Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35896
Trapped Gene
5330417C22Rik (ENSMUSG00000040412)
Vector Insertion
Chr 3: 108294916 - 108339436
Public Clones IST11504E3 (tigm) IST12858E7 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000711246 (Chr3:108339214..108339435 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AAAAACTGAAAGGCGCACAC Chr3:108339300..108339319 60.29 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000711246 (Chr3:108339214..108339435 -)
Downstram Exon
ENSMUSE00000670694 (Chr3:108294917..108295037 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AAAAACTGAAAGGCGCACAC Chr3:108339300..108339319 60.29 45 CGCACGCTGTGTACTCAAAA Chr3:108294985..108295004 61.04 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000670678 Chr3:108339214..108339444 AAAAACTGAAAGGCGCACAC Chr3:108339300..108339319 60.29 45
upstream ENSMUSE00000711246 Chr3:108339214..108339435 AAAAACTGAAAGGCGCACAC Chr3:108339300..108339319 60.29 45
upstream ENSMUSE00000716391 Chr3:108339214..108339435 AAAAACTGAAAGGCGCACAC Chr3:108339300..108339319 60.29 45
upstream ENSMUSE00000670694 Chr3:108294917..108295037 GAGTACACAGCGTGCGACAG Chr3:108295003..108295022 60.68 60

*** Putative Vector Insertion (Chr 3: 108294916 - 108339436) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000587565 Chr3:108291748..108291940 AGTGGACTCCGAGATGCTGT Chr3:108291740..108291759 59.87 55
downstream ENSMUSE00000670693 Chr3:108291748..108291940 AGTGGACTCCGAGATGCTGT Chr3:108291740..108291759 59.87 55
downstream ENSMUSE00000587564 Chr3:108285249..108285396 GACGGCATACATCAGTGTGG Chr3:108285299..108285318 59.99 55
downstream ENSMUSE00000670692 Chr3:108284712..108284780 TCATCCACCTGGAGTCATCA Chr3:108284710..108284729 60.05 50
downstream ENSMUSE00000587563 Chr3:108284700..108284780 TCATCCACCTGGAGTCATCA Chr3:108284710..108284729 60.05 50
downstream ENSMUSE00000564704 Chr3:108284182..108284287 ACACCGAGAAAGCTGTGGTT Chr3:108284208..108284227 59.77 50
downstream ENSMUSE00000587560 Chr3:108283894..108284043 GCAGGACGTTTCTCCTTTGT Chr3:108283900..108283919 59.33 50
downstream ENSMUSE00000587559 Chr3:108277879..108277967 TTGCAGGTGGAAGATCCTTT Chr3:108277924..108277943 59.67 45
downstream ENSMUSE00000587558 Chr3:108275641..108275818 TTTTGGTATGGCCCATTTGT Chr3:108275764..108275783 60.05 40
downstream ENSMUSE00000274871 Chr3:108274887..108275015 GCAGTGTGTTCCACCATTTG Chr3:108274925..108274944 60.01 50
downstream ENSMUSE00000274865 Chr3:108274266..108274356 AGTCGTTGTCTGAGGCACCA Chr3:108274278..108274297 61.9 55
downstream ENSMUSE00000274859 Chr3:108272820..108272925 CTGGCCACCTCTTTGTTCTC Chr3:108272856..108272875 59.84 55
downstream ENSMUSE00000274851 Chr3:108272446..108272583 TTTCATGAAGGGTGGTCCTC Chr3:108272426..108272445 59.9 50
downstream ENSMUSE00000335040 Chr3:108270671..108270934 AATCCCGGTTGATGTAATGG Chr3:108270753..108270772 59.51 45
downstream ENSMUSE00000373240 Chr3:108268524..108268697 GGTGCAGTCGTTGTAGCAGA Chr3:108268646..108268665 60.06 55
downstream ENSMUSE00000364934 Chr3:108267173..108267353 ACCTGGCAGACATAGGCTGT Chr3:108267231..108267250 59.75 55
downstream ENSMUSE00000402645 Chr3:108266388..108266484 TTCAACTGGGGAGACGATTC Chr3:108266416..108266435 60.05 50
downstream ENSMUSE00000362165 Chr3:108265808..108265909 AGCAGCTTTCATTGGATTGC Chr3:108265809..108265828 60.36 45
downstream ENSMUSE00000274935 Chr3:108264114..108264240 ATCACAGGTCCCATCAGAGC Chr3:108264194..108264213 60.08 55
downstream ENSMUSE00000274927 Chr3:108263857..108264035 TTGGTTCTCGCCACATGTAA Chr3:108263986..108264005 60.11 45
downstream ENSMUSE00000670677 Chr3:108262722..108262768 AGCGTTCATTACCAACTTGGAG Chr3:108262710..108262731 60.53 45.46
downstream ENSMUSE00000670680 Chr3:108262721..108262768 AGCGTTCATTACCAACTTGGAG Chr3:108262710..108262731 60.53 45.46
downstream ENSMUSE00000274917 Chr3:108262603..108262768 ATCCTCCACGTCCTCTCCTT Chr3:108262641..108262660 60.07 55
downstream ENSMUSE00000670679 Chr3:108261160..108261205 No primer for this exon
downstream ENSMUSE00000670676 Chr3:108261102..108261206 TTGAGGCAAGCGTAGAGACA Chr3:108261106..108261125 59.74 50
downstream ENSMUSE00000587557 Chr3:108260987..108261386 ACCGAGTCAAATCCATCAGG Chr3:108261339..108261358 59.93 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GGGACAGAATGTGACCATCC Chr3:108309396..108309416 60.18 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGGACAGAATGTGACCATCC Chr3:108309396..108309416 60.18 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040412