Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10340
Trapped Gene
Pml (ENSMUSG00000036986)
Vector Insertion
Chr 9: 58095246 - 58097347
Public Clones (sanger) XA129 (baygenomics) E061A07 (ggtc) 5SE285C04 (ggtc) D159C05 (ggtc)
PST25865-NR (escells) IST12571G4 (tigm) IST12873G12 (tigm) IST14138B7 (tigm)
IST11507D1 (tigm) IST10325G1 (tigm) IST10806A9 (tigm) IST10031C1 (tigm)
IST12571G4 (tigm) IST11692F3 (tigm) IST13051H2 (tigm) IST10921E6 (tigm)
IST10763E6 (tigm)
Private Clones OST219894 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000485399 (Chr9:58097348..58097593 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGTCGACAACAGGACTCTGC Chr9:58097424..58097443 60.03 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000485399 (Chr9:58097348..58097593 -)
Downstram Exon
ENSMUSE00000254921 (Chr9:58094782..58095245 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGTCGACAACAGGACTCTGC Chr9:58097424..58097443 60.03 55 TATTGGACTTGCGCGTACTG Chr9:58094803..58094822 59.9 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000485399 Chr9:58097348..58097593 TGTCGACAACAGGACTCTGC Chr9:58097424..58097443 60.03 55

*** Putative Vector Insertion (Chr 9: 58095246 - 58097347) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000254921 Chr9:58094782..58095245 TATTGGACTTGCGCGTACTG Chr9:58094803..58094822 59.9 50
downstream ENSMUSE00000254901 Chr9:58082160..58082740 TCATGCCACTGCTGAATCTC Chr9:58082608..58082627 59.95 50
downstream ENSMUSE00000254882 Chr9:58080960..58081054 TGGTTGTCACTGGGTGAGTG Chr9:58080961..58080980 60.63 55
downstream ENSMUSE00000457341 Chr9:58078298..58078435 CATAGCCACAGGTTGGGTCT Chr9:58078348..58078367 59.99 55
downstream ENSMUSE00000254861 Chr9:58077635..58077893 GTCCTCGTTCTCCTCTGTGG Chr9:58077773..58077792 59.83 60
downstream ENSMUSE00000254833 Chr9:58077162..58077214 CAGATTCTCGGTGTCCGAAT Chr9:58077140..58077159 60.07 50
downstream ENSMUSE00000254804 Chr9:58069522..58069672 GCTGCTATCGTCCAACTCGT Chr9:58069624..58069643 60.43 55
downstream ENSMUSE00000534036 Chr9:58066349..58068376 TCAGTGTGTGGAAACGGGTA Chr9:58067039..58067058 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATAATCGCCTTGCAGCACA Chr9:58097278..58097298 60.38 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGTTTACGTGACTGGGAAAA Chr9:58097282..58097302 58.67 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 CCCTGTCTCACTTCCTCTCG Chr9:58097585..58097605 59.98 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CCCTGTCTCACTTCCTCTCG Chr9:58097585..58097605 59.98 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036986