Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6710
Trapped Gene
Cdk5rap2 (ENSMUSG00000039298)
Vector Insertion
Chr 4: 69933810 - 69937507
Public Clones HMA561 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 55% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000526526 (Chr4:69937508..69937742 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AATTCAAAACCCGCAACAAG Chr4:69937584..69937603 59.97 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000526526 (Chr4:69937508..69937742 -)
Downstram Exon
ENSMUSE00000526525 (Chr4:69933678..69933809 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AATTCAAAACCCGCAACAAG Chr4:69937584..69937603 59.97 40 TTGTCCTGGAAGGCTGTTCT Chr4:69933745..69933764 59.84 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000720534 Chr4:70071246..70071401 CTCTGCGTTCACGATGGACT Chr4:70071295..70071314 61.42 55
upstream ENSMUSE00000720857 Chr4:70071246..70071401 CTCTGCGTTCACGATGGACT Chr4:70071295..70071314 61.42 55
upstream ENSMUSE00000632276 Chr4:70064508..70064575 ACCCTGTTCTGCCAAGTGAC Chr4:70064548..70064567 60.16 55
upstream ENSMUSE00000672864 Chr4:70064508..70064575 ACCCTGTTCTGCCAAGTGAC Chr4:70064548..70064567 60.16 55
upstream ENSMUSE00000632275 Chr4:70062279..70062346 CCGGAACATGAAGGACTTTG Chr4:70062284..70062303 60.49 50
upstream ENSMUSE00000672863 Chr4:70062279..70062346 CCGGAACATGAAGGACTTTG Chr4:70062284..70062303 60.49 50
upstream ENSMUSE00000178367 Chr4:70041225..70041335 CCGAGCACATCTACAAGACG Chr4:70041225..70041244 59.47 55
upstream ENSMUSE00000672862 Chr4:70041225..70041335 CCGAGCACATCTACAAGACG Chr4:70041225..70041244 59.47 55
upstream ENSMUSE00000178366 Chr4:70037827..70037903 No primer for this exon
upstream ENSMUSE00000672861 Chr4:70037827..70037903 No primer for this exon
upstream ENSMUSE00000632274 Chr4:70025041..70025164 GTGGAGAGCCTAGCAGAACG Chr4:70025138..70025157 60.16 60
upstream ENSMUSE00000672860 Chr4:70025041..70025164 GTGGAGAGCCTAGCAGAACG Chr4:70025138..70025157 60.16 60
upstream ENSMUSE00000632273 Chr4:70021845..70021999 GGACCTGGAGATGACTCTGG Chr4:70021864..70021883 59.64 60
upstream ENSMUSE00000672859 Chr4:70021845..70021999 GGACCTGGAGATGACTCTGG Chr4:70021864..70021883 59.64 60
upstream ENSMUSE00000178370 Chr4:70015747..70015909 CGAGAACGTGTCATCTGGAG Chr4:70015800..70015819 59.42 55
upstream ENSMUSE00000672858 Chr4:70015747..70015909 CGAGAACGTGTCATCTGGAG Chr4:70015800..70015819 59.42 55
upstream ENSMUSE00000632272 Chr4:70014644..70014685 GGCAGAAGGAGAGAAACCAC Chr4:70014662..70014681 58.87 55
upstream ENSMUSE00000672857 Chr4:70014644..70014685 GGCAGAAGGAGAGAAACCAC Chr4:70014662..70014681 58.87 55
upstream ENSMUSE00000632271 Chr4:70013703..70013822 CAGGGTCTAACCATGGCATTA Chr4:70013721..70013741 59.83 47.62
upstream ENSMUSE00000672856 Chr4:70013703..70013822 CAGGGTCTAACCATGGCATTA Chr4:70013721..70013741 59.83 47.62
upstream ENSMUSE00000500594 Chr4:70010178..70010279 TCCCCAGATTCCAGCTAAGA Chr4:70010181..70010200 59.77 50
upstream ENSMUSE00000672855 Chr4:70010178..70010279 TCCCCAGATTCCAGCTAAGA Chr4:70010181..70010200 59.77 50
upstream ENSMUSE00000494901 Chr4:69998375..69998593 AAGCTGCGCTGGTAGAGAAG Chr4:69998558..69998577 59.92 55
upstream ENSMUSE00000672854 Chr4:69998375..69998593 AAGCTGCGCTGGTAGAGAAG Chr4:69998558..69998577 59.92 55
upstream ENSMUSE00000632270 Chr4:69978461..69978631 TTCCAGGTGAAAGCAAGACA Chr4:69978533..69978552 59.42 45
upstream ENSMUSE00000672853 Chr4:69978461..69978631 TTCCAGGTGAAAGCAAGACA Chr4:69978533..69978552 59.42 45
upstream ENSMUSE00000672852 Chr4:69976358..69976498 TTGGGAGCGATGGCTTAATA Chr4:69976409..69976428 60.55 45
upstream ENSMUSE00000672878 Chr4:69976358..69976498 TTGGGAGCGATGGCTTAATA Chr4:69976409..69976428 60.55 45
upstream ENSMUSE00000672851 Chr4:69968229..69968323 GGCTGACTGGGGACTTAAAA Chr4:69968279..69968298 59.17 50
upstream ENSMUSE00000672876 Chr4:69968229..69968323 GGCTGACTGGGGACTTAAAA Chr4:69968279..69968298 59.17 50
upstream ENSMUSE00000632266 Chr4:69963118..69963248 GTTCTTGCCTACCGGAACCT Chr4:69963165..69963184 60.5 55
upstream ENSMUSE00000672850 Chr4:69963118..69963248 GTTCTTGCCTACCGGAACCT Chr4:69963165..69963184 60.5 55
upstream ENSMUSE00000526530 Chr4:69961600..69961709 TTGCCTTGAAGAGCACAATC Chr4:69961644..69961663 59 45
upstream ENSMUSE00000672849 Chr4:69961600..69961709 TTGCCTTGAAGAGCACAATC Chr4:69961644..69961663 59 45
upstream ENSMUSE00000632265 Chr4:69959854..69959982 CACACAGACAACCAGCACCT Chr4:69959930..69959949 59.78 55
upstream ENSMUSE00000672848 Chr4:69959854..69959982 CACACAGACAACCAGCACCT Chr4:69959930..69959949 59.78 55
upstream ENSMUSE00000526521 Chr4:69952866..69952961 CGGACGTTGAGACTCCTTTC Chr4:69952899..69952918 59.84 55
upstream ENSMUSE00000672847 Chr4:69952866..69952961 CGGACGTTGAGACTCCTTTC Chr4:69952899..69952918 59.84 55
upstream ENSMUSE00000632264 Chr4:69950879..69951063 GGCTGCAAAAGTGGATATGG Chr4:69951020..69951039 60.47 50
upstream ENSMUSE00000672846 Chr4:69950879..69951063 GGCTGCAAAAGTGGATATGG Chr4:69951020..69951039 60.47 50
upstream ENSMUSE00000526527 Chr4:69942124..69942556 ACACGGTGGAGCTGAAGAGT Chr4:69942307..69942326 59.91 55
upstream ENSMUSE00000672845 Chr4:69942124..69942556 ACACGGTGGAGCTGAAGAGT Chr4:69942307..69942326 59.91 55
upstream ENSMUSE00000526526 Chr4:69937508..69937742 AATTCAAAACCCGCAACAAG Chr4:69937584..69937603 59.97 40
upstream ENSMUSE00000672844 Chr4:69937508..69937742 AATTCAAAACCCGCAACAAG Chr4:69937584..69937603 59.97 40

*** Putative Vector Insertion (Chr 4: 69933810 - 69937507) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000526525 Chr4:69933678..69933809 TTGTCCTGGAAGGCTGTTCT Chr4:69933745..69933764 59.84 50
downstream ENSMUSE00000672843 Chr4:69933678..69933809 TTGTCCTGGAAGGCTGTTCT Chr4:69933745..69933764 59.84 50
downstream ENSMUSE00000526524 Chr4:69927509..69928082 GGTTTGCAAGTCGTGGATTT Chr4:69927846..69927865 59.98 45
downstream ENSMUSE00000672836 Chr4:69927509..69927735 GGGTTAGTGGACGGAGGATT Chr4:69927638..69927657 60.19 55
downstream ENSMUSE00000672842 Chr4:69927509..69928082 GGTTTGCAAGTCGTGGATTT Chr4:69927846..69927865 59.98 45
downstream ENSMUSE00000526523 Chr4:69925525..69925757 GAAACAGCCTCTCCAGTTGC Chr4:69925509..69925528 60 55
downstream ENSMUSE00000632260 Chr4:69925525..69925757 GAAACAGCCTCTCCAGTTGC Chr4:69925509..69925528 60 55
downstream ENSMUSE00000486410 Chr4:69918369..69918417 GTGGTTCCACTCTGGCTGAT Chr4:69918372..69918391 60.12 55
downstream ENSMUSE00000446627 Chr4:69915670..69915848 GGGTAAGTTGCCTTCCACAG Chr4:69915799..69915818 59.59 55
downstream ENSMUSE00000446604 Chr4:69911387..69911506 TGTTTCCGGAGCTTCTCATT Chr4:69911397..69911416 59.81 45
downstream ENSMUSE00000672835 Chr4:69910477..69910532 No primer for this exon
downstream ENSMUSE00000632259 Chr4:69907982..69908008 No primer for this exon
downstream ENSMUSE00000405083 Chr4:69906415..69906531 TCATACTGAGGGCCTCGTTC Chr4:69906414..69906433 60.22 55
downstream ENSMUSE00000225395 Chr4:69904430..69904619 CCTAGCCAGGGACTCACGTA Chr4:69904554..69904573 60.27 60
downstream ENSMUSE00000225387 Chr4:69903505..69903629 CTTGACTTCGCCTCTTCCTG Chr4:69903584..69903603 60.13 55
downstream ENSMUSE00000225383 Chr4:69900319..69900396 GCCTGGGTGGATTCAAATAG Chr4:69900314..69900333 59.39 50
downstream ENSMUSE00000714958 Chr4:69899214..69899479 CACAGGAGAGCGAGTCAACA Chr4:69899407..69899426 60.18 55
downstream ENSMUSE00000716218 Chr4:69899214..69899479 CACAGGAGAGCGAGTCAACA Chr4:69899407..69899426 60.18 55
downstream ENSMUSE00000339304 Chr4:69896381..69896524 AAGAGCTTCAGCAACCTGGA Chr4:69896411..69896430 60.13 50
downstream ENSMUSE00000672840 Chr4:69896381..69896524 AAGAGCTTCAGCAACCTGGA Chr4:69896411..69896430 60.13 50
downstream ENSMUSE00000411303 Chr4:69889632..69889758 GACTTTCTCCTGGTGCTTGC Chr4:69889623..69889642 60 55
downstream ENSMUSE00000672839 Chr4:69889632..69889758 GACTTTCTCCTGGTGCTTGC Chr4:69889623..69889642 60 55
downstream ENSMUSE00000339245 Chr4:69884564..69884610 AAGGACTTGGTGGGTGATGA Chr4:69884566..69884585 60.36 50
downstream ENSMUSE00000672838 Chr4:69884564..69884610 AAGGACTTGGTGGGTGATGA Chr4:69884566..69884585 60.36 50
downstream ENSMUSE00000380045 Chr4:69884058..69884148 GGGCCACAAGCTTTATTAGC Chr4:69884038..69884057 58.86 50
downstream ENSMUSE00000672837 Chr4:69884058..69884148 GGGCCACAAGCTTTATTAGC Chr4:69884038..69884057 58.86 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
  No PCR available

Come back to gene ENSMUSG00000039298