Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI10189
Trapped Gene
2810407C02Rik (ENSMUSG00000075700)
Vector Insertion
Chr 3: 58390001 - 58392367
Public Clones DTM024 (baygenomics)
Private Clones OST379096 (lexicon)
Severity of mutation (?) Insertion after 64% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000173238 (Chr3:58389874..58390000 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCTCCTAGCATCTGGCAGT Chr3:58389964..58389983 59.22 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000173238 (Chr3:58389874..58390000 +)
Downstram Exon
ENSMUSE00000173240 (Chr3:58392368..58392455 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCTCCTAGCATCTGGCAGT Chr3:58389964..58389983 59.22 55 TCTCAATCATGTTGCTCAGGA Chr3:58392415..58392435 59.38 42.86

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000674842 Chr3:58380558..58380795 GCGGCTGTCTCAATTACGAT Chr3:58380641..58380660 60.24 50
upstream ENSMUSE00000660055 Chr3:58380603..58380795 GCGGCTGTCTCAATTACGAT Chr3:58380641..58380660 60.24 50
upstream ENSMUSE00000660056 Chr3:58389153..58389263 GTTATCAGCCAGCGGTATCC Chr3:58389196..58389215 59.56 55
upstream ENSMUSE00000173238 Chr3:58389874..58390000 AGCTCCTAGCATCTGGCAGT Chr3:58389964..58389983 59.22 55

*** Putative Vector Insertion (Chr 3: 58390001 - 58392367) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000173240 Chr3:58392368..58392455 TCTCAATCATGTTGCTCAGGA Chr3:58392415..58392435 59.38 42.86
downstream ENSMUSE00000660057 Chr3:58394086..58394213 TGATCGATGATGTGGGATTG Chr3:58394213..58394232 60.29 45
downstream ENSMUSE00000674839 Chr3:58394089..58394242 TTCGGTGCTGATAGGTAGGG Chr3:58394236..58394255 60.09 55
downstream ENSMUSE00000674838 Chr3:58394617..58397055 TCTCCCATTGCAGTTCCTTC Chr3:58395878..58395897 60.19 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGGGGCCAAGAAAATAAGGT Chr3:58389984..58390004 60.66 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGGGGCCAAGAAAATAAGGT Chr3:58389984..58390004 60.66 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000075700