Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3973
Trapped Gene
Rrp1b (ENSMUSG00000058392)
Vector Insertion
Chr 17: 32195610 - 32196218
Public Clones AS0035 (sanger) PST23242-NR (escells)
Private Clones OST880 (lexicon)
Severity of mutation (?) Insertion after 88% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000312759 (Chr17:32195469..32195609 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAAACGGAGGACGACTTTG Chr17:32195498..32195517 59.71 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000312759 (Chr17:32195469..32195609 +)
Downstram Exon
ENSMUSE00000312742 (Chr17:32196219..32196282 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAAACGGAGGACGACTTTG Chr17:32195498..32195517 59.71 50 TCTTGGAACTGGAGGGTGTT Chr17:32196249..32196268 59.55 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000547752 Chr17:32173107..32173549 CAACTAACCGCCCTGTCAAT Chr17:32173189..32173208 59.99 50
upstream ENSMUSE00000313039 Chr17:32182874..32182956 No primer for this exon
upstream ENSMUSE00000313011 Chr17:32184619..32184676 CCCAACTCATCCACGTTGTA Chr17:32184641..32184660 59.42 50
upstream ENSMUSE00000547741 Chr17:32185498..32185583 ATGAATCGAGAGTGGCAAGG Chr17:32185530..32185549 60.22 50
upstream ENSMUSE00000312955 Chr17:32186371..32186432 GAAGTTCTCAAGCGGAATGC Chr17:32186401..32186420 59.96 50
upstream ENSMUSE00000312926 Chr17:32186894..32187023 GCGTGAGAACCCACTTGATT Chr17:32186962..32186981 60.12 50
upstream ENSMUSE00000312898 Chr17:32188091..32188155 CTTAGCGGACCAGAACCTCA Chr17:32188093..32188112 60.39 55
upstream ENSMUSE00000312877 Chr17:32188628..32188794 GTAGCGAGGGGTGTTTTTGA Chr17:32188647..32188666 60.11 50
upstream ENSMUSE00000312854 Chr17:32189684..32189772 GACATCTGTGCAGCCTTGAA Chr17:32189731..32189750 59.99 50
upstream ENSMUSE00000137510 Chr17:32190802..32190899 GCTGATCGACTCCTGGAAAT Chr17:32190820..32190839 59.24 50
upstream ENSMUSE00000479782 Chr17:32192050..32192069 No primer for this exon
upstream ENSMUSE00000137513 Chr17:32192856..32192942 AGGACAACGGTCAGAGAAGG Chr17:32192883..32192902 59.3 55
upstream ENSMUSE00000312778 Chr17:32193501..32194201 CAAAGTACCGGATTCGGAGA Chr17:32193625..32193644 60.07 50
upstream ENSMUSE00000312759 Chr17:32195469..32195609 GAAAACGGAGGACGACTTTG Chr17:32195498..32195517 59.71 50

*** Putative Vector Insertion (Chr 17: 32195610 - 32196218) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000312742 Chr17:32196219..32196282 TCTTGGAACTGGAGGGTGTT Chr17:32196249..32196268 59.55 50
downstream ENSMUSE00000609261 Chr17:32197293..32197547 GGGGCTGACCAGGATACTCT Chr17:32197333..32197352 60.48 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACACGTAGGCAGGTGTGCTA Chr17:32195628..32195648 59.39 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACACGTAGGCAGGTGTGCTA Chr17:32195628..32195648 59.39 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000058392