Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27663
Trapped Gene
8430427H17Rik (ENSMUSG00000061411)
Vector Insertion
Chr 2: 153262084 - 153270092
Public Clones (ggtc) (ggtc) IST14997F11 (tigm)
Private Clones OST54265 (lexicon)
Severity of mutation (?) Insertion after 34% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000681596 (Chr2:153270093..153270215 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCGGTTCACTCCCAGAGCTA Chr2:153270125..153270144 62.65 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000681596 (Chr2:153270093..153270215 -)
Downstram Exon
ENSMUSE00000276502 (Chr2:153261942..153262083 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCGGTTCACTCCCAGAGCTA Chr2:153270125..153270144 62.65 60 TCCATGCGGAGTCATTCATA Chr2:153262010..153262029 60.03 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000555729 Chr2:153355178..153355709 CGACTCGGCTAAAACCAAGA Chr2:153355372..153355391 60.38 50
upstream ENSMUSE00000504458 Chr2:153309423..153309578 CTACTCGATGCACGTGGAGA Chr2:153309482..153309501 60.01 55
upstream ENSMUSE00000276516 Chr2:153303607..153303718 GAGAGGCTGTGACTCGGTTC Chr2:153303671..153303690 59.99 60
upstream ENSMUSE00000276509 Chr2:153296424..153296533 TGATTACAACATGCCCCTCA Chr2:153296477..153296496 59.92 45
upstream ENSMUSE00000681596 Chr2:153270093..153270215 CCGGTTCACTCCCAGAGCTA Chr2:153270125..153270144 62.65 60

*** Putative Vector Insertion (Chr 2: 153262084 - 153270092) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000276502 Chr2:153261942..153262083 TCCATGCGGAGTCATTCATA Chr2:153262010..153262029 60.03 45
downstream ENSMUSE00000460716 Chr2:153246268..153246545 GTGGATGGGTTCAGGGTAGA Chr2:153246466..153246485 59.78 55
downstream ENSMUSE00000461586 Chr2:153243696..153243881 ATCGTCATCGTCATCTGCTG Chr2:153243752..153243771 59.82 50
downstream ENSMUSE00000471602 Chr2:153243424..153243615 GGTTCTCATCCACGAAGAGC Chr2:153243563..153243582 59.81 55
downstream ENSMUSE00000463499 Chr2:153243099..153243221 AGGTCAGATGCGGAGGAGTA Chr2:153243172..153243191 59.83 55
downstream ENSMUSE00000384147 Chr2:153242380..153242581 AGTCCCGAGAGTGCTGCTTA Chr2:153242520..153242539 60.16 55
downstream ENSMUSE00000466561 Chr2:153233202..153237565 CAGACAGAATGCGGTAAGCA Chr2:153235321..153235340 60.01 50
downstream ENSMUSE00000681598 Chr2:153233198..153237565 CAGACAGAATGCGGTAAGCA Chr2:153235321..153235340 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACTTCTGCTCGTGGGTGGTA Chr2:153267039..153267059 60.71 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GATGCAAATGGCTGAGCTTC Chr2:153267097..153267117 60.9 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CTGGCACTGAATTCTCGGTA Chr2:153267227..153267247 58.87 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CGGTAAATCCTCCTCCCTTT Chr2:153264212..153264232 59.42 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000061411