Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4048
Trapped Gene
Kpna3 (ENSMUSG00000021929)
Vector Insertion
Chr 14: 62006347 - 62010000
Public Clones AQ0326 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 38% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000557946 (Chr14:62010001..62010096 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGAAATCCACCAATTGATGACC Chr14:62010056..62010077 60.06 40.91 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000557946 (Chr14:62010001..62010096 -)
Downstram Exon
ENSMUSE00000557944 (Chr14:62006261..62006346 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGAAATCCACCAATTGATGACC Chr14:62010056..62010077 60.06 40.91 GCAGAAGTTCCCGATGCTAT Chr14:62006265..62006284 59.3 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000280941 Chr14:62058560..62058711 GAGAACCACCGCATCAAGAG Chr14:62058588..62058607 60.8 55
upstream ENSMUSE00000280938 Chr14:62021835..62021879 ACGATGCGAAGACACAGAAA Chr14:62021860..62021879 59.44 45
upstream ENSMUSE00000122186 Chr14:62010593..62010682 AATGTTCCCCAAGAAGAAAGC Chr14:62010629..62010649 59.58 42.86
upstream ENSMUSE00000122183 Chr14:62010385..62010414 No primer for this exon
upstream ENSMUSE00000122184 Chr14:62010236..62010288 AGTCCAGTTGAGTGCTGTGC Chr14:62010246..62010265 59.05 55
upstream ENSMUSE00000557946 Chr14:62010001..62010096 AGAAATCCACCAATTGATGACC Chr14:62010056..62010077 60.06 40.91

*** Putative Vector Insertion (Chr 14: 62006347 - 62010000) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000557944 Chr14:62006261..62006346 GCAGAAGTTCCCGATGCTAT Chr14:62006265..62006284 59.3 50
downstream ENSMUSE00000122187 Chr14:62003940..62004026 ATGGAGGAGTCGCAGAAAAA Chr14:62003973..62003992 59.81 45
downstream ENSMUSE00000557942 Chr14:62003425..62003594 ATGTGACGTTCCGAAGGAAG Chr14:62003465..62003484 60.11 50
downstream ENSMUSE00000122199 Chr14:62002072..62002116 CACACACAAAGCTGGCAAAA Chr14:62002074..62002093 60.88 45
downstream ENSMUSE00000122188 Chr14:61993121..61993252 AAGTATGACAGCGCCCAAAC Chr14:61993196..61993215 60.14 50
downstream ENSMUSE00000363635 Chr14:61991882..61991923 CTATGTTCCCAACCGCTCTG Chr14:61991871..61991890 60.65 55
downstream ENSMUSE00000406313 Chr14:61991823..61991877 GGAAGTGGGACAGGACATCA Chr14:61991811..61991830 60.93 55
downstream ENSMUSE00000122193 Chr14:61991795..61991923 TCTGCTCATCAGTGCCAGTC Chr14:61991850..61991869 60.15 55
downstream ENSMUSE00000687117 Chr14:61991240..61991247 No primer for this exon
downstream ENSMUSE00000122189 Chr14:61989708..61989812 CTGCTGATTGCCTGCTGTTA Chr14:61989746..61989765 60.16 50
downstream ENSMUSE00000122195 Chr14:61989539..61989610 AGTTGCTAATTGCCCAAGCA Chr14:61989543..61989562 60.77 45
downstream ENSMUSE00000122196 Chr14:61989220..61989382 CATCACCAGCCATTATCAGG Chr14:61989237..61989256 58.95 50
downstream ENSMUSE00000122192 Chr14:61986965..61987059 CATGTTGCTGCAAAACTTCAA Chr14:61987005..61987025 59.9 38.1
downstream ENSMUSE00000387588 Chr14:61984023..61986566 TGCTGTCTTATCGCTTGGTG Chr14:61986375..61986394 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AATAATCGCCTTGCAGCACA Chr14:62009931..62009951 61.69 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTAAACGTGACTGGGAAAACC Chr14:62009933..62009954 58.98 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000021929