Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9776
Trapped Gene
Cirh1a (ENSMUSG00000041438)
Vector Insertion
Chr 8: 109432202 - 109434841
Public Clones XH230 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 54% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000394164 (Chr8:109432105..109432201 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCATCACTTGGAACTGTGGA Chr8:109432158..109432177 59.68 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000394164 (Chr8:109432105..109432201 +)
Downstram Exon
ENSMUSE00000356226 (Chr8:109434842..109434906 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCATCACTTGGAACTGTGGA Chr8:109432158..109432177 59.68 50 GCAGGAGATGATCTGCGTTT Chr8:109434895..109434914 60.37 50

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
upstream ENSMUSE00000517277 Chr8:109422342..109422426 TGAAGATGGCTCCGTGAAAC Chr8:109422350..109422369 61.19 50
upstream ENSMUSE00000337709 Chr8:109424746..109424835 GTCGCAGCTGGTTCCTTAGA Chr8:109424787..109424806 60.54 55
upstream ENSMUSE00000383129 Chr8:109428133..109428344 ATAGGCAACACCTGGGAGTG Chr8:109428160..109428179 59.99 55
upstream ENSMUSE00000329996 Chr8:109430025..109430196 AGCTGGTGTCCATGACTTCC Chr8:109430077..109430096 60.12 55
upstream ENSMUSE00000380591 Chr8:109430290..109430381 GCTGCTCTCCGAAAGATCAC Chr8:109430352..109430371 60.1 55
upstream ENSMUSE00000394164 Chr8:109432105..109432201 GCATCACTTGGAACTGTGGA Chr8:109432158..109432177 59.68 50

*** Putative Vector Insertion (Chr 8: 109432202 - 109434841) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 AAAACTGCGTGACTGGGAAA Chr8:109432246..109432266 60.67 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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