Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10645
Trapped Gene
Ccnt2 (ENSMUSG00000026349)
Vector Insertion
Chr 1: 129696131 - 129698182
Public Clones W048F02 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 36% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000158250 (Chr1:129695967..129696130 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGTCCAATTGGGAGATTCCT Chr1:129696044..129696063 60.13 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000158250 (Chr1:129695967..129696130 +)
Downstram Exon
ENSMUSE00000158242 (Chr1:129698183..129698253 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGTCCAATTGGGAGATTCCT Chr1:129696044..129696063 60.13 50 TCCAGTTTCGAATCCTCTTCA Chr1:129698253..129698273 59.8 42.86

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000344861 Chr1:129670741..129670962 GAAGCGGATGAAGAGCTGTC Chr1:129670889..129670908 60.1 55
upstream ENSMUSE00000710550 Chr1:129670741..129670962 GAAGCGGATGAAGAGCTGTC Chr1:129670889..129670908 60.1 55
upstream ENSMUSE00000158247 Chr1:129671678..129671759 ATATGCACCATTCCTTCACCA Chr1:129671725..129671745 60.21 42.86
upstream ENSMUSE00000158249 Chr1:129688182..129688310 ACGCTTGTCTTCATCCCCTA Chr1:129688264..129688283 59.69 50
upstream ENSMUSE00000158245 Chr1:129689935..129689995 No primer for this exon
upstream ENSMUSE00000158243 Chr1:129691832..129691894 ATCACCATTGAACACCCACA Chr1:129691840..129691859 59.66 45
upstream ENSMUSE00000320862 Chr1:129694418..129694463 GGATTTGGCACAGACATCCT Chr1:129694425..129694444 59.93 50
upstream ENSMUSE00000158250 Chr1:129695967..129696130 GGTCCAATTGGGAGATTCCT Chr1:129696044..129696063 60.13 50

*** Putative Vector Insertion (Chr 1: 129696131 - 129698182) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000158242 Chr1:129698183..129698253 TCCAGTTTCGAATCCTCTTCA Chr1:129698253..129698273 59.8 42.86
downstream ENSMUSE00000158248 Chr1:129698739..129699870 TGCACGGCTATCTTGAACAG Chr1:129698942..129698961 60.01 50
downstream ENSMUSE00000692282 Chr1:129698739..129701414 GCACCACATTCCCGTCTAGT Chr1:129700792..129700811 60 55
downstream ENSMUSE00000692276 Chr1:129699969..129702509 GCACCACATTCCCGTCTAGT Chr1:129700792..129700811 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATGTGGACCCCACGGTTAC Chr1:129696095..129696115 60.49 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCTTCTCGTGACTGGGAAAA Chr1:129696176..129696196 60.22 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026349