Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI243
Trapped Gene
Jam2 (ENSMUSG00000053062)
Vector Insertion
Chr 16: 84774367 - 84774799
Public Clones GC0388 (tigem) RST515 (baygenomics) M124A10 (ggtc) P082F01 (ggtc)
G007C04 (ggtc) P066B02 (ggtc) Q009D05 (ggtc) M058C08 (ggtc) G064A07 (ggtc)
P089C05 (ggtc) W203D08 (ggtc) P024D02 (ggtc) W173C05 (ggtc) W203C08 (ggtc)
G026D05 (ggtc) P078B01 (ggtc) P012G01 (ggtc) Q017A02 (ggtc) P111H12 (ggtc)
P090D09 (ggtc) G004D03 (ggtc) P068E05 (ggtc) Q020B05 (ggtc) G038A09 (ggtc)
D007B12 (ggtc) G074A03 (ggtc) G057F02 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000698472 (Chr16:84774368..84774798 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTCCTAGGGCCAGAAGACCT Chr16:84774523..84774542 59.7 60 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000698472 (Chr16:84774368..84774798 +)
Downstram Exon
ENSMUSE00000465097 (Chr16:84774528..84774798 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTCCTAGGGCCAGAAGACCT Chr16:84774523..84774542 59.7 60 GGGCGACGATCAAGTAGTGT Chr16:84774795..84774814 60.14 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC

*** Putative Vector Insertion (Chr 16: 84774367 - 84774799) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000698472 Chr16:84774368..84774798 GGGCGACGATCAAGTAGTGT Chr16:84774795..84774814 60.14 55
downstream ENSMUSE00000465097 Chr16:84774528..84774798 GGGCGACGATCAAGTAGTGT Chr16:84774795..84774814 60.14 55
downstream ENSMUSE00000698466 Chr16:84774631..84774798 GGGCGACGATCAAGTAGTGT Chr16:84774795..84774814 60.14 55
downstream ENSMUSE00000268247 Chr16:84801815..84801883 TTGACGGTGGTCTTTTGATG Chr16:84801861..84801880 59.54 45
downstream ENSMUSE00000268240 Chr16:84807080..84807187 TGGGGTTTTACAAGCCAAAA Chr16:84807108..84807127 60.33 40
downstream ENSMUSE00000496500 Chr16:84809589..84809741 CACAGCGATACTCTCCAGCA Chr16:84809678..84809697 60.16 55
downstream ENSMUSE00000634408 Chr16:84809589..84811241 TTCCAGACCCTAGCATGGAC Chr16:84809998..84810017 60.07 55
downstream ENSMUSE00000131665 Chr16:84813144..84813343 CCTTCTTTATCCTGGCATCG Chr16:84813231..84813250 59.66 50
downstream ENSMUSE00000131671 Chr16:84815414..84815513 CTCCACTGTCCATCTTGGAA Chr16:84815450..84815469 58.64 50
downstream ENSMUSE00000131673 Chr16:84816511..84816618 ACCACCACAACCGTTGCTAT Chr16:84816556..84816575 60.3 50
downstream ENSMUSE00000698469 Chr16:84819005..84819020 No primer for this exon
downstream ENSMUSE00000131670 Chr16:84821505..84821547 No primer for this exon
downstream ENSMUSE00000404528 Chr16:84823032..84823128 TTTGGTGCAGCTCAAAACTG Chr16:84823095..84823114 60.03 45
downstream ENSMUSE00000698468 Chr16:84823032..84826173 TTTGGTGCAGCTCAAAACTG Chr16:84823095..84823114 60.03 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGTTCTCCCTCAAGAGGCTA Chr16:84774396..84774416 58.47 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCCCTCAAGAGGCTAGTCGT Chr16:84774401..84774421 59.04 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000053062