Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI23799
Trapped Gene
Plekha1 (ENSMUSG00000040268)
Vector Insertion
Chr 7: 138021409 - 138025843
Public Clones IST14978H9 (tigm)
Private Clones OST244508 (lexicon) OST197685 (lexicon)
Severity of mutation (?) Insertion after 13% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000303418 (Chr7:138021248..138021408 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GACAGAATCGCATCTGTGGA Chr7:138021284..138021303 59.79 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000303418 (Chr7:138021248..138021408 +)
Downstram Exon
ENSMUSE00000303415 (Chr7:138025844..138025900 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GACAGAATCGCATCTGTGGA Chr7:138021284..138021303 59.79 50 No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000722344 Chr7:138009270..138009497 TAGTGTTCGCGGTAGGGAGT Chr7:138009320..138009339 59.76 55
upstream ENSMUSE00000587719 Chr7:138009412..138009514 No primer for this exon
upstream ENSMUSE00000303424 Chr7:138009424..138009497 No primer for this exon
upstream ENSMUSE00000303418 Chr7:138021248..138021408 GACAGAATCGCATCTGTGGA Chr7:138021284..138021303 59.79 50
upstream ENSMUSE00000710017 Chr7:138021248..138021408 GACAGAATCGCATCTGTGGA Chr7:138021284..138021303 59.79 50

*** Putative Vector Insertion (Chr 7: 138021409 - 138025843) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000303415 Chr7:138025844..138025900 No primer for this exon
downstream ENSMUSE00000433230 Chr7:138028917..138028962 TCTGCCTTTGGCCTTAACTT Chr7:138028954..138028973 58.97 45
downstream ENSMUSE00000433218 Chr7:138035695..138035792 CCACTCCACTAAGTCCTGCTG Chr7:138035761..138035781 59.92 57.14
downstream ENSMUSE00000303411 Chr7:138040839..138040964 GGCTGTGAGTCTGACTGCTTT Chr7:138040866..138040886 59.66 52.38
downstream ENSMUSE00000303403 Chr7:138044031..138044174 GAAGGTGGCTTAGGAGCAAA Chr7:138044128..138044147 59.45 50
downstream ENSMUSE00000303397 Chr7:138045691..138045759 No primer for this exon
downstream ENSMUSE00000303392 Chr7:138048384..138048448 AAGTGGTATCACCCGCAGAG Chr7:138048416..138048435 60.13 55
downstream ENSMUSE00000526658 Chr7:138048905..138048968 TCGTCACGATTTCAAACAGG Chr7:138048948..138048967 59.69 45
downstream ENSMUSE00000303374 Chr7:138051850..138051939 GCGCCAGAGACTGCTTTAAT Chr7:138051902..138051921 59.62 50
downstream ENSMUSE00000511504 Chr7:138053102..138053142 AAGGGTTCGACAGCCTTCTG Chr7:138053135..138053154 61.71 55
downstream ENSMUSE00000717258 Chr7:138053102..138053249 GCTGTAAGGAGGAGCGAGTC Chr7:138053240..138053259 59.19 60
downstream ENSMUSE00000512089 Chr7:138054346..138056816 GTGCTGGGCAACTAAAGAGC Chr7:138056162..138056181 60.02 55
downstream ENSMUSE00000526656 Chr7:138054346..138054997 AGGACGGACAGTGAATTTGG Chr7:138054393..138054412 59.97 50
downstream ENSMUSE00000668952 Chr7:138054346..138054997 AGGACGGACAGTGAATTTGG Chr7:138054393..138054412 59.97 50
downstream ENSMUSE00000714336 Chr7:138054346..138056826 GTGCTGGGCAACTAAAGAGC Chr7:138056162..138056181 60.02 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TATTAATCGCCTTGCAGCAC Chr7:138021457..138021477 58.94 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGTGTATATCGTGACTGGGAAAA Chr7:138021451..138021474 60.12 43.48 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040268