Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI2605
Trapped Gene
Ddx42 (ENSMUSG00000020705)
Vector Insertion
Chr 11: 106098438 - 106099821
Public Clones XR0874 (sanger) XR0882 (sanger) IST13558A7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 41% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000327917 (Chr11:106098309..106098437 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000327917 (Chr11:106098309..106098437 +)
Downstram Exon
ENSMUSE00000327910 (Chr11:106099822..106099921 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000367069 Chr11:106078240..106078470 No primer for this exon
upstream ENSMUSE00000360968 Chr11:106085395..106085632 No primer for this exon
upstream ENSMUSE00000385834 Chr11:106086098..106086248 No primer for this exon
upstream ENSMUSE00000328098 Chr11:106090077..106090138 No primer for this exon
upstream ENSMUSE00000328092 Chr11:106091644..106091680 No primer for this exon
upstream ENSMUSE00000328087 Chr11:106092446..106092595 No primer for this exon
upstream ENSMUSE00000380490 Chr11:106094120..106094224 No primer for this exon
upstream ENSMUSE00000327928 Chr11:106096166..106096285 No primer for this exon
upstream ENSMUSE00000327922 Chr11:106096921..106097097 No primer for this exon
upstream ENSMUSE00000327917 Chr11:106098309..106098437 No primer for this exon

*** Putative Vector Insertion (Chr 11: 106098438 - 106099821) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000327910 Chr11:106099822..106099921 No primer for this exon
downstream ENSMUSE00000327900 Chr11:106100450..106100497 No primer for this exon
downstream ENSMUSE00000327891 Chr11:106101316..106101413 No primer for this exon
downstream ENSMUSE00000327880 Chr11:106102865..106103141 No primer for this exon
downstream ENSMUSE00000108271 Chr11:106104189..106104415 No primer for this exon
downstream ENSMUSE00000108273 Chr11:106106641..106106751 No primer for this exon
downstream ENSMUSE00000108270 Chr11:106108090..106108191 No primer for this exon
downstream ENSMUSE00000108278 Chr11:106108806..106110453 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTTCAGGAAGGGGCAGAGAT Chr11:106098403..106098423 60.72 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATTGCTCGTGACTGGGAAAA Chr11:106098483..106098503 60.64 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000020705