Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12577
Trapped Gene
Adh5 (ENSMUSG00000028138)
Vector Insertion
Chr 3: 138117771 - 138118048
Public Clones W052B06 (ggtc)
Private Clones OST31264 (lexicon)
Severity of mutation (?) Insertion after 98% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000176727 (Chr3:138117632..138117770 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AATTTGTGACCGGCAATCTC Chr3:138117701..138117720 59.94 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000176727 (Chr3:138117632..138117770 +)
Downstram Exon
ENSMUSE00000331984 (Chr3:138118049..138118463 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AATTTGTGACCGGCAATCTC Chr3:138117701..138117720 59.94 45 GTTGCACAATGAGCAGCAAT Chr3:138118254..138118273 59.88 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000176694 Chr3:138106128..138106157 No primer for this exon
upstream ENSMUSE00000176729 Chr3:138108254..138108355 AAGGCTCATGAAGTTCGGATT Chr3:138108332..138108352 60.09 42.86
upstream ENSMUSE00000176691 Chr3:138110047..138110188 CTATACCCTGAGCGGAGCTG Chr3:138110079..138110098 59.99 60
upstream ENSMUSE00000176714 Chr3:138110816..138110903 CATCCCACTCTACATCCCACA Chr3:138110826..138110846 60.78 52.38
upstream ENSMUSE00000176685 Chr3:138113863..138114082 TGGGGACTAGCACATTTTCC Chr3:138113940..138113959 59.93 50
upstream ENSMUSE00000176731 Chr3:138114208..138114468 CATCCCGGATCATTGGTATC Chr3:138114290..138114309 59.97 50
upstream ENSMUSE00000176690 Chr3:138116706..138116841 GTGGGAGTAGCTGCTTCAGG Chr3:138116754..138116773 60.01 60
upstream ENSMUSE00000176727 Chr3:138117632..138117770 AATTTGTGACCGGCAATCTC Chr3:138117701..138117720 59.94 45

*** Putative Vector Insertion (Chr 3: 138117771 - 138118048) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000331984 Chr3:138118049..138118463 GTTGCACAATGAGCAGCAAT Chr3:138118254..138118273 59.88 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGTTCCAGAATCTGCCTGTG Chr3:138117791..138117811 59.83 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGTGGTGTTAAAAGCCGTGA Chr3:138117807..138117827 60.15 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000028138