Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35988
Trapped Gene
Bbs9 (ENSMUSG00000035919)
Vector Insertion
Chr 9: 22616988 - 22692024
Public Clones IST13084H11 (tigm) IST13084H11 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 95% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000280764 (Chr9:22616765..22616987 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCCTGTCGAAGAGTTCCAAG Chr9:22616814..22616833 59.99 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000280764 (Chr9:22616765..22616987 +)
Downstram Exon
ENSMUSE00000280735 (Chr9:22692025..22692132 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCCTGTCGAAGAGTTCCAAG Chr9:22616814..22616833 59.99 55 TGAGGTGCTTGTGGTTGGTA Chr9:22692114..22692133 60.15 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000422462 Chr9:22280189..22280499 TTGGGAACGTGGAAAACTTC Chr9:22280459..22280478 59.95 45
upstream ENSMUSE00000422449 Chr9:22295262..22295384 CCCGTGACTGGTGGTCTACT Chr9:22295289..22295308 60.03 60
upstream ENSMUSE00000422429 Chr9:22301153..22301303 TGGAAGTCGGGAAGTTTGTC Chr9:22301282..22301301 60.09 50
upstream ENSMUSE00000422423 Chr9:22308489..22308553 TCCCGGAAGCTCTGTGTCTA Chr9:22308523..22308542 60.93 55
upstream ENSMUSE00000333776 Chr9:22318424..22318537 TGACGTATGGACCCTTTGGT Chr9:22318508..22318527 60.23 50
upstream ENSMUSE00000392637 Chr9:22372149..22372323 TGATGGTGTTTGAGCAGGAA Chr9:22372188..22372207 60.24 45
upstream ENSMUSE00000281096 Chr9:22379555..22379639 GCCACAGATGCAGACAAGAA Chr9:22379574..22379593 59.99 50
upstream ENSMUSE00000281078 Chr9:22383081..22383264 CTGAATATTGGCGAGCAAGC Chr9:22383093..22383112 60.88 50
upstream ENSMUSE00000281061 Chr9:22383908..22384037 GCCGTCAGAGTAGGCTGTTT Chr9:22384015..22384034 59.5 55
upstream ENSMUSE00000280973 Chr9:22433386..22433564 TCACCTGCAGTGCTCGTATC Chr9:22433425..22433444 60.02 55
upstream ENSMUSE00000280946 Chr9:22440055..22440131 GTTTGGCCCTTGACTGAACA Chr9:22440057..22440076 61.08 50
upstream ENSMUSE00000280929 Chr9:22443174..22443227 GACTCTGTCCCGTCCATCAC Chr9:22443201..22443220 60.54 60
upstream ENSMUSE00000280891 Chr9:22448189..22448291 TGGTGTTGCAGAAGGTCAAG Chr9:22448208..22448227 59.87 50
upstream ENSMUSE00000362135 Chr9:22450408..22450512 No primer for this exon
upstream ENSMUSE00000702380 Chr9:22452464..22452478 No primer for this exon
upstream ENSMUSE00000362779 Chr9:22459669..22459809 CAGTCTGCTCGGTCTCTTCC Chr9:22459787..22459806 60.13 60
upstream ENSMUSE00000379729 Chr9:22463494..22463589 GCGCTCGAGTGACTCTTCTT Chr9:22463554..22463573 59.9 55
upstream ENSMUSE00000341359 Chr9:22475229..22475401 ATACCGCATTCAGAGCGAAC Chr9:22475233..22475252 60.24 50
upstream ENSMUSE00000377404 Chr9:22483356..22483508 CTGTACAATTTCGGGCCATT Chr9:22483402..22483421 59.82 45
upstream ENSMUSE00000280795 Chr9:22598195..22598377 CTGAAGAGTGCCACCCATTT Chr9:22598258..22598277 60.11 50
upstream ENSMUSE00000280764 Chr9:22616765..22616987 GCCTGTCGAAGAGTTCCAAG Chr9:22616814..22616833 59.99 55

*** Putative Vector Insertion (Chr 9: 22616988 - 22692024) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000280735 Chr9:22692025..22692132 TGAGGTGCTTGTGGTTGGTA Chr9:22692114..22692133 60.15 50
downstream ENSMUSE00000354999 Chr9:22692306..22692718 AGGCAGCAACCATTTTCTTG Chr9:22692560..22692579 60.25 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCACCGTCTTCATTCATGT Chr9:22688940..22688960 60.94 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGTTGAGTGGGGAATAAAATA Chr9:22689011..22689033 59.1 40.91 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035919