Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1992
Trapped Gene
Acy1 (ENSMUSG00000023262)
Vector Insertion
Chr 9: 106336930 - 106337015
Public Clones BB0713 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 70% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000262115 (Chr9:106337016..106337160 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGTGACTTCGGTGAATCTGA Chr9:106337108..106337127 59.83 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000262115 (Chr9:106337016..106337160 -)
Downstram Exon
ENSMUSE00000134181 (Chr9:106336861..106336929 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGTGACTTCGGTGAATCTGA Chr9:106337108..106337127 59.83 50 CTCAAAGGTGACCCCCTCTC Chr9:106336848..106336867 61.02 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000371257 Chr9:106340464..106340552 CACAGGACTGAGACGTGGAG Chr9:106340472..106340491 59.44 60
upstream ENSMUSE00000262331 Chr9:106339960..106340068 CTGTGCAACCCAATCCAGAC Chr9:106339964..106339983 61.53 55
upstream ENSMUSE00000262317 Chr9:106339220..106339284 TGGGTCTGAGCTGTCAGAAA Chr9:106339226..106339245 59.54 50
upstream ENSMUSE00000262290 Chr9:106339027..106339131 CACTCCCCTCCATCTTGCTA Chr9:106339060..106339079 60.21 55
upstream ENSMUSE00000262263 Chr9:106338457..106338551 AAGGATTCCGAGGGCTACAT Chr9:106338499..106338518 59.92 50
upstream ENSMUSE00000262239 Chr9:106338115..106338191 CCATCCACATGACCTTTGTG Chr9:106338119..106338138 59.81 50
upstream ENSMUSE00000262216 Chr9:106337946..106338035 CACAAGGGGATGGAGTTGTT Chr9:106337999..106338018 59.82 50
upstream ENSMUSE00000262191 Chr9:106337799..106337855 TAGTGAGCGGAGTCCTTGGT Chr9:106337799..106337818 59.87 55
upstream ENSMUSE00000262170 Chr9:106337427..106337500 ATGCCTCACGCTTCATTGAG Chr9:106337448..106337467 61.35 50
upstream ENSMUSE00000262140 Chr9:106337296..106337345 No primer for this exon
upstream ENSMUSE00000262115 Chr9:106337016..106337160 CGTGACTTCGGTGAATCTGA Chr9:106337108..106337127 59.83 50

*** Putative Vector Insertion (Chr 9: 106336930 - 106337015) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000134181 Chr9:106336861..106336929 CTCAAAGGTGACCCCCTCTC Chr9:106336848..106336867 61.02 60
downstream ENSMUSE00000134180 Chr9:106335898..106335977 AATCATCCGTGGGTGTCATT Chr9:106335919..106335938 60.06 45
downstream ENSMUSE00000134183 Chr9:106335693..106335753 TCTGGCTCCAGAGTGAGGTT Chr9:106335711..106335730 59.99 55
downstream ENSMUSE00000362473 Chr9:106335322..106335576 ATATCCTCATGCAGCCGTTC Chr9:106335469..106335488 60.07 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGAGTGGCACCAGATGTAGA Chr9:106337021..106337041 59.85 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGAGTGCCAGCTTTGACTTC Chr9:106337041..106337061 59.17 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000023262