Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9376
Trapped Gene
Ube2n (ENSMUSG00000074781)
Vector Insertion
Chr 10: 95004086 - 95004271
Public Clones XH066 (baygenomics)
Private Clones OST12961 (lexicon) OST12674 (lexicon) OST8217 (lexicon) OST6145 (lexicon)
Severity of mutation (?) Insertion after 61% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000640785 (Chr10:95003839..95004085 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCAATGGCAGCACCTAAAGT Chr10:95003995..95004014 60.13 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000640785 (Chr10:95003839..95004085 +)
Downstram Exon
ENSMUSE00000640784 (Chr10:95004272..95004412 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCAATGGCAGCACCTAAAGT Chr10:95003995..95004014 60.13 50 TTGCTCGGCTACATCATTTG Chr10:95004381..95004400 59.83 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000640786 Chr10:95003783..95003815 No primer for this exon
upstream ENSMUSE00000640785 Chr10:95003839..95004085 CCAATGGCAGCACCTAAAGT Chr10:95003995..95004014 60.13 50

*** Putative Vector Insertion (Chr 10: 95004086 - 95004271) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000640784 Chr10:95004272..95004412 TTGCTCGGCTACATCATTTG Chr10:95004381..95004400 59.83 45
downstream ENSMUSE00000640783 Chr10:95004906..95008292 GCAGGAGGACTCAAAACTGC Chr10:95006138..95006157 60 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTTGTTTGTCACCCTGTGC Chr10:95004092..95004112 60.62 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGTGTCCTTTTTGTCCTCGT Chr10:95004120..95004140 60.15 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

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