Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI32955
Trapped Gene
Gria4 (ENSMUSG00000025892)
Vector Insertion
Chr 9: 4537634 - 4665008
Public Clones IST12643B6 (tigm) IST10922D6 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000260428 (Chr9:4664768..4665007 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGAGAGCCAGTTCGTGCTT Chr9:4664859..4664878 59.75 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000260428 (Chr9:4664768..4665007 -)
Downstram Exon
ENSMUSE00000260405 (Chr9:4537635..4537819 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGAGAGCCAGTTCGTGCTT Chr9:4664859..4664878 59.75 55 CACTGACATGCCATCCATTC Chr9:4537738..4537757 59.92 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000455153 Chr9:4795845..4796142 CGACTTGGAGGGCATAAAAA Chr9:4796004..4796023 60.07 45
upstream ENSMUSE00000455170 Chr9:4795187..4795363 GCAGGCAGATTGTCTTGTTG Chr9:4795242..4795261 59.44 50
upstream ENSMUSE00000153926 Chr9:4793810..4793968 GAAGCCCCTTTCAATTTGGT Chr9:4793863..4793882 60.3 45
upstream ENSMUSE00000260428 Chr9:4664768..4665007 GAGAGAGCCAGTTCGTGCTT Chr9:4664859..4664878 59.75 55
upstream ENSMUSE00000260405 Chr9:4537635..4537819 GGCATGTCAGTGCGATATGT Chr9:4537752..4537771 59.56 50

*** Putative Vector Insertion (Chr 9: 4537634 - 4665008) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000260376 Chr9:4519486..4519539 GGTAGCCTTTGACGTGCTTC Chr9:4519484..4519503 59.88 55
downstream ENSMUSE00000260353 Chr9:4513223..4513381 CCAGCGATCCATTAGTTTCG Chr9:4513249..4513268 60.6 50
downstream ENSMUSE00000540099 Chr9:4503562..4503729 TTCAGCCATTACCAAGACACC Chr9:4503663..4503683 59.99 47.62
downstream ENSMUSE00000260319 Chr9:4502374..4502478 TTGAACATTCCCAGTCAGTCC Chr9:4502424..4502444 59.96 47.62
downstream ENSMUSE00000260300 Chr9:4480178..4480288 CAAGAGTAGGCGCATCTTGA Chr9:4480209..4480228 59.17 50
downstream ENSMUSE00000540096 Chr9:4472012..4472218 TGTTTCGCAATTTCAGATGC Chr9:4472096..4472115 59.82 40
downstream ENSMUSE00000540095 Chr9:4464114..4464484 CACTGGGTCCTTCTTTTCCA Chr9:4464180..4464199 60.08 50
downstream ENSMUSE00000540094 Chr9:4461906..4462104 ACCATACGCCTCCAACAATC Chr9:4462048..4462067 59.82 50
downstream ENSMUSE00000540092 Chr9:4456005..4456252 CTCCCACTTTCATCGTGTCA Chr9:4456038..4456057 59.68 50
downstream ENSMUSE00000540086 Chr9:4432773..4432887 TTGTCCAAGAGGCCTTGTTC Chr9:4432812..4432831 60.23 50
downstream ENSMUSE00000540091 Chr9:4427030..4427144 TCTAAGACGCCTGCCTCACT Chr9:4427072..4427091 60.16 55
downstream ENSMUSE00000540090 Chr9:4424320..4424454 CCTCTGCCCTGGACTTGTAA Chr9:4424312..4424331 60.25 55
downstream ENSMUSE00000455093 Chr9:4417896..4420316 CCTAAGGTACCCCACCCACT Chr9:4419889..4419908 60.1 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGATCCAAAGCTGATTACCG Chr9:4587012..4587033 60.08 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTGAAAATGCCATGGAACC Chr9:4554008..4554028 60.84 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025892