Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI4004
Trapped Gene
AC175246.2 (ENSMUSG00000026361)
Vector Insertion
Chr 1: 145518559 - 145524768
Public Clones AR0076 (sanger) AM0056 (sanger) AM0055 (sanger) A062C05 (ggtc)
Private Clones not available
Severity of mutation (?) Insertion after 46% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000158425 (Chr1:145524769..145524985 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CTGAAGCCATGTCAGTGGAA Chr1:145524958..145524977 59.83 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000158425 (Chr1:145524769..145524985 -)
Downstram Exon
ENSMUSE00000158419 (Chr1:145518460..145518558 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CTGAAGCCATGTCAGTGGAA Chr1:145524958..145524977 59.83 50 ACGACCTTCTTCTCTGGCTTT Chr1:145518477..145518497 59.52 47.62

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000335477 Chr1:145549624..145549814 TGAAGTGATCTTCGGGGAGT Chr1:145549667..145549686 59.65 50
upstream ENSMUSE00000158420 Chr1:145546347..145546452 TAATGTGCACCTTTCGCATC Chr1:145546370..145546389 59.69 45
upstream ENSMUSE00000158422 Chr1:145542523..145542592 TTAGAAGACCCGACCGAAAA Chr1:145542554..145542573 59.68 45
upstream ENSMUSE00000158427 Chr1:145538544..145538606 GAGTGCCCCCTTGGAAATAG Chr1:145538565..145538584 60.82 55
upstream ENSMUSE00000279140 Chr1:145538405..145538457 AGCAAAGAAACCACGGATTG Chr1:145538407..145538426 60.11 45
upstream ENSMUSE00000279133 Chr1:145533053..145533141 TCGTTTGGAAGGCCATAAAG Chr1:145533081..145533100 60.07 45
upstream ENSMUSE00000158425 Chr1:145524769..145524985 CTGAAGCCATGTCAGTGGAA Chr1:145524958..145524977 59.83 50

*** Putative Vector Insertion (Chr 1: 145518559 - 145524768) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000158419 Chr1:145518460..145518558 ACGACCTTCTTCTCTGGCTTT Chr1:145518477..145518497 59.52 47.62
downstream ENSMUSE00000158416 Chr1:145517120..145517198 GCAGCTGGAATAGGCTGTTT Chr1:145517139..145517158 59.48 50
downstream ENSMUSE00000158418 Chr1:145514755..145514819 CCATGGTAGGTGCCCATAGT Chr1:145514755..145514774 59.69 55
downstream ENSMUSE00000279102 Chr1:145482162..145482219 GGCTGCAGGAGTTTGAGTCT Chr1:145482159..145482178 59.6 55
downstream ENSMUSE00000279097 Chr1:145474976..145475011 No primer for this exon
downstream ENSMUSE00000279089 Chr1:145474632..145474719 AATAATGGGTGTCCGTGACC Chr1:145474678..145474697 59.53 50
downstream ENSMUSE00000279080 Chr1:145464409..145464570 CCTGGTTGCATCTGGTCTTT Chr1:145464459..145464478 60.11 50
downstream ENSMUSE00000158413 Chr1:145462433..145462533 AAACAGCCACAACTCGATCC Chr1:145462492..145462511 60.12 50
downstream ENSMUSE00000158423 Chr1:145456500..145456641 CCCAGAAACGTAAGAAAACTGG Chr1:145456491..145456512 60.03 45.46
downstream ENSMUSE00000595574 Chr1:145454630..145455687 TCGGATACACACAGGCTGAC Chr1:145455110..145455129 59.71 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TAATCGCCTTGCAGCACATC Chr1:145521697..145521717 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGAAACGTGACTGGGAAAAC Chr1:145524702..145524723 60 42.86 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026361