Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12002
Trapped Gene
Cntfr (ENSMUSG00000028444)
Vector Insertion
Chr 4: 41616861 - 41617874
Public Clones G056F02 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 29% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000416099 (Chr4:41617875..41618108 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACGTGCAGTATGAGCGTCTG Chr4:41618080..41618099 60.08 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000416099 (Chr4:41617875..41618108 -)
Downstram Exon
ENSMUSE00000632943 (Chr4:41616706..41616860 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACGTGCAGTATGAGCGTCTG Chr4:41618080..41618099 60.08 55 CTCCTCGAGGTTTCCATCAG Chr4:41616749..41616768 59.8 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000660886 Chr4:41644010..41644074 GTCTGTATCCTGGGGAGCTG Chr4:41644012..41644031 59.68 60
upstream ENSMUSE00000675346 Chr4:41644010..41644123 ATCACCAACGCTCCGTATTT Chr4:41644074..41644093 59.46 45
upstream ENSMUSE00000660882 Chr4:41642343..41642474 No primer for this exon
upstream ENSMUSE00000675345 Chr4:41642343..41642477 No primer for this exon
upstream ENSMUSE00000660885 Chr4:41633829..41633918 CCAGGAAGACTTTGGTCTGG Chr4:41633877..41633896 59.69 55
upstream ENSMUSE00000605086 Chr4:41622052..41622136 CGCTGTCTACACGCAGAAAC Chr4:41622064..41622083 59.66 55
upstream ENSMUSE00000711160 Chr4:41622052..41622136 CGCTGTCTACACGCAGAAAC Chr4:41622064..41622083 59.66 55
upstream ENSMUSE00000416099 Chr4:41617875..41618108 ACGTGCAGTATGAGCGTCTG Chr4:41618080..41618099 60.08 55

*** Putative Vector Insertion (Chr 4: 41616861 - 41617874) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000632943 Chr4:41616706..41616860 CTCCTCGAGGTTTCCATCAG Chr4:41616749..41616768 59.8 55
downstream ENSMUSE00000294045 Chr4:41610571..41610688 AAGCCCTTGGGGTAAGTGTT Chr4:41610612..41610631 59.86 50
downstream ENSMUSE00000179195 Chr4:41610233..41610399 GTGATGGCCGTAGTGTTGTG Chr4:41610231..41610250 60.03 55
downstream ENSMUSE00000179194 Chr4:41609004..41609167 CACCACGTTTTCTGGAGGAT Chr4:41609117..41609136 59.97 50
downstream ENSMUSE00000179193 Chr4:41605812..41605992 CACTCCATGTCCCAATCTCA Chr4:41605865..41605884 59.47 50
downstream ENSMUSE00000660884 Chr4:41605272..41605440 GGGTCACAGATCTTCGTGGT Chr4:41605358..41605377 59.97 55
downstream ENSMUSE00000660883 Chr4:41604532..41605183 TAGCTGCATGGTCCTCCTCT Chr4:41604932..41604951 59.97 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCTCCTATTGGATGCCTTAGC Chr4:41617829..41617850 60.07 52.38 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTGTTCGTGACTGGGAAAAC Chr4:41617808..41617829 60 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028444