Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5422
Trapped Gene
Paics (ENSMUSG00000029247)
Vector Insertion
Chr 5: 77380829 - 77380861
Public Clones CSD075 (baygenomics) CSD085 (baygenomics) CSJ163 (baygenomics) P023B10 (ggtc)
W071E06 (ggtc) Q012D03 (ggtc) (ggtc) M121A08 (ggtc) W266C03 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000710719 (Chr5:77380794..77380860 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCGGTCTGCTCCTCTAGTTC Chr5:77380815..77380834 59.19 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000710719 (Chr5:77380794..77380860 +)
Downstram Exon
ENSMUSE00000408986 (Chr5:77380830..77380860 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCGGTCTGCTCCTCTAGTTC Chr5:77380815..77380834 59.19 60 GCCATTATCCGAGGTGAACT Chr5:77380852..77380871 59.01 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000722120 Chr5:77380373..77380693 GTGGGAGGCTCCGTTATTTT Chr5:77380393..77380412 60.32 50
upstream ENSMUSE00000712346 Chr5:77380393..77380426 GTGGGAGGCTCCGTTATTTT Chr5:77380393..77380412 60.32 50
upstream ENSMUSE00000710719 Chr5:77380794..77380860 GCGGTCTGCTCCTCTAGTTC Chr5:77380815..77380834 59.19 60

*** Putative Vector Insertion (Chr 5: 77380829 - 77380861) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000408986 Chr5:77380830..77380860 GCCATTATCCGAGGTGAACT Chr5:77380852..77380871 59.01 50
downstream ENSMUSE00000695715 Chr5:77383980..77383989 No primer for this exon
downstream ENSMUSE00000349614 Chr5:77385568..77385768 CGTAGAGCTTCTTCCCGATG Chr5:77385600..77385619 59.97 55
downstream ENSMUSE00000485689 Chr5:77385571..77385768 CGTAGAGCTTCTTCCCGATG Chr5:77385600..77385619 59.97 55
downstream ENSMUSE00000234501 Chr5:77388340..77388518 CTGTACCCCAGGGTTCCTTT Chr5:77388476..77388495 60.22 55
downstream ENSMUSE00000187310 Chr5:77390135..77390314 CAAGGCCAGCAAAACAGAAT Chr5:77390210..77390229 60.25 45
downstream ENSMUSE00000187314 Chr5:77390418..77390531 ATGGCCATAGTCTCCAGGAA Chr5:77390502..77390521 59.51 50
downstream ENSMUSE00000187313 Chr5:77391452..77391535 GGTCTGCAACCCACTCAAAG Chr5:77391530..77391549 60.69 55
downstream ENSMUSE00000187309 Chr5:77393467..77393647 GGTCCTTTATGCGCAGATGT Chr5:77393615..77393634 60.1 50
downstream ENSMUSE00000187315 Chr5:77395272..77395430 CACTGGGCAGTCGAAGAGAT Chr5:77395433..77395452 60.41 55
downstream ENSMUSE00000390527 Chr5:77395673..77396528 CAAATTCAGGTCGTCTGCAA Chr5:77396296..77396315 59.84 45
downstream ENSMUSE00000709158 Chr5:77395673..77396338 CAAATTCAGGTCGTCTGCAA Chr5:77396296..77396315 59.84 45
downstream ENSMUSE00000710468 Chr5:77395673..77396534 CAAATTCAGGTCGTCTGCAA Chr5:77396296..77396315 59.84 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTCCAGAACACTGCCCTTT Chr5:77380788..77380808 59.71 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTCCAGAACACTGCCCTTT Chr5:77380788..77380808 59.71 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029247