Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1880
Trapped Gene
Srprb (ENSMUSG00000032553)
Vector Insertion
Chr 9: 103101197 - 103103616
Public Clones AY0799 (sanger)
Private Clones OST419361 (lexicon) OST42133 (lexicon)
Severity of mutation (?) Insertion after 30% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000220699 (Chr9:103103617..103103711 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGGAAAACGTTGCTGTTTGT Chr9:103103621..103103640 60.01 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000220699 (Chr9:103103617..103103711 -)
Downstram Exon
ENSMUSE00000220705 (Chr9:103101119..103101196 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGGAAAACGTTGCTGTTTGT Chr9:103103621..103103640 60.01 45 TGGCAGAACTATCGGTAATGG Chr9:103101120..103101140 59.97 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000398828 Chr9:103104242..103104437 CCAGCCTTACCTCGACTCCT Chr9:103104320..103104339 60.78 60
upstream ENSMUSE00000220699 Chr9:103103617..103103711 GGGAAAACGTTGCTGTTTGT Chr9:103103621..103103640 60.01 45

*** Putative Vector Insertion (Chr 9: 103101197 - 103103616) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000220705 Chr9:103101119..103101196 TGGCAGAACTATCGGTAATGG Chr9:103101120..103101140 59.97 47.62
downstream ENSMUSE00000220707 Chr9:103099868..103099950 GGGAGGTCGATCAGAGTCAG Chr9:103099900..103099919 59.79 60
downstream ENSMUSE00000320245 Chr9:103094543..103094679 AATTCGGCCACATCTTTCAC Chr9:103094595..103094614 59.94 45
downstream ENSMUSE00000220708 Chr9:103093399..103093453 ACTTCGCTGATTTTGCCATT Chr9:103093405..103093424 59.71 40
downstream ENSMUSE00000396391 Chr9:103091420..103092751 CCCTACTCTCAAAGCGATGC Chr9:103092243..103092262 59.98 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGGGAAAACGTTGCTGTTT Chr9:103103621..103103641 60.15 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CTGGGAAAACGTTGCTGTTT Chr9:103103621..103103641 60.15 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032553