Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI29961
Trapped Gene
Slc35f2 (ENSMUSG00000042195)
Vector Insertion
Chr 9: 53619702 - 53645644
Public Clones (sanger) (sanger) D177G05 (ggtc) D086F05 (ggtc) (ggtc)
D057D11 (ggtc) CMHD-GT_402H3-3 (cmhd) IST14656C5 (tigm) IST14096B3 (tigm)
IST10653E5 (tigm) IST14329D6 (tigm) IST10126E11 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 10% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000534833 (Chr9:53619544..53619701 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATCCGACGCAAACTCTTCAC Chr9:53619679..53619698 60.26 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000534833 (Chr9:53619544..53619701 +)
Downstram Exon
ENSMUSE00000472752 (Chr9:53645645..53645820 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATCCGACGCAAACTCTTCAC Chr9:53619679..53619698 60.26 50 GCCAAATACTGGCTGGTGAT Chr9:53645728..53645747 59.96 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000534833 Chr9:53619544..53619701 ATCCGACGCAAACTCTTCAC Chr9:53619679..53619698 60.26 50

*** Putative Vector Insertion (Chr 9: 53619702 - 53645644) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000472752 Chr9:53645645..53645820 GCCAAATACTGGCTGGTGAT Chr9:53645728..53645747 59.96 50
downstream ENSMUSE00000275372 Chr9:53648818..53648945 GGACACTGGTCAGAGTCGTG Chr9:53648946..53648965 59.28 60
downstream ENSMUSE00000275352 Chr9:53654425..53654584 CTTTGTATCTTGCCCGGAGA Chr9:53654497..53654516 60.21 50
downstream ENSMUSE00000275333 Chr9:53655853..53656009 TGTATGCCGCTGATGATTGT Chr9:53656009..53656028 60.1 45
downstream ENSMUSE00000275310 Chr9:53657493..53657545 GAATCCGGGCAATGTCTTTA Chr9:53657530..53657549 59.9 45
downstream ENSMUSE00000275287 Chr9:53658682..53658836 GACTGAAGTGGCACTCGTGA Chr9:53658773..53658792 60.03 55
downstream ENSMUSE00000636885 Chr9:53664590..53665960 CAGAGTCTGTGGCTTGTCCA Chr9:53664802..53664821 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAACTGGGAACCCAAACCAC Chr9:53631710..53631730 59.69 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAACTGGGAACCCAAACCAC Chr9:53631710..53631730 59.69 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042195