Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1125
Trapped Gene
Ctdspl2 (ENSMUSG00000033411)
Vector Insertion
Chr 2: 121795016 - 121803066
Public Clones AQ0546 (sanger) AL0220 (sanger) AC0247 (sanger) CC0180 (sanger)
AL0368 (sanger) AL0236 (sanger) AY0480 (sanger) AL0241 (sanger)
XB557 (baygenomics) RRX125 (baygenomics) RRU391 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000395240 (Chr2:121794806..121795015 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAACACGGAAGGCTTCTCAG Chr2:121794840..121794859 59.99 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000395240 (Chr2:121794806..121795015 +)
Downstram Exon
ENSMUSE00000349038 (Chr2:121803067..121803205 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAACACGGAAGGCTTCTCAG Chr2:121794840..121794859 59.99 55 ACTCCGCTTCGAAGGATTTT Chr2:121803099..121803118 60.21 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000641657 Chr2:121781737..121782353 GAGGGATAAGCGGGAAAGAC Chr2:121782268..121782287 60.04 55
upstream ENSMUSE00000641653 Chr2:121782147..121782353 GAGGGATAAGCGGGAAAGAC Chr2:121782268..121782287 60.04 55
upstream ENSMUSE00000684445 Chr2:121782395..121782493 GTCCGTAGGCATGCACTGTT Chr2:121782466..121782485 61.13 55
upstream ENSMUSE00000395240 Chr2:121794806..121795015 GAACACGGAAGGCTTCTCAG Chr2:121794840..121794859 59.99 55
upstream ENSMUSE00000707978 Chr2:121794806..121795015 GAACACGGAAGGCTTCTCAG Chr2:121794840..121794859 59.99 55
upstream ENSMUSE00000684442 Chr2:121794818..121795015 GAACACGGAAGGCTTCTCAG Chr2:121794840..121794859 59.99 55

*** Putative Vector Insertion (Chr 2: 121795016 - 121803066) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000349038 Chr2:121803067..121803205 ACTCCGCTTCGAAGGATTTT Chr2:121803099..121803118 60.21 45
downstream ENSMUSE00000390724 Chr2:121804628..121804777 CTCGGAGGACTACCAGAGCA Chr2:121804715..121804734 60.54 60
downstream ENSMUSE00000684451 Chr2:121804631..121804777 CTCGGAGGACTACCAGAGCA Chr2:121804715..121804734 60.54 60
downstream ENSMUSE00000372909 Chr2:121806888..121807100 GTAAGCCGCTCCATTAGCTG Chr2:121807012..121807031 60 55
downstream ENSMUSE00000410609 Chr2:121812685..121812763 GGCTGACGAGTACCCACTCT Chr2:121812722..121812741 59.33 60
downstream ENSMUSE00000292135 Chr2:121814526..121814637 AGAGGCGGAACATGTTTGAT Chr2:121814558..121814577 59.56 45
downstream ENSMUSE00000292126 Chr2:121819082..121819168 AGTGAGCGCTGCATCTTCTA Chr2:121819138..121819157 58.93 50
downstream ENSMUSE00000641652 Chr2:121819082..121819255 AGTGAGCGCTGCATCTTCTA Chr2:121819138..121819157 58.93 50
downstream ENSMUSE00000641655 Chr2:121819406..121819492 CCCAGTCTTAACGTGGCAAG Chr2:121819470..121819489 60.68 55
downstream ENSMUSE00000365988 Chr2:121829637..121829699 TCCAGGAATTCCCTGAAGAA Chr2:121829680..121829699 59.6 45
downstream ENSMUSE00000292117 Chr2:121829804..121829883 No primer for this exon
downstream ENSMUSE00000292112 Chr2:121832599..121832725 AGGCTTGTGGTGAGTTGTCA Chr2:121832717..121832736 59.31 50
downstream ENSMUSE00000292105 Chr2:121833457..121833552 GCTTCTCCAGAAATGGAATCA Chr2:121833543..121833563 59.26 42.86
downstream ENSMUSE00000684441 Chr2:121836299..121839327 CAGCATAAAGATGCCCAGGT Chr2:121838307..121838326 60.1 50
downstream ENSMUSE00000684444 Chr2:121836299..121836459 AGCAAATCATGCAATCGAAA Chr2:121836354..121836373 59.26 35
downstream ENSMUSE00000684450 Chr2:121836299..121838124 GAAAGCAAGACGGGGTACAA Chr2:121836485..121836504 60.11 50
downstream ENSMUSE00000684457 Chr2:121836299..121837903 GAAAGCAAGACGGGGTACAA Chr2:121836485..121836504 60.11 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAAAGGAAGCACACCCAAGG Chr2:121797998..121798018 60.1 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAAAGGAAGCACACCCAAGG Chr2:121797998..121798018 60.1 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000033411