Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI19577
Trapped Gene
Shroom3 (ENSMUSG00000029381)
Vector Insertion
Chr 5: 93112858 - 93209778
Public Clones IST14206G6 (tigm) IST12485H6 (tigm) IST11825B2 (tigm) IST12588E3 (tigm)
IST10885F3 (tigm) IST12646C2 (tigm) IST12726D10 (tigm) IST12427H12 (tigm)
IST12421F12 (tigm) IST13960F6 (tigm) IST12726D10 (tigm) IST12810G1 (tigm)
IST14623C2 (tigm) IST14317E7 (tigm) IST14313E7 (tigm) IST11825B1 (tigm)
Private Clones OST388613 (lexicon) OST300595 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000475607 (Chr5:93112461..93112857 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCCACGGAGAGATTCGTTTA Chr5:93112750..93112769 60.07 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000475607 (Chr5:93112461..93112857 +)
Downstram Exon
ENSMUSE00000321238 (Chr5:93209779..93209933 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCCACGGAGAGATTCGTTTA Chr5:93112750..93112769 60.07 50 TATGACTTCGTCCCCAGCTT Chr5:93209844..93209863 59.69 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000475607 Chr5:93112461..93112857 CCCACGGAGAGATTCGTTTA Chr5:93112750..93112769 60.07 50

*** Putative Vector Insertion (Chr 5: 93112858 - 93209778) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000321238 Chr5:93209779..93209933 TATGACTTCGTCCCCAGCTT Chr5:93209844..93209863 59.69 50
downstream ENSMUSE00000694089 Chr5:93238414..93238587 CCTCAGTGATCTGCTGGATG Chr5:93238556..93238575 59.37 55
downstream ENSMUSE00000694084 Chr5:93327024..93327246 No primer for this exon
downstream ENSMUSE00000321233 Chr5:93348671..93348802 CCTCCTGACCATGTTGCTTT Chr5:93348781..93348800 60.11 50
downstream ENSMUSE00000694088 Chr5:93348671..93348802 CCTCCTGACCATGTTGCTTT Chr5:93348781..93348800 60.11 50
downstream ENSMUSE00000321231 Chr5:93362780..93362911 GTAGCTCTGGTGCCAAGGAG Chr5:93362906..93362925 60.01 60
downstream ENSMUSE00000694087 Chr5:93362780..93362911 GTAGCTCTGGTGCCAAGGAG Chr5:93362906..93362925 60.01 60
downstream ENSMUSE00000694094 Chr5:93369003..93372165 TAGGAGCGCTTCTTCTGCTC Chr5:93371459..93371478 60 55
downstream ENSMUSE00000188405 Chr5:93377430..93377503 No primer for this exon
downstream ENSMUSE00000188402 Chr5:93379510..93380346 CAGGGCTTCTTGGACTGGTA Chr5:93379865..93379884 60.25 55
downstream ENSMUSE00000321188 Chr5:93381565..93382056 TTTCCTCTTTGCGCCACTAT Chr5:93382015..93382034 59.85 45
downstream ENSMUSE00000321182 Chr5:93384287..93384437 CTCCGGCATGTCTTTGATTT Chr5:93384395..93384414 60.07 45
downstream ENSMUSE00000321177 Chr5:93391117..93391389 TTCAGCTTGATGTCCGTGAG Chr5:93391202..93391221 59.98 50
downstream ENSMUSE00000483674 Chr5:93393382..93394785 TTGCCTACATCCACCACAAA Chr5:93394287..93394306 59.96 45

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GAGCGTGGAGAACCGTTAAT Chr5:93124829..93124849 59.2 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGACATGATCTGTGGGTTGG Chr5:93124883..93124903 60.38 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029381