Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31286
Trapped Gene
AC153521.7 (ENSMUSG00000078446)
Vector Insertion
Chr 10: 55934755 - 55944532
Public Clones IST14103A9 (tigm) IST14633C8 (tigm) IST11094G2 (tigm) IST13172F11 (tigm)
IST13682A10 (tigm) IST13750C10 (tigm) IST11094G2 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 50% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000576249 (Chr10:55944370..55944531 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GACACGGTTGTTCAGCATGT Chr10:55944397..55944416 59.6 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000576249 (Chr10:55944370..55944531 -)
Downstram Exon
ENSMUSE00000513428 (Chr10:55934756..55934924 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GACACGGTTGTTCAGCATGT Chr10:55944397..55944416 59.6 50 TCACTGTCGGAGCAGTTGTC Chr10:55934750..55934769 60.03 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000576250 Chr10:55948284..55948474 GTGGTTGCGGAGATTTGACT Chr10:55948449..55948468 60.12 50
upstream ENSMUSE00000576249 Chr10:55944370..55944531 GACACGGTTGTTCAGCATGT Chr10:55944397..55944416 59.6 50
upstream ENSMUSE00000513428 Chr10:55934756..55934924 GACAACTGCTCCGACAGTGA Chr10:55934772..55934791 60.03 55

*** Putative Vector Insertion (Chr 10: 55934755 - 55944532) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000512496 Chr10:55921694..55921762 CAACCGTAGTTTCCCTTGACA Chr10:55921708..55921728 60.02 47.62
downstream ENSMUSE00000507487 Chr10:55918241..55918366 GGGAGCTGAGCACAATGTTT Chr10:55918306..55918325 60.26 50
downstream ENSMUSE00000502099 Chr10:55916624..55916672 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTAGAGCTGAGGGGATGCAG Chr10:55941524..55941544 59.97 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAACATGTTGGGGCGTGACT Chr10:55941474..55941494 61.35 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000078446