAAG Chr5:4003623..4003642 60.61 50
upstream ENSMUSE00000184844 Chr5:4004803..4004943 CCACAGCAGTACGCAAACAC Chr5:4004922..4004941 60.37 55
upstream ENSMUSE00000703012 Chr5:4004803..4004943 CCACAGCAGTACGCAAACAC Chr5:4004922..4004941 60.37 55
upstream ENSMUSE00000299683 Chr5:4005410..4005513 TGGACATGACGATCAGGAAG Chr5:4005412..4005431 59.63 50
upstream ENSMUSE00000550041 Chr5:4005410..4005513 TGGACATGACGATCAGGAAG Chr5:4005412..4005431 59.63 50
upstream ENSMUSE00000299676 Chr5:4008344..4008549 GCACCAGAAGATTGTGCAAG Chr5:4008528..4008547 59.44 50
upstream ENSMUSE00000703011 Chr5:4008344..4008549 GCACCAGAAGATTGTGCAAG Chr5:4008528..4008547 59.44 50
upstream ENSMUSE00000184840 Chr5:4013850..4014079 CTGGAACTGCCATAGCAACA Chr5:4013877..4013896 59.86 50
upstream ENSMUSE00000703010 Chr5:4013850..4014079 CTGGAACTGCCATAGCAACA Chr5:4013877..4013896 59.86 50
upstream ENSMUSE00000299661 Chr5:4028374..4028536 CAGAGTTGATGCGTGAGTCC Chr5:4028399..4028418 59.42 55
upstream ENSMUSE00000703009 Chr5:4028374..4028536 CAGAGTTGATGCGTGAGTCC Chr5:4028399..4028418 59.42 55
upstream ENSMUSE00000517054 Chr5:4029840..4030052 TGATGGGTACTCGGATGAAA Chr5:4029847..4029866 58.92 45
upstream ENSMUSE00000703008 Chr5:4029840..4030052 TGATGGGTACTCGGATGAAA Chr5:4029847..4029866 58.92 45
upstream ENSMUSE00000416357 Chr5:4032681..4032913 AGCTGAAAAAGTCCGTGGTG Chr5:4032736..4032755 60.29 50
upstream ENSMUSE00000703007 Chr5:4032681..4032913 AGCTGAAAAAGTCCGTGGTG Chr5:4032736..4032755 60.29 50
upstream ENSMUSE00000416333 Chr5:4034748..4034867 AAGGCTGTGCCTAGAATCCA Chr5:4034820..4034839 59.84 50
upstream ENSMUSE00000703006 Chr5:4034748..4034867 AAGGCTGTGCCTAGAATCCA Chr5:4034820..4034839 59.84 50
upstream ENSMUSE00000416325 Chr5:4038529..4038705 GCTGCTATCCAAGGAGCAAC Chr5:4038582..4038601 59.99 55
upstream ENSMUSE00000703005 Chr5:4038529..4038705 GCTGCTATCCAAGGAGCAAC Chr5:4038582..4038601 59.99 55
upstream ENSMUSE00000416319 Chr5:4039239..4039343 GAGCGGGATGCTACAGACAG Chr5:4039311..4039330 60.97 60
upstream ENSMUSE00000703004 Chr5:4039239..4039343 GAGCGGGATGCTACAGACAG Chr5:4039311..4039330 60.97 60
upstream ENSMUSE00000416314 Chr5:4043918..4044070 CAGTTTCGGGAAGAACTGGA Chr5:4043945..4043964 60.22 50
upstream ENSMUSE00000703003 Chr5:4043918..4044070 CAGTTTCGGGAAGAACTGGA Chr5:4043945..4043964 60.22 50
upstream ENSMUSE00000416308 Chr5:4044799..4044978 AAACTTGGGTTTGCCATGAA Chr5:4044811..4044830 60.34 40
upstream ENSMUSE00000703002 Chr5:4044799..4044978 AAACTTGGGTTTGCCATGAA Chr5:4044811..4044830 60.34 40
upstream ENSMUSE00000416301 Chr5:4045898..4046941 AGGAGTATGTGCCGTTCCAC Chr5:4046631..4046650 60 55
upstream ENSMUSE00000703001 Chr5:4045898..4046941 AGGAGTATGTGCCGTTCCAC Chr5:4046631..4046650 60 55
upstream ENSMUSE00000416296 Chr5:4050155..4050643 AGCTACATGCCGCTGAGATT Chr5:4050495..4050514 60.01 50
upstream ENSMUSE00000703000 Chr5:4050155..4050643 AGCTACATGCCGCTGAGATT Chr5:4050495..4050514 60.01 50
upstream ENSMUSE00000416292 Chr5:4051036..4051099 CCATTCCTGAATTGGCAGAT Chr5:4051043..4051062 59.89 45
upstream ENSMUSE00000702999 Chr5:4051036..4051099 CCATTCCTGAATTGGCAGAT Chr5:4051043..4051062 59.89 45
upstream ENSMUSE00000416289 Chr5:4051210..4051310 GCAATAGAAGGCCGAGAAGA Chr5:4051251..4051270 59.55 50
upstream ENSMUSE00000702998 Chr5:4051210..4051310 GCAATAGAAGGCCGAGAAGA Chr5:4051251..4051270 59.55 50
upstream ENSMUSE00000416283 Chr5:4055161..4055352 CGGAATCTTGGCTGAAAGAG Chr5:4055258..4055277 59.95 50
upstream ENSMUSE00000702997 Chr5:4055161..4055352 CGGAATCTTGGCTGAAAGAG Chr5:4055258..4055277 59.95 50
upstream ENSMUSE00000416276 Chr5:4055592..4055768 CAGACTGGCGAGGTGAACTT Chr5:4055614..4055633 60.44 55
upstream ENSMUSE00000702996 Chr5:4055592..4055768 CAGACTGGCGAGGTGAACTT Chr5:4055614..4055633 60.44 55
upstream ENSMUSE00000416270 Chr5:4058436..4058580 CTCAGATTAATGGCGGGAAA Chr5:4058518..4058537 60.03 45
upstream ENSMUSE00000702995 Chr5:4058436..4058580 CTCAGATTAATGGCGGGAAA Chr5:4058518..4058537 60.03 45
upstream ENSMUSE00000416267 Chr5:4060282..4060495 GGTGGTTGCGGAACTAAAAA Chr5:4060394..4060413 59.97 45
upstream ENSMUSE00000702994 Chr5:4060282..4060495 GGTGGTTGCGGAACTAAAAA Chr5:4060394..4060413 59.97 45
upstream ENSMUSE00000416262 Chr5:4061138..4061288 AGGGACGGGAAAAAGAAGAA Chr5:4061263..4061282 60.05 45
upstream ENSMUSE00000702993 Chr5:4061138..4061288 AGGGACGGGAAAAAGAAGAA Chr5:4061263..4061282 60.05 45
upstream ENSMUSE00000339553 Chr5:4064071..4064739 AAGAACAAGGCCGCAACTTA Chr5:4064210..4064229 59.88 45
upstream ENSMUSE00000702992 Chr5:4064071..4064739 AAGAACAAGGCCGCAACTTA Chr5:4064210..4064229 59.88 45
upstream ENSMUSE00000299843 Chr5:4065181..4065386 AGCCACCTGGAACTTCACTG Chr5:4065183..4065202 60.3 55
upstream ENSMUSE00000702991 Chr5:4065181..4065386 AGCCACCTGGAACTTCACTG Chr5:4065183..4065202 60.3 55
upstream ENSMUSE00000299837 Chr5:4065805..4065910 No primer for this exon
upstream ENSMUSE00000702990 Chr5:4065805..4065910 No primer for this exon
upstream ENSMUSE00000299830 Chr5:4067740..4067922 CACCTTACGGAGCATTGTCA Chr5:4067847..4067866 59.72 50
upstream ENSMUSE00000702989 Chr5:4067740..4067922 CACCTTACGGAGCATTGTCA Chr5:4067847..4067866 59.72 50

*** Putative Vector Insertion (Chr 5: 4067923 - 4069006) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000299823 Chr5:4069007..4069207 GCAAGGCATCGTTTCGTAGT Chr5:4069169..4069188 60.28 50
downstream ENSMUSE00000702988 Chr5:4069007..4069207 GCAAGGCATCGTTTCGTAGT Chr5:4069169..4069188 60.28 50
downstream ENSMUSE00000299806 Chr5:4070299..4070531 GGGTGACGTCTTCACACTCC Chr5:4070413..4070432 60.57 60
downstream ENSMUSE00000702987 Chr5:4070299..4070531 GGGTGACGTCTTCACACTCC Chr5:4070413..4070432 60.57 60
downstream ENSMUSE00000407283 Chr5:4072615..4072700 CAGTCCAAATCCATCCCTGT Chr5:4072696..4072715 59.78 50
downstream ENSMUSE00000702986 Chr5:4072615..4072700 CAGTCCAAATCCATCCCTGT Chr5:4072696..4072715 59.78 50
downstream ENSMUSE00000332095 Chr5:4077186..4077315 GCCCACCAGGAGAATGATAG Chr5:4077230..4077249 59.51 55
downstream ENSMUSE00000702985 Chr5:4077186..4077315 GCCCACCAGGAGAATGATAG Chr5:4077230..4077249 59.51 55
downstream ENSMUSE00000364998 Chr5:4077828..4077967 TAGCTCCAAGTCGCCTTCTC Chr5:4077961..4077980 59.72 55
downstream ENSMUSE00000702984 Chr5:4077828..4077967 TAGCTCCAAGTCGCCTTCTC Chr5:4077961..4077980 59.72 55
downstream ENSMUSE00000403453 Chr5:4079659..4080204 TACTCGTCCAGCAGCACTGT Chr5:4080018..4080037 59.65 55
downstream ENSMUSE00000702983 Chr5:4079659..4080204 TACTCGTCCAGCAGCACTGT Chr5:4080018..4080037 59.65 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACACAGGAGCCAGCAGAGAC Chr5:4067901..4067921 60.62 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACACAGGAGCCAGCAGAGAC Chr5:4067901..4067921 60.62 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040407