Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27979
Trapped Gene
Rnaseh2b (ENSMUSG00000021932)
Vector Insertion
Chr 14: 62984139 - 62989308
Public Clones not available
Private Clones OST43062 (lexicon)
Severity of mutation (?) Insertion after 80% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000122207 (Chr14:62984096..62984138 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATTGACCAACCCTCCATCAA Chr14:62984117..62984136 60.17 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000122207 (Chr14:62984096..62984138 +)
Downstram Exon
ENSMUSE00000122212 (Chr14:62989309..62989389 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATTGACCAACCCTCCATCAA Chr14:62984117..62984136 60.17 45 TGCCGGTCTTCAAGTCTTTAG Chr14:62989389..62989409 59.5 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000445440 Chr14:62950941..62951013 CCAGGCAGCTAGTGTTCCTA Chr14:62950987..62951006 58.13 55
upstream ENSMUSE00000122211 Chr14:62965405..62965479 GCCTCCTGTTCGTAAAGCTG Chr14:62965444..62965463 60.01 55
upstream ENSMUSE00000445402 Chr14:62967358..62967465 No primer for this exon
upstream ENSMUSE00000122217 Chr14:62969237..62969313 TCCTAAAGGCTGGCAAAGAG Chr14:62969294..62969313 59.59 50
upstream ENSMUSE00000122213 Chr14:62972360..62972474 GTCGATGACACGTTTCCAGA Chr14:62972390..62972409 59.68 50
upstream ENSMUSE00000445391 Chr14:62979300..62979364 AGACATTGAAGTGGCTGGAGA Chr14:62979339..62979359 59.86 47.62
upstream ENSMUSE00000280565 Chr14:62980166..62980271 CCAAACTGTGGTGGCACTAA Chr14:62980171..62980190 59.61 50
upstream ENSMUSE00000122206 Chr14:62982867..62982948 ATGCCCATGGTCTGATCTCT Chr14:62982882..62982901 59.49 50
upstream ENSMUSE00000122207 Chr14:62984096..62984138 ATTGACCAACCCTCCATCAA Chr14:62984117..62984136 60.17 45

*** Putative Vector Insertion (Chr 14: 62984139 - 62989308) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000122212 Chr14:62989309..62989389 TGCCGGTCTTCAAGTCTTTAG Chr14:62989389..62989409 59.5 47.62
downstream ENSMUSE00000336995 Chr14:62991197..62991337 CTGAGCTGCAGTCATTTTGC Chr14:62991226..62991245 59.75 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATTGACCAACCCTCCATCAA Chr14:62987118..62987138 60.17 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TAGGCTTCCAGAACCTCCAG Chr14:62984094..62984114 59.42 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000021932