Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14821
Trapped Gene
Xrcc1 (ENSMUSG00000051768)
Vector Insertion
Chr 7: 25356171 - 25357227
Public Clones PST10341-NL (escells) PST10341-NR (escells)
Private Clones not available
Severity of mutation (?) Insertion after 85% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000414942 (Chr7:25356034..25356170 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GACAGTGAGACCCCCTCAGA Chr7:25356122..25356141 60.24 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000414942 (Chr7:25356034..25356170 +)
Downstram Exon
ENSMUSE00000414939 (Chr7:25357228..25357318 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GACAGTGAGACCCCCTCAGA Chr7:25356122..25356141 60.24 60 AAGTGTTTGCCCTCGAAGAA Chr7:25357252..25357271 59.85 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000356098 Chr7:25332213..25332378 GCTGCAACCCTTCTTCTTCA Chr7:25332274..25332293 60.52 50
upstream ENSMUSE00000199591 Chr7:25332809..25332901 TCTTCTCAAGGCGGACACTT Chr7:25332826..25332845 59.99 50
upstream ENSMUSE00000199606 Chr7:25344755..25344871 AAGGAGGAGCAGATCCACAG Chr7:25344761..25344780 59.4 55
upstream ENSMUSE00000415211 Chr7:25350555..25350713 GTGTTCGCATTTTTGGACCT Chr7:25350619..25350638 59.98 45
upstream ENSMUSE00000415208 Chr7:25351238..25351312 CCATACGGCCTGAGTTTTGT Chr7:25351244..25351263 59.99 50
upstream ENSMUSE00000415205 Chr7:25351408..25351519 GGAGGATGACAGTGCCAACT Chr7:25351449..25351468 60.12 55
upstream ENSMUSE00000415202 Chr7:25351877..25351986 ACTGCAGGCCTCTAGTGCAG Chr7:25351920..25351939 60.75 60
upstream ENSMUSE00000415199 Chr7:25352058..25352163 CACCCTCAAGAGACCCAAAT Chr7:25352144..25352163 58.99 50
upstream ENSMUSE00000415192 Chr7:25352333..25352591 TCTACCCCAGCACAGAGAGC Chr7:25352371..25352390 60.56 60
upstream ENSMUSE00000414958 Chr7:25352829..25352945 CCGGATTGTGCGTAAAGAGT Chr7:25352880..25352899 60.13 50
upstream ENSMUSE00000414953 Chr7:25355235..25355328 GACGAAGGGGACTCTCACAG Chr7:25355269..25355288 59.83 60
upstream ENSMUSE00000414951 Chr7:25355468..25355597 GGACCCCAGGACAATAGTGA Chr7:25355558..25355577 59.78 55
upstream ENSMUSE00000414945 Chr7:25355891..25355945 ACACCGAGGATGAACTGAGG Chr7:25355924..25355943 60.11 55
upstream ENSMUSE00000414942 Chr7:25356034..25356170 GACAGTGAGACCCCCTCAGA Chr7:25356122..25356141 60.24 60

*** Putative Vector Insertion (Chr 7: 25356171 - 25357227) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000414939 Chr7:25357228..25357318 AAGTGTTTGCCCTCGAAGAA Chr7:25357252..25357271 59.85 45
downstream ENSMUSE00000414933 Chr7:25358073..25358148 ACTGGACCCGCTCATTCATA Chr7:25358110..25358129 60.48 50
downstream ENSMUSE00000415215 Chr7:25358244..25358453 CATAGAGCTGATGGGGGAGT Chr7:25358340..25358359 59.12 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GACAGTGAGACCCCCTCAGA Chr7:25356123..25356143 60.24 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTAGGTCCCCTGGGTCTCTC Chr7:25356203..25356223 60.07 65 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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