Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI19064
Trapped Gene
Plekha1 (ENSMUSG00000040268)
Vector Insertion
Chr 7: 138021247 - 138021409
Public Clones CMHD-GT_465E7-3 (cmhd)
Private Clones OST405816 (lexicon) OST371001 (lexicon) OST315144 (lexicon) OST288440 (lexicon)
OST286287 (lexicon) OST280386 (lexicon) OST276880 (lexicon) OST212536 (lexicon)
OST204625 (lexicon) OST111213 (lexicon) OST111205 (lexicon) OST57171 (lexicon)
OST35546 (lexicon)
Severity of mutation (?) Insertion after 0% 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
ENSMUSE00000710017 (Chr7:138021248..138021408 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GACAGAATCGCATCTGTGGA Chr7:138021284..138021303 59.79 50 AGATGCGATTCTGTCGATCC Chr7:138021301..138021320 60.19 50

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

*** Putative Vector Insertion (Chr 7: 138021247 - 138021409) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000303418 Chr7:138021248..138021408 AGATGCGATTCTGTCGATCC Chr7:138021301..138021320 60.19 50
downstream ENSMUSE00000710017 Chr7:138021248..138021408 AGATGCGATTCTGTCGATCC Chr7:138021301..138021320 60.19 50
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 AAGCCCAGAAATGCCTTATG Chr7:138021259..138021279 59.18 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACAGAATCGCATCGTGACTG Chr7:138021286..138021306 59.86 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040268