Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI30596
Trapped Gene
Atp9a (ENSMUSG00000027546)
Vector Insertion
Chr 2: 168516465 - 168530732
Public Clones (cmhd) IST11053F2 (tigm) IST12443B1 (tigm) IST12445B1 (tigm) IST13115D12 (tigm)
IST14024E9 (tigm) IST13092E8 (tigm) IST13660D5 (tigm) IST12443B1BBF1 (tigm)
IST12445A1 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 12% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000718900 (Chr2:168530623..168530731 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATCCGATGTTATGTGCGTGA Chr2:168530667..168530686 59.96 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000718900 (Chr2:168530623..168530731 -)
Downstram Exon
ENSMUSE00000710545 (Chr2:168516466..168516524 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATCCGATGTTATGTGCGTGA Chr2:168530667..168530686 59.96 45 CCCACCTGGATGTTTGAACT Chr2:168516466..168516485 59.82 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000679310 Chr2:168567655..168567821 ATTGATGCCACAGGGTGTGT Chr2:168567779..168567798 61.27 50
upstream ENSMUSE00000679327 Chr2:168567588..168567633 GGAGCGAGCAGGAGAGAATG Chr2:168567599..168567618 62.53 60
upstream ENSMUSE00000232466 Chr2:168567182..168567464 AAGAAGCGGGTGGACAGTAG Chr2:168567194..168567213 59.35 55
upstream ENSMUSE00000679269 Chr2:168567182..168567300 AAGAAGCGGGTGGACAGTAG Chr2:168567194..168567213 59.35 55
upstream ENSMUSE00000679313 Chr2:168567182..168567462 AAGAAGCGGGTGGACAGTAG Chr2:168567194..168567213 59.35 55
upstream ENSMUSE00000679312 Chr2:168559521..168559540 No primer for this exon
upstream ENSMUSE00000679274 Chr2:168536576..168536580 No primer for this exon
upstream ENSMUSE00000679311 Chr2:168536530..168536543 No primer for this exon
upstream ENSMUSE00000416040 Chr2:168536332..168536476 CGTACTGTCTGGTTGGGACA Chr2:168536411..168536430 59.59 55
upstream ENSMUSE00000416034 Chr2:168531695..168531808 AGTTCGTCCCAGAGATGAGG Chr2:168531728..168531747 59.25 55
upstream ENSMUSE00000679268 Chr2:168531363..168531365 No primer for this exon
upstream ENSMUSE00000716903 Chr2:168530623..168530731 ATCCGATGTTATGTGCGTGA Chr2:168530667..168530686 59.96 45
upstream ENSMUSE00000718900 Chr2:168530623..168530731 ATCCGATGTTATGTGCGTGA Chr2:168530667..168530686 59.96 45
upstream ENSMUSE00000679272 Chr2:168516466..168516524 CAAACATCCAGGTGGGAGAC Chr2:168516484..168516503 60.36 55
upstream ENSMUSE00000708606 Chr2:168516466..168516524 CAAACATCCAGGTGGGAGAC Chr2:168516484..168516503 60.36 55
upstream ENSMUSE00000710545 Chr2:168516466..168516524 CAAACATCCAGGTGGGAGAC Chr2:168516484..168516503 60.36 55

*** Putative Vector Insertion (Chr 2: 168516465 - 168530732) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000170425 Chr2:168514799..168514850 CCTCAGGAAGATCATGTCAGC Chr2:168514793..168514813 59.82 52.38
downstream ENSMUSE00000679308 Chr2:168514799..168514850 CCTCAGGAAGATCATGTCAGC Chr2:168514793..168514813 59.82 52.38
downstream ENSMUSE00000170420 Chr2:168512841..168512935 CCGAAGCTTCCAGTCTGTCT Chr2:168512858..168512877 59.6 55
downstream ENSMUSE00000679305 Chr2:168512841..168512935 CCGAAGCTTCCAGTCTGTCT Chr2:168512858..168512877 59.6 55
downstream ENSMUSE00000170433 Chr2:168509213..168509293 GAATGTCGATGTTGGGCTCT Chr2:168509217..168509236 60.08 50
downstream ENSMUSE00000679300 Chr2:168509213..168509293 GAATGTCGATGTTGGGCTCT Chr2:168509217..168509236 60.08 50
downstream ENSMUSE00000170424 Chr2:168507476..168507551 ACTGATCGGAGGGTCACTGT Chr2:168507506..168507525 59.56 55
downstream ENSMUSE00000679298 Chr2:168507476..168507551 ACTGATCGGAGGGTCACTGT Chr2:168507506..168507525 59.56 55
downstream ENSMUSE00000170422 Chr2:168501642..168501718 TGACACTCCGCAGTTCTCTG Chr2:168501646..168501665 60.18 55
downstream ENSMUSE00000679297 Chr2:168501642..168501718 TGACACTCCGCAGTTCTCTG Chr2:168501646..168501665 60.18 55
downstream ENSMUSE00000170421 Chr2:168500701..168500861 GGATCTTGGTGAGGCAGTTC Chr2:168500797..168500816 59.66 55
downstream ENSMUSE00000679296 Chr2:168500701..168500861 GGATCTTGGTGAGGCAGTTC Chr2:168500797..168500816 59.66 55
downstream ENSMUSE00000232408 Chr2:168500292..168500434 GGAATTGTGCTGGAACGAAC Chr2:168500314..168500333 60.5 50
downstream ENSMUSE00000679295 Chr2:168500292..168500434 GGAATTGTGCTGGAACGAAC Chr2:168500314..168500333 60.5 50
downstream ENSMUSE00000170440 Chr2:168498977..168499089 CCATCTCATTCTGGGTCAGG Chr2:168499044..168499063 60.47 55
downstream ENSMUSE00000679294 Chr2:168498977..168499089 CCATCTCATTCTGGGTCAGG Chr2:168499044..168499063 60.47 55
downstream ENSMUSE00000170430 Chr2:168493506..168493718 GTGTCACGTTGTGGCAGAGT Chr2:168493579..168493598 59.79 55
downstream ENSMUSE00000679293 Chr2:168493506..168493718 GTGTCACGTTGTGGCAGAGT Chr2:168493579..168493598 59.79 55
downstream ENSMUSE00000170436 Chr2:168487429..168487590 TAGGTGAACGGGAAGACCTG Chr2:168487438..168487457 60.1 55
downstream ENSMUSE00000679291 Chr2:168487429..168487590 TAGGTGAACGGGAAGACCTG Chr2:168487438..168487457 60.1 55
downstream ENSMUSE00000170432 Chr2:168479676..168479768 TCCAGCCAGTCGTTGTACTG Chr2:168479661..168479680 59.9 55
downstream ENSMUSE00000679290 Chr2:168479676..168479768 TCCAGCCAGTCGTTGTACTG Chr2:168479661..168479680 59.9 55
downstream ENSMUSE00000170423 Chr2:168478994..168479077 GGACTTCTTGGCTACCACCA Chr2:168479002..168479021 60.11 55
downstream ENSMUSE00000679289 Chr2:168478994..168479077 GGACTTCTTGGCTACCACCA Chr2:168479002..168479021 60.11 55
downstream ENSMUSE00000415943 Chr2:168478068..168478238 CAGCTTAGCCTGGACGTAGC Chr2:168478193..168478212 60.18 60
downstream ENSMUSE00000679288 Chr2:168478068..168478238 CAGCTTAGCCTGGACGTAGC Chr2:168478193..168478212 60.18 60
downstream ENSMUSE00000170439 Chr2:168475029..168475127 GCTTGTCCCCTGTTAGCATC Chr2:168475081..168475100 59.7 55
downstream ENSMUSE00000679287 Chr2:168475029..168475127 GCTTGTCCCCTGTTAGCATC Chr2:168475081..168475100 59.7 55
downstream ENSMUSE00000170438 Chr2:168474291..168474380 CTACGGAAGGCATTCAGCTC Chr2:168474312..168474331 59.98 55
downstream ENSMUSE00000679286 Chr2:168474291..168474380 CTACGGAAGGCATTCAGCTC Chr2:168474312..168474331 59.98 55
downstream ENSMUSE00000170427 Chr2:168474055..168474199 TACTGCACAGGTGAGCTTCC Chr2:168474034..168474053 59.04 55
downstream ENSMUSE00000679285 Chr2:168474055..168474199 TACTGCACAGGTGAGCTTCC Chr2:168474034..168474053 59.04 55
downstream ENSMUSE00000170431 Chr2:168473185..168473249 CAGTCGGATTCCTGGATCAT Chr2:168473185..168473204 59.89 50
downstream ENSMUSE00000679284 Chr2:168473185..168473249 CAGTCGGATTCCTGGATCAT Chr2:168473185..168473204 59.89 50
downstream ENSMUSE00000232333 Chr2:168469362..168469517 No primer for this exon
downstream ENSMUSE00000679283 Chr2:168469362..168469517 No primer for this exon
downstream ENSMUSE00000232326 Chr2:168466131..168466195 TGGTAGAGAGGAACGGATGC Chr2:168466127..168466146 60.22 55
downstream ENSMUSE00000679282 Chr2:168466131..168466195 TGGTAGAGAGGAACGGATGC Chr2:168466127..168466146 60.22 55
downstream ENSMUSE00000232318 Chr2:168465382..168465490 GAGAACACGGGAAACATCGT Chr2:168465433..168465452 59.97 50
downstream ENSMUSE00000679281 Chr2:168465382..168465490 GAGAACACGGGAAACATCGT Chr2:168465433..168465452 59.97 50
downstream ENSMUSE00000170442 Chr2:168464570..168464627 AAGAACGTCTTGTAGGACAGTGG Chr2:168464577..168464599 59.73 47.83
downstream ENSMUSE00000679279 Chr2:168464570..168464627 AAGAACGTCTTGTAGGACAGTGG Chr2:168464577..168464599 59.73 47.83
downstream ENSMUSE00000170444 Chr2:168463001..168463204 GAAGGAGATTGCCACGATGT Chr2:168463112..168463131 60.08 50
downstream ENSMUSE00000679277 Chr2:168463001..168463204 GAAGGAGATTGCCACGATGT Chr2:168463112..168463131 60.08 50
downstream ENSMUSE00000679270 Chr2:168460261..168460408 AGGTGATGACGGACACCTTC Chr2:168460333..168460352 59.97 55
downstream ENSMUSE00000416049 Chr2:168459963..168460408 AGGTGATGACGGACACCTTC Chr2:168460333..168460352 59.97 55
downstream ENSMUSE00000679275 Chr2:168459963..168460408 AGGTGATGACGGACACCTTC Chr2:168460333..168460352 59.97 55
downstream ENSMUSE00000679315 Chr2:168459938..168460408 AGGTGATGACGGACACCTTC Chr2:168460333..168460352 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATCCGTGAGGCAGTAGAGGA Chr2:168521686..168521706 59.83 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATCCGTGAGGCAGTAGAGGA Chr2:168521686..168521706 59.83 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027546