Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI34516
Trapped Gene
Pcnp (ENSMUSG00000071533)
Vector Insertion
Chr 16: 56018584 - 56022243
Public Clones IST10087C11 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 80% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000618092 (Chr16:56022168..56022242 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTGCTCCAAAAACTCTGTCG Chr16:56022198..56022217 59.05 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000618092 (Chr16:56022168..56022242 -)
Downstram Exon
ENSMUSE00000618091 (Chr16:56018585..56018640 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTGCTCCAAAAACTCTGTCG Chr16:56022198..56022217 59.05 45 TCTTTGCTTCTGGAGGCATT Chr16:56018585..56018604 59.96 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000655002 Chr16:56029716..56029830 GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60
upstream ENSMUSE00000717002 Chr16:56029716..56029809 GGGAGAGGAGAAGCCAGAGA Chr16:56029743..56029762 61.01 60
upstream ENSMUSE00000699358 Chr16:56024647..56024781 GCCTCTTGTACTGCCACACA Chr16:56024718..56024737 59.9 55
upstream ENSMUSE00000618093 Chr16:56024337..56024551 AATGGAGGGGAAAGTTCCAG Chr16:56024479..56024498 60.3 50
upstream ENSMUSE00000720388 Chr16:56024337..56024741 AATGGAGGGGAAAGTTCCAG Chr16:56024479..56024498 60.3 50
upstream ENSMUSE00000618092 Chr16:56022168..56022242 TTGCTCCAAAAACTCTGTCG Chr16:56022198..56022217 59.05 45
upstream ENSMUSE00000618091 Chr16:56018585..56018640 AATGCCTCCAGAAGCAAAGA Chr16:56018607..56018626 59.96 45

*** Putative Vector Insertion (Chr 16: 56018584 - 56022243) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000718790 Chr16:56018233..56018640 TCTTTGCTTCTGGAGGCATT Chr16:56018585..56018604 59.96 45
downstream ENSMUSE00000699357 Chr16:56017304..56017430 GTCTTGGTCGTGGACGTTTC Chr16:56017288..56017307 60.56 55
downstream ENSMUSE00000699366 Chr16:56015621..56017430 CTAGAATGGCCCGAAACAAA Chr16:56016719..56016738 60.07 45
downstream ENSMUSE00000717074 Chr16:56007358..56007595 GCAGAGTGAGTGCTGCTGTC Chr16:56007408..56007427 59.93 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCCCCCACATACACAAAATAGAG Chr16:56019267..56019290 60.12 43.48 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTCCCCCACATACACAAAATAG Chr16:56019269..56019291 58.74 40.91 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000071533