Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28632
Trapped Gene
Fxr1 (ENSMUSG00000027680)
Vector Insertion
Chr 3: 33967175 - 33967838
Public Clones CMHD-GT_457E2-3 (cmhd)
Private Clones OST24911 (lexicon) OST21961 (lexicon)
Severity of mutation (?) Insertion after 100% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000172144 (Chr3:33967083..33967174 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAACCTCCCAAGGGAAACT Chr3:33967131..33967150 59.42 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000172144 (Chr3:33967083..33967174 +)
Downstram Exon
ENSMUSE00000514715 (Chr3:33967839..33968259 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAACCTCCCAAGGGAAACT Chr3:33967131..33967150 59.42 50 CCTTTTCTGAAGGACCATGC Chr3:33967881..33967900 59.67 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000489359 Chr3:33919030..33919085 No primer for this exon
upstream ENSMUSE00000450747 Chr3:33938449..33938501 GTCCACGAAGACTCCCTCAC Chr3:33938464..33938483 59.69 60
upstream ENSMUSE00000639573 Chr3:33939985..33940078 AACGCCAGGTTCCGTTTAAT Chr3:33939996..33940015 60.72 45
upstream ENSMUSE00000639572 Chr3:33944954..33945025 GCTGGCTAAAGTTCGGATGA Chr3:33944995..33945014 60.35 50
upstream ENSMUSE00000639571 Chr3:33945359..33945507 TTCGGCCTGTCAATCAAAAT Chr3:33945423..33945442 60.45 40
upstream ENSMUSE00000639570 Chr3:33945888..33945981 AAAGCAGTAGGAGCATGCAGA Chr3:33945922..33945942 60.17 47.62
upstream ENSMUSE00000639569 Chr3:33946554..33946670 ATTCGGACGAAGTTGATGCT Chr3:33946614..33946633 59.7 45
upstream ENSMUSE00000639568 Chr3:33948075..33948245 GGAACGCATGGCAGTAACAT Chr3:33948147..33948166 60.92 50
upstream ENSMUSE00000639567 Chr3:33948997..33949075 No primer for this exon
upstream ENSMUSE00000639566 Chr3:33953144..33953253 GGATAAATCTGGTGTGGTTCG Chr3:33953187..33953207 59.3 47.62
upstream ENSMUSE00000639564 Chr3:33955252..33955338 AGCATTGGGAATGTGCAAGT Chr3:33955288..33955307 60.53 45
upstream ENSMUSE00000172139 Chr3:33956946..33957153 TGCCACTGATGAAAGTACCG Chr3:33957056..33957075 59.72 50
upstream ENSMUSE00000520260 Chr3:33956946..33957003 GGAACGTCTGCAGATTGATG Chr3:33956966..33956985 59.24 50
upstream ENSMUSE00000515423 Chr3:33957091..33957153 No primer for this exon
upstream ENSMUSE00000639563 Chr3:33960750..33960953 AACCCCTCCGAAACAGAATC Chr3:33960770..33960789 60.31 50
upstream ENSMUSE00000592734 Chr3:33963041..33963245 TCCGATCAGACTGCAGACAC Chr3:33963091..33963110 59.99 55
upstream ENSMUSE00000592745 Chr3:33963041..33963241 TCCGATCAGACTGCAGACAC Chr3:33963091..33963110 59.99 55
upstream ENSMUSE00000172137 Chr3:33963896..33963976 GGGGTCAGGCAGAAGATAGA Chr3:33963950..33963969 59.24 55
upstream ENSMUSE00000675906 Chr3:33965422..33965431 No primer for this exon
upstream ENSMUSE00000172144 Chr3:33967083..33967174 GAAACCTCCCAAGGGAAACT Chr3:33967131..33967150 59.42 50

*** Putative Vector Insertion (Chr 3: 33967175 - 33967838) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000514715 Chr3:33967839..33968259 CCTTTTCTGAAGGACCATGC Chr3:33967881..33967900 59.67 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACCTCCCAAGGGAAACTTTG Chr3:33967135..33967155 60.33 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACCTCCCAAGGGAAACTTTG Chr3:33967135..33967155 60.33 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027680