Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI25205
Trapped Gene
CAAA01179078.1.1.20098 (ENSMUSG00000053338)
Vector Insertion
Chr 7: 3497853 - 3498305
Public Clones IST15087F10 (tigm)
Private Clones OST191759 (lexicon)
Severity of mutation (?) Insertion after 42% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000422437 (Chr7:3498306..3498596 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAGAATGATGGCGGACACTA Chr7:3498383..3498402 59.67 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000422437 (Chr7:3498306..3498596 -)
Downstram Exon
ENSMUSE00000422430 (Chr7:3497556..3497852 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAGAATGATGGCGGACACTA Chr7:3498383..3498402 59.67 50 AGCTGTATTCCCCCGAGTCT Chr7:3497606..3497625 60.1 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000633587 Chr7:3503313..3503433 GCTGAAGACCTTTGGACCAG Chr7:3503360..3503379 59.84 55
upstream ENSMUSE00000422442 Chr7:3499077..3499112 TGTTGGGCAAACAGACATTC Chr7:3499086..3499105 59.55 45
upstream ENSMUSE00000422437 Chr7:3498306..3498596 CAGAATGATGGCGGACACTA Chr7:3498383..3498402 59.67 50

*** Putative Vector Insertion (Chr 7: 3497853 - 3498305) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000422430 Chr7:3497556..3497852 AGCTGTATTCCCCCGAGTCT Chr7:3497606..3497625 60.1 55
downstream ENSMUSE00000422425 Chr7:3496807..3496872 GAAAGTCGAGGCAGCAAGAT Chr7:3496813..3496832 59.58 50
downstream ENSMUSE00000422450 Chr7:3489957..3490102 ACCGACCCGGATGAGATTAT Chr7:3490025..3490044 60.55 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAGCAATGCCCTTTTCTTGT Chr7:3498313..3498333 60.25 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGCAATGCCCTTTTCTTGT Chr7:3498313..3498333 60.25 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 AAGCTCCGGTCTGTTTCCTT Chr7:3498599..3498619 60.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 AAGCTCCGGTCTGTTTCCTT Chr7:3498599..3498619 60.25 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053338