Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4145
Trapped Gene
Ddx6 (ENSMUSG00000032097)
Vector Insertion
Chr 9: 44420975 - 44422294
Public Clones AN0164 (sanger) E068H10 (ggtc) E068H10 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 18% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000216524 (Chr9:44420911..44420974 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACCTGGTGATGACTGGAAAAA Chr9:44420911..44420931 59.44 42.86 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000216524 (Chr9:44420911..44420974 +)
Downstram Exon
ENSMUSE00000216526 (Chr9:44422295..44422399 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACCTGGTGATGACTGGAAAAA Chr9:44420911..44420931 59.44 42.86 CCAGCCCATTTCAAAAATTC Chr9:44422381..44422400 59.39 40

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000435404 Chr9:44412979..44413035 GGGAGCTTCGAGTCAACAAT Chr9:44412979..44412998 59.29 50
upstream ENSMUSE00000260519 Chr9:44415206..44415675 CCTGTGCAGCTAACAAAGCA Chr9:44415457..44415476 60.19 50
upstream ENSMUSE00000216524 Chr9:44420911..44420974 ACCTGGTGATGACTGGAAAAA Chr9:44420911..44420931 59.44 42.86

*** Putative Vector Insertion (Chr 9: 44420975 - 44422294) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000216526 Chr9:44422295..44422399 CCAGCCCATTTCAAAAATTC Chr9:44422381..44422400 59.39 40
downstream ENSMUSE00000216525 Chr9:44431702..44431831 TCAGGTCCAGCCTTTCAAGT Chr9:44431816..44431835 59.84 50
downstream ENSMUSE00000216535 Chr9:44432558..44432704 TGACCTGGATGCAAATCTGA Chr9:44432623..44432642 60.2 45
downstream ENSMUSE00000216528 Chr9:44434471..44434565 CCACGCCTTTCTTGATGAGA Chr9:44434530..44434549 61.32 50
downstream ENSMUSE00000461271 Chr9:44435721..44435843 GCACAAAATCCTGTGACAACA Chr9:44435753..44435773 59.61 42.86
downstream ENSMUSE00000216533 Chr9:44436724..44436852 TTGAGGCAGTGCACTTTTTG Chr9:44436839..44436858 60.03 45
downstream ENSMUSE00000216531 Chr9:44438107..44438223 TGCAGAAAATGATGGACTGG Chr9:44438140..44438159 59.65 45
downstream ENSMUSE00000473047 Chr9:44439466..44439529 CAAACAAGATTGCGGCATAA Chr9:44439527..44439546 59.7 40
downstream ENSMUSE00000216530 Chr9:44442176..44442277 TAGGTCTCTGCCAGCTTTGG Chr9:44442257..44442276 60.53 55
downstream ENSMUSE00000216534 Chr9:44443766..44443948 AGGCTCTTGTCGATGTTGCT Chr9:44443895..44443914 60.02 50
downstream ENSMUSE00000637410 Chr9:44444572..44446427 CTTTACAGCGAGTGCCTTCC Chr9:44445445..44445464 60.01 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCCCTCCAAAGGATCTAAGAA Chr9:44420943..44420965 58.85 45.46 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032097