Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI530
Trapped Gene
Cstf3 (ENSMUSG00000027176)
Vector Insertion
Chr 2: 104430860 - 104449027
Public Clones XS1003 (sanger) (sanger) (sanger) AQ0179 (sanger) (sanger)
(sanger) CF0713 (sanger) (sanger) XS1001 (sanger) (sanger)
(sanger) (sanger) AZ0021 (sanger) (sanger) AL0354 (sanger) (sanger)
(sanger) CA0057 (sanger) (sanger) RHA082 (baygenomics) P126F08 (ggtc)
E047G10 (ggtc) P027E12 (ggtc) D128D10 (ggtc) (ggtc) H011A09 (ggtc)
D178E09 (ggtc) M124F11 (ggtc) D056G12 (ggtc) (ggtc) H011A09 (ggtc)
P126F08 (ggtc) D144G10 (ggtc) 3SE287B10 (ggtc) IST10126B6 (tigm) IST13566E9 (tigm)
IST14657G8 (tigm) IST10880F9 (tigm) IST11622E8 (tigm)
Private Clones OST465727 (lexicon) OST448825 (lexicon) OST440770 (lexicon) OST425553 (lexicon)
OST419291 (lexicon) OST402342 (lexicon) OST391165 (lexicon) OST359043 (lexicon)
OST356979 (lexicon) OST329646 (lexicon) OST328994 (lexicon) OST322968 (lexicon)
OST309033 (lexicon) OST307609 (lexicon) OST307592 (lexicon) OST299345 (lexicon)
OST286068 (lexicon) OST268907 (lexicon) OST266469 (lexicon) OST242334 (lexicon)
OST241427 (lexicon) OST237847 (lexicon) OST237758 (lexicon) OST207606 (lexicon)
OST205894 (lexicon) OST171414 (lexicon) OST170471 (lexicon) OST169063 (lexicon)
OST167258 (lexicon) OST142000 (lexicon) OST141971 (lexicon) OST131687 (lexicon)
OST108240 (lexicon) OST102206 (lexicon) OST89743 (lexicon) OST89058 (lexicon)
OST86605 (lexicon) OST83463 (lexicon) OST83427 (lexicon) OST82332 (lexicon)
OST76521 (lexicon) OST68354 (lexicon) OST67170 (lexicon) OST60899 (lexicon)
OST56570 (lexicon) OST44874 (lexicon) OST43250 (lexicon) OST41132 (lexicon)
OST39960 (lexicon) OST37908 (lexicon) OST31213 (lexicon)
Severity of mutation (?) Insertion after 1% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000376863 (Chr2:104430680..104430859 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGGTGCGTACGTTGTAGTCC Chr2:104430804..104430823 59.64 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000376863 (Chr2:104430680..104430859 +)
Downstram Exon
ENSMUSE00000226273 (Chr2:104449028..104449129 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGGTGCGTACGTTGTAGTCC Chr2:104430804..104430823 59.64 55 GCTCCAAGCATCAAGGTCAT Chr2:104449111..104449130 60.23 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000376863 Chr2:104430680..104430859 TGGTGCGTACGTTGTAGTCC Chr2:104430804..104430823 59.64 55

*** Putative Vector Insertion (Chr 2: 104430860 - 104449027) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000226273 Chr2:104449028..104449129 GCTCCAAGCATCAAGGTCAT Chr2:104449111..104449130 60.23 50
downstream ENSMUSE00000166584 Chr2:104449248..104449343 GCAACAAGGCGTTCGTAAGT Chr2:104449297..104449316 60.31 50
downstream ENSMUSE00000166573 Chr2:104484446..104484478 No primer for this exon
downstream ENSMUSE00000340815 Chr2:104485136..104485233 TGTAGCTGGGCAGTTTACCC Chr2:104485235..104485254 60.13 55
downstream ENSMUSE00000226254 Chr2:104486557..104486623 No primer for this exon
downstream ENSMUSE00000166559 Chr2:104486766..104486800 No primer for this exon
downstream ENSMUSE00000226243 Chr2:104486881..104487007 No primer for this exon
downstream ENSMUSE00000166568 Chr2:104488327..104488404 No primer for this exon
downstream ENSMUSE00000166567 Chr2:104489610..104489772 CCACATGTCCACTTGCTGAG Chr2:104489705..104489724 60.31 55
downstream ENSMUSE00000226232 Chr2:104491799..104491908 TTCTGCAAGCAGCTTACTCG Chr2:104491905..104491924 59.51 50
downstream ENSMUSE00000166579 Chr2:104492602..104492718 AACGTGCTTATGGCTCTTTCA Chr2:104492671..104492691 59.9 42.86
downstream ENSMUSE00000166575 Chr2:104493161..104493235 CAATGTCCTCAATTGCCAGA Chr2:104493227..104493246 59.65 45
downstream ENSMUSE00000166565 Chr2:104494318..104494461 TCCATGAGGGCTGCAGTTAC Chr2:104494448..104494467 61.21 55
downstream ENSMUSE00000166560 Chr2:104495846..104495948 No primer for this exon
downstream ENSMUSE00000226206 Chr2:104499423..104499492 No primer for this exon
downstream ENSMUSE00000392214 Chr2:104500676..104500871 AAGCTGTTTCCTTGCCTTCA Chr2:104500800..104500819 59.99 45
downstream ENSMUSE00000166562 Chr2:104503451..104503604 GTGCTAAATGTCGTGGCTGA Chr2:104503607..104503626 59.87 50
downstream ENSMUSE00000166566 Chr2:104504226..104504320 GAGGTGGGAGCAGTTTCATC Chr2:104504309..104504328 59.66 55
downstream ENSMUSE00000166570 Chr2:104504454..104504514 TCCATCAGCTCATCCACTTG Chr2:104504488..104504507 59.79 50
downstream ENSMUSE00000342603 Chr2:104504874..104505575 GATGTGGCGTTGTCATTTTG Chr2:104505333..104505352 59.97 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGGCGACCTCTTCTCTCTCT Chr2:104433888..104433908 59.28 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TATTTCGTGACTGGGAAAACC Chr2:104433906..104433927 58.94 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027176