Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28523
Trapped Gene
1700009P17Rik (ENSMUSG00000026649)
Vector Insertion
Chr 1: 173056342 - 173056694
Public Clones CMHD-GT_405A1-3 (cmhd)
Private Clones OST28934 (lexicon) OST28932 (lexicon) OST28567 (lexicon) OST28272 (lexicon)
OST24381 (lexicon) OST16732 (lexicon) OST16630 (lexicon) OST13698 (lexicon)
OST12395 (lexicon) OST2239 (lexicon)
Severity of mutation (?) Insertion after 61% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000479738 (Chr1:173056165..173056341 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACTACAGCTGCCGACAACCT Chr1:173056249..173056268 59.94 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000479738 (Chr1:173056165..173056341 +)
Downstram Exon
ENSMUSE00000706641 (Chr1:173056695..173056916 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACTACAGCTGCCGACAACCT Chr1:173056249..173056268 59.94 55 TCTGGGTTGTCTCCTTGGAT Chr1:173056813..173056832 59.51 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000495823 Chr1:173051792..173051952 AACCTGGTTGGCTCACATTT Chr1:173051906..173051925 59.45 45
upstream ENSMUSE00000494744 Chr1:173053177..173053324 TGCCAGGCAACAAGTGTAAA Chr1:173053266..173053285 60.29 45
upstream ENSMUSE00000496838 Chr1:173055165..173055227 ACCCACGTACCTGCAGAACT Chr1:173055182..173055201 59.65 55
upstream ENSMUSE00000535859 Chr1:173055166..173055227 ACCCACGTACCTGCAGAACT Chr1:173055182..173055201 59.65 55
upstream ENSMUSE00000535860 Chr1:173055401..173055481 GCTGCCCATGAAGGTTACAC Chr1:173055407..173055426 60.53 55
upstream ENSMUSE00000658698 Chr1:173055401..173055416 No primer for this exon
upstream ENSMUSE00000519216 Chr1:173055419..173055481 AACGATCGAGGGCATCTCTT Chr1:173055440..173055459 61.13 50
upstream ENSMUSE00000479738 Chr1:173056165..173056341 ACTACAGCTGCCGACAACCT Chr1:173056249..173056268 59.94 55

*** Putative Vector Insertion (Chr 1: 173056342 - 173056694) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000687473 Chr1:173056695..173057098 CAGCATGGCATAGATCTGGA Chr1:173056957..173056976 59.78 50
downstream ENSMUSE00000706641 Chr1:173056695..173056916 TCTGGGTTGTCTCCTTGGAT Chr1:173056813..173056832 59.51 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAACCCCCATTTCTTTCCAG Chr1:173056367..173056387 60.16 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AAACCCCCATTTCTTTCCAG Chr1:173056367..173056387 60.16 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026649