Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4228
Trapped Gene
Ate1 (ENSMUSG00000030850)
Vector Insertion
Chr 7: 137562083 - 137607644
Public Clones AL0039 (sanger) AD0874 (sanger) AC0060 (sanger)
Private Clones OST409341 (lexicon)
Severity of mutation (?) Insertion after 81% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000204318 (Chr7:137607645..137607744 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCATGAGAAAACATCGCAAC Chr7:137607701..137607720 59.28 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000204318 (Chr7:137607645..137607744 -)
Downstram Exon
ENSMUSE00000204316 (Chr7:137561962..137562082 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCATGAGAAAACATCGCAAC Chr7:137607701..137607720 59.28 45 TGAAACGGCAGTACTTGGAG Chr7:137561958..137561977 58.92 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000587759 Chr7:137663391..137663475 CTGAAGGCCGGCTACTACTG Chr7:137663429..137663448 60.03 60
upstream ENSMUSE00000423413 Chr7:137662870..137663053 AAGAACAAGTTGGGCAGTCG Chr7:137662878..137662897 60.29 50
upstream ENSMUSE00000204315 Chr7:137659619..137659682 TTCCATGACAGTGCAGGATT Chr7:137659650..137659669 59.09 45
upstream ENSMUSE00000204314 Chr7:137657276..137657338 TGTCATGGATCAAACATGCTG Chr7:137657294..137657314 60.53 42.86
upstream ENSMUSE00000304983 Chr7:137654325..137654428 No primer for this exon
upstream ENSMUSE00000304975 Chr7:137652521..137652772 TGTTGACGGTGACTTTGCAT Chr7:137652722..137652741 60.16 45
upstream ENSMUSE00000368332 Chr7:137650996..137651213 GTAAGCCTCCATGTCGGAAA Chr7:137651176..137651195 60.07 50
upstream ENSMUSE00000204317 Chr7:137648208..137648336 CCTGATAAGCCAACCGTGAG Chr7:137648212..137648231 60.65 55
upstream ENSMUSE00000304959 Chr7:137647236..137647364 TGGCTATACACCAGGAAGCA Chr7:137647260..137647279 59.3 50
upstream ENSMUSE00000204319 Chr7:137625197..137625229 ATTCCTTTGCAGCTCACCAT Chr7:137625202..137625221 59.7 45
upstream ENSMUSE00000204324 Chr7:137610770..137610951 GCTGTGGGGGTGTTAGACAT Chr7:137610854..137610873 59.85 55
upstream ENSMUSE00000204318 Chr7:137607645..137607744 GCATGAGAAAACATCGCAAC Chr7:137607701..137607720 59.28 45

*** Putative Vector Insertion (Chr 7: 137562083 - 137607644) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000204316 Chr7:137561962..137562082 TGAAACGGCAGTACTTGGAG Chr7:137561958..137561977 58.92 50
downstream ENSMUSE00000668997 Chr7:137535040..137538250 CCTGGACAGACACCCAAAGT Chr7:137537282..137537301 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGCTATTTAATCGCCTTGCAG Chr7:137598579..137598600 60.36 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TACTGTCGTGACTGGGAAAACC Chr7:137598577..137598599 61.32 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000030850