Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4205
Trapped Gene
Sipa1l1 (ENSMUSG00000042700)
Vector Insertion
Chr 12: 83526443 - 83533739
Public Clones AL0763 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 80% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000447703 (Chr12:83526000..83526442 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGCAGATCGGACCTTAGAG Chr12:83526286..83526305 60.35 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000447703 (Chr12:83526000..83526442 +)
Downstram Exon
ENSMUSE00000447698 (Chr12:83533740..83533979 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGCAGATCGGACCTTAGAG Chr12:83526286..83526305 60.35 55 TCCCACGGAGTTAATGGTTC Chr12:83533965..83533984 59.79 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000471823 Chr12:83270407..83271063 AGTGAGCGGAAAGTCAGTGC Chr12:83270479..83270498 60.6 55
upstream ENSMUSE00000472867 Chr12:83335450..83335515 CAATTTGGACTCACAAGCAAGA Chr12:83335467..83335488 60.28 40.91
upstream ENSMUSE00000653649 Chr12:83392452..83392472 No primer for this exon
upstream ENSMUSE00000447771 Chr12:83412336..83412396 GTGTGGACGCTGCTGTCTTA Chr12:83412350..83412369 60.06 55
upstream ENSMUSE00000468208 Chr12:83441649..83443486 CTCGTCATGAGCTGTCCGTA Chr12:83443216..83443235 60.01 55
upstream ENSMUSE00000448627 Chr12:83458220..83458350 GTGAGCATTCGAAGGGAAAA Chr12:83458267..83458286 60.19 45
upstream ENSMUSE00000247831 Chr12:83463930..83464118 CTCATGAAACTGGACGAGCA Chr12:83464095..83464114 59.98 50
upstream ENSMUSE00000612143 Chr12:83473355..83473529 ACGAGTCCGGCTAAAAGGAT Chr12:83473477..83473496 60.1 50
upstream ENSMUSE00000479751 Chr12:83485638..83485741 CATGCTGCCCTACACACCTA Chr12:83485708..83485727 59.74 55
upstream ENSMUSE00000447752 Chr12:83488542..83488699 CGAAAAACATCCGGTCTCAC Chr12:83488618..83488637 60.49 50
upstream ENSMUSE00000447746 Chr12:83497180..83497753 TCTTCTATGAGCGGGGAGAA Chr12:83497671..83497690 59.91 50
upstream ENSMUSE00000345516 Chr12:83498333..83498607 GTGGCGGATGTAGAACCCTA Chr12:83498423..83498442 59.96 55
upstream ENSMUSE00000447731 Chr12:83503897..83504166 TGCCAGTGATGGAGTACCAG Chr12:83503920..83503939 59.7 55
upstream ENSMUSE00000447725 Chr12:83517891..83518037 CAGCAACTTGTCTTCGTCCA Chr12:83517966..83517985 60.03 50
upstream ENSMUSE00000447718 Chr12:83521525..83521649 AGAAGTGAGGACAGCCTTGC Chr12:83521619..83521638 59.6 55
upstream ENSMUSE00000447711 Chr12:83523362..83523480 TCGAAGGTACTGCCTGCTTT Chr12:83523388..83523407 60.01 50
upstream ENSMUSE00000447703 Chr12:83526000..83526442 TGGCAGATCGGACCTTAGAG Chr12:83526286..83526305 60.35 55

*** Putative Vector Insertion (Chr 12: 83526443 - 83533739) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000447698 Chr12:83533740..83533979 TCCCACGGAGTTAATGGTTC Chr12:83533965..83533984 59.79 50
downstream ENSMUSE00000447692 Chr12:83534676..83534841 TGAGGCTCGAAGCCTAGTGT Chr12:83534730..83534749 60.16 55
downstream ENSMUSE00000447685 Chr12:83538675..83538921 GTGGAAGTGACTTGGGGAGA Chr12:83538882..83538901 60.09 55
downstream ENSMUSE00000358226 Chr12:83541802..83541948 GCGGCATCTACTAGGTTGGA Chr12:83541937..83541956 60.24 55
downstream ENSMUSE00000275863 Chr12:83547804..83547918 CTCCTCCAGCTGGTCACTGT Chr12:83547889..83547908 60.46 60
downstream ENSMUSE00000371292 Chr12:83550297..83550378 TTCTCGAAGCATTTTCAGCA Chr12:83550369..83550388 59.69 40
downstream ENSMUSE00000683518 Chr12:83550297..83550391 TTCTCGAAGCATTTTCAGCA Chr12:83550369..83550388 59.69 40
downstream ENSMUSE00000412789 Chr12:83550888..83551258 GCTGTGCACTGTCCGATATG Chr12:83551163..83551182 60.3 55
downstream ENSMUSE00000683517 Chr12:83550888..83552769 CCAGGGCAAGTGGTTTTCTA Chr12:83552253..83552272 60.1 50
downstream ENSMUSE00000683520 Chr12:83550888..83552769 CCAGGGCAAGTGGTTTTCTA Chr12:83552253..83552272 60.1 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAAGCAACTAGGCGGAATGT Chr12:83532463..83532483 58.86 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAAGCAACTAGGCGGAATGT Chr12:83526463..83526483 58.86 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042700