Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI38515
Trapped Gene
Igsf3 (ENSMUSG00000042035)
Vector Insertion
Chr 3: 101243703 - 101254806
Public Clones (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 57% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000456935 (Chr3:101243298..101243702 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGGTGACCTTCACACGAGA Chr3:101243456..101243475 59.86 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000456935 (Chr3:101243298..101243702 +)
Downstram Exon
ENSMUSE00000370610 (Chr3:101254807..101255217 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGGTGACCTTCACACGAGA Chr3:101243456..101243475 59.86 55 CGTAGGTCCCGTACTCGAAG Chr3:101255013..101255032 59.75 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000503310 Chr3:101181048..101181125 No primer for this exon
upstream ENSMUSE00000456978 Chr3:101181729..101182415 CGAATGAGCGATCTCAGACA Chr3:101181944..101181963 60.1 50
upstream ENSMUSE00000456959 Chr3:101229374..101229751 TGAGCGCTACTTTGGGAGTT Chr3:101229708..101229727 60.01 50
upstream ENSMUSE00000456951 Chr3:101230953..101231363 GAAGCACCTTTCGTCTCACC Chr3:101231208..101231227 59.85 55
upstream ENSMUSE00000456946 Chr3:101235127..101235516 AAAGAGTTCACCGTGCGTCT Chr3:101235129..101235148 59.91 50
upstream ENSMUSE00000244853 Chr3:101239254..101239655 GTGTCGTCCTTGAGGGAGAG Chr3:101239290..101239309 59.83 60
upstream ENSMUSE00000456935 Chr3:101243298..101243702 CTGGTGACCTTCACACGAGA Chr3:101243456..101243475 59.86 55

*** Putative Vector Insertion (Chr 3: 101243703 - 101254806) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000370610 Chr3:101254807..101255217 CGTAGGTCCCGTACTCGAAG Chr3:101255013..101255032 59.75 60
downstream ENSMUSE00000456923 Chr3:101259028..101259435 GTCCTGTACCGCCACATTCT Chr3:101259326..101259345 60 55
downstream ENSMUSE00000456919 Chr3:101261546..101262031 TAGGGAATACCAGGCCACAG Chr3:101261679..101261698 59.95 55
downstream ENSMUSE00000515848 Chr3:101263710..101264773 TCCGGCTGAAGGAAGAGATA Chr3:101264614..101264633 59.91 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGACATGGGATGGCTAAAAA Chr3:101246678..101246699 60.31 38.1 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGGACACAGGACCGTGACTG Chr3:101246742..101246762 61.21 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042035