Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4017
Trapped Gene
Fbxl10 (ENSMUSG00000029475)
Vector Insertion
Chr 5: 123397890 - 123399078
Public Clones AQ1011 (sanger)
Private Clones OST419990 (lexicon)
Severity of mutation (?) Insertion after 0% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000328651 (Chr5:123399079..123399172 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACCTCCGTGTGGTACCATGT Chr5:123399095..123399114 60.16 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000328651 (Chr5:123399079..123399172 -)
Downstram Exon
ENSMUSE00000328643 (Chr5:123397736..123397889 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACCTCCGTGTGGTACCATGT Chr5:123399095..123399114 60.16 55 ACCCACTCCTCGTACAAAGC Chr5:123397812..123397831 59.21 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000717210 Chr5:123439634..123439832 CGCAAATGGATAAGGGTCTG Chr5:123439731..123439750 60.46 50
upstream ENSMUSE00000518745 Chr5:123438877..123438909 No primer for this exon
upstream ENSMUSE00000714097 Chr5:123438877..123439315 TTACGTTCCGGGGATTATGA Chr5:123439130..123439149 60.15 45
upstream ENSMUSE00000593008 Chr5:123438476..123438542 GGGGAGTCTCCTTAGGAAGTG Chr5:123438516..123438536 59.19 57.14
upstream ENSMUSE00000338385 Chr5:123437671..123437815 TATACCAGGGGGACTTCGTG Chr5:123437690..123437709 59.81 55
upstream ENSMUSE00000376150 Chr5:123434471..123434549 TTCGGGACAAGGATGGACTA Chr5:123434479..123434498 60.45 50
upstream ENSMUSE00000328593 Chr5:123432786..123432832 TGATTTCACAGTCCGAGACG Chr5:123432801..123432820 59.83 50
upstream ENSMUSE00000328661 Chr5:123411419..123411597 CCAGAAGGGTACCGAGATGA Chr5:123411541..123411560 60.06 55
upstream ENSMUSE00000328656 Chr5:123411022..123411128 GTGGCCTCAGCATCTAAAGG Chr5:123411080..123411099 59.84 55
upstream ENSMUSE00000328651 Chr5:123399079..123399172 ACCTCCGTGTGGTACCATGT Chr5:123399095..123399114 60.16 55

*** Putative Vector Insertion (Chr 5: 123397890 - 123399078) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000328643 Chr5:123397736..123397889 ACCCACTCCTCGTACAAAGC Chr5:123397812..123397831 59.21 55
downstream ENSMUSE00000328635 Chr5:123390962..123391077 CACGTTGAAGCTATGCAGGA Chr5:123390982..123391001 60.01 50
downstream ENSMUSE00000328629 Chr5:123384742..123384868 TAACGGAACTTGGGCTGAAC Chr5:123384827..123384846 60.11 50
downstream ENSMUSE00000331402 Chr5:123382476..123382960 CCGGAAGGGACTCTAGCTTT Chr5:123382516..123382535 59.84 55
downstream ENSMUSE00000382139 Chr5:123371394..123371480 CATCCACGTGCTCTTTCAGT Chr5:123371434..123371453 58.88 50
downstream ENSMUSE00000537526 Chr5:123350158..123350359 GGCTCCGATTCATAGTCGTC Chr5:123350143..123350162 59.66 55
downstream ENSMUSE00000328745 Chr5:123338539..123338763 AGTGGCACTCTCCACACTCC Chr5:123338591..123338610 60.31 60
downstream ENSMUSE00000437855 Chr5:123333328..123333471 GTGGATGATCTCGTTGCAGA Chr5:123333321..123333340 59.79 50
downstream ENSMUSE00000247403 Chr5:123332411..123332497 GAAGCTCATCGTTGACCACA Chr5:123332439..123332458 59.84 50
downstream ENSMUSE00000437831 Chr5:123331973..123332233 CTTGTTGTCCCGGTTCATCT Chr5:123332128..123332147 59.97 50
downstream ENSMUSE00000437825 Chr5:123331646..123331759 GGCTGAGACTGCTGCCTAGA Chr5:123331662..123331681 60.84 60
downstream ENSMUSE00000437822 Chr5:123331029..123331067 No primer for this exon
downstream ENSMUSE00000412900 Chr5:123330182..123330861 GTGAGCTGGAACGTGACTGA Chr5:123330701..123330720 60.03 55
downstream ENSMUSE00000189235 Chr5:123329498..123329661 CCAACTGAGGTCAAGGGAGA Chr5:123329525..123329544 60.23 55
downstream ENSMUSE00000189228 Chr5:123329254..123329415 CCTCATCTGGGCATCCTTTA Chr5:123329266..123329285 60.03 50
downstream ENSMUSE00000189233 Chr5:123328444..123328662 AGGCGCAGCTCTACAATGTT Chr5:123328592..123328611 60.04 50
downstream ENSMUSE00000716214 Chr5:123321714..123321906 AGCGTTTGAAGAAGGACAGG Chr5:123321840..123321859 59.47 50
downstream ENSMUSE00000593009 Chr5:123320690..123321906 TGCATCAGGGAAAGGTTAGG Chr5:123320702..123320721 60.07 50
downstream ENSMUSE00000719227 Chr5:123320688..123321906 TGCATCAGGGAAAGGTTAGG Chr5:123320702..123320721 60.07 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACCTCCGTGTGGTACCATGT Chr5:123399093..123399113 60.16 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACCTCCGTGTGGTACCATGT Chr5:123399093..123399113 60.16 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029475