Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI14702
Trapped Gene
Shroom3 (ENSMUSG00000029381)
Vector Insertion
Chr 5: 93348670 - 93348803
Public Clones FHCRC-GT-ROSA53 (fhcrc)
Private Clones OST64793 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000321233 (Chr5:93348671..93348802 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGAGCTGCTCACCTGCAGTC Chr5:93348728..93348747 60.92 60 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000321233 (Chr5:93348671..93348802 +)
Downstram Exon
ENSMUSE00000694088 (Chr5:93348671..93348802 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGAGCTGCTCACCTGCAGTC Chr5:93348728..93348747 60.92 60 CCTCCTGACCATGTTGCTTT Chr5:93348781..93348800 60.11 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
upstream ENSMUSE00000321238 Chr5:93209779..93209933 AAGCTGGGGACGAAGTCATA Chr5:93209822..93209841 59.69 50
upstream ENSMUSE00000694089 Chr5:93238414..93238587 ACCAGCTCGACTGTGTGTCA Chr5:93238501..93238520 60.53 55
upstream ENSMUSE00000694084 Chr5:93327024..93327246 No primer for this exon

*** Putative Vector Insertion (Chr 5: 93348670 - 93348803) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 TCAGCTGTTGGCTTTCTTGTT Chr5:93348642..93348663 60.04 42.86 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGTCCCGTGACTGGGAAAAC Chr5:93348716..93348736 61.32 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029381