Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12364
Trapped Gene
Cirh1a (ENSMUSG00000041438)
Vector Insertion
Chr 8: 109422152 - 109422341
Public Clones W081C04 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 17% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000514199 (Chr8:109421960..109422151 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGACTGAACGGAGAAATCC Chr8:109422031..109422050 60.05 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000514199 (Chr8:109421960..109422151 +)
Downstram Exon
ENSMUSE00000517277 (Chr8:109422342..109422426 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGACTGAACGGAGAAATCC Chr8:109422031..109422050 60.05 50 TGCCGATCAAAATTTCTTGC Chr8:109422424..109422443 61.08 40

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000634542 Chr8:109417534..109417569 No primer for this exon
upstream ENSMUSE00000634541 Chr8:109417572..109417608 No primer for this exon
upstream ENSMUSE00000447964 Chr8:109417590..109417612 No primer for this exon
upstream ENSMUSE00000634539 Chr8:109418488..109418549 GGGTGAATTTAAGGTCCATCG Chr8:109418495..109418515 60.55 47.62
upstream ENSMUSE00000447951 Chr8:109418491..109418651 CATCAGGTATCCGGTGTGTG Chr8:109418539..109418558 59.83 55
upstream ENSMUSE00000514199 Chr8:109421960..109422151 TGGACTGAACGGAGAAATCC Chr8:109422031..109422050 60.05 50

*** Putative Vector Insertion (Chr 8: 109422152 - 109422341) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000517277 Chr8:109422342..109422426 TGCCGATCAAAATTTCTTGC Chr8:109422424..109422443 61.08 40
downstream ENSMUSE00000337709 Chr8:109424746..109424835 GTGCCAGCAGAGACTGAGAA Chr8:109424774..109424793 59.29 55
downstream ENSMUSE00000383129 Chr8:109428133..109428344 CACTCCCAGGTGTTGCCTAT Chr8:109428182..109428201 59.99 55
downstream ENSMUSE00000329996 Chr8:109430025..109430196 CTGCTGTTGGAAGTCATGGA Chr8:109430107..109430126 59.83 50
downstream ENSMUSE00000380591 Chr8:109430290..109430381 TCCATGAGAGGCCGAATAAC Chr8:109430329..109430348 60.04 50
downstream ENSMUSE00000394164 Chr8:109432105..109432201 CTCCACAGTTCCAAGTGATGC Chr8:109432180..109432200 60.71 52.38
downstream ENSMUSE00000356226 Chr8:109434842..109434906 GCAGGAGATGATCTGCGTTT Chr8:109434895..109434914 60.37 50
downstream ENSMUSE00000362234 Chr8:109436126..109436248 AGGCTATCCAGCTTCCACAC Chr8:109436183..109436202 59.31 55
downstream ENSMUSE00000390288 Chr8:109437248..109437404 AGCTTCCTTCCGACAGATGA Chr8:109437374..109437393 59.95 50
downstream ENSMUSE00000344388 Chr8:109440056..109440162 CATCTGGACTGACTGCCAAA Chr8:109440100..109440119 59.83 50
downstream ENSMUSE00000329875 Chr8:109441482..109441577 GCTGGTCAGAATGAGCAATG Chr8:109441578..109441597 59.4 50
downstream ENSMUSE00000329844 Chr8:109442520..109442705 GCTGGTGAAATCCTTGCTTC Chr8:109442598..109442617 59.82 50
downstream ENSMUSE00000329810 Chr8:109446072..109446182 TCATTTTTCGGAGGAAGTGG Chr8:109446127..109446146 60.04 45
downstream ENSMUSE00000394911 Chr8:109446765..109446987 GGTGGGAGTTGAGCAATGAT Chr8:109446853..109446872 59.93 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGGCTCTCAACTTTTGGTCA Chr8:109422137..109422157 59.42 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGGCTCTCAACTTTTGGTCA Chr8:109422137..109422157 59.42 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000041438