Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13104
Trapped Gene
Pik3ip1 (ENSMUSG00000034614)
Vector Insertion
Chr 11: 3233968 - 3241525
Public Clones CMHD-GT_314H08-3 (cmhd) CMHD-GT_391G12-3 (cmhd) CMHD-GT_485H1-3 (cmhd) CMHD-GT_326E11-3 (cmhd)
CMHD-GT_439D4-3 (cmhd) CMHD-GT_489B7-3 (cmhd) FHCRC-GT-S18-3D1 (fhcrc) IST12963C7 (tigm)
IST13309D3 (tigm) IST12229B5 (tigm) IST12124B3 (tigm) IST14161C7 (tigm)
Private Clones OST235800 (lexicon)
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000682486 (Chr11:3233508..3233967 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACATCAGCTTCTTGGCGTCT Chr11:3233649..3233668 60.02 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000682486 (Chr11:3233508..3233967 +)
Downstram Exon
ENSMUSE00000314282 (Chr11:3241526..3242973 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACATCAGCTTCTTGGCGTCT Chr11:3233649..3233668 60.02 50 TCCTTCAGGTCTTTCGCAGT Chr11:3242663..3242682 59.99 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000314311 Chr11:3230793..3231007 TGGACACTGGCTGTTGAGTC Chr11:3230895..3230914 59.87 55
upstream ENSMUSE00000595383 Chr11:3230811..3231007 TGGACACTGGCTGTTGAGTC Chr11:3230895..3230914 59.87 55
upstream ENSMUSE00000314307 Chr11:3231918..3232034 ACCTGTACCGGGAGGACCAG Chr11:3231939..3231958 63.56 65
upstream ENSMUSE00000314300 Chr11:3232112..3232231 ACCACAACTACTGCCGGAAC Chr11:3232121..3232140 60.03 55
upstream ENSMUSE00000314294 Chr11:3233212..3233415 AGTGATCGGGATCAGTCAGC Chr11:3233351..3233370 60.23 55
upstream ENSMUSE00000314288 Chr11:3233508..3233586 GGCATTATCGTGGGCTACAC Chr11:3233558..3233577 60.36 55
upstream ENSMUSE00000682486 Chr11:3233508..3233967 ACATCAGCTTCTTGGCGTCT Chr11:3233649..3233668 60.02 50

*** Putative Vector Insertion (Chr 11: 3233968 - 3241525) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000314282 Chr11:3241526..3242973 TCCTTCAGGTCTTTCGCAGT Chr11:3242663..3242682 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGGGTTGTGAGCTGCCATA Chr11:3236928..3236948 61.21 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CATCTTTCGTGACTGGGAAA Chr11:3237012..3237032 58.69 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000034614