Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI35599
Trapped Gene
Zcchc7 (ENSMUSG00000035649)
Vector Insertion
Chr 4: 44924932 - 44938846
Public Clones IST14742F3 (tigm) IST13003B6 (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
ENSMUSE00000527451 (Chr4:44921323..44924931 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCGATGGACTGCCATCTATT Chr4:44923099..44923118 60.07 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000527451 (Chr4:44921323..44924931 +)
Downstram Exon
ENSMUSE00000674534 (Chr4:44938847..44938942 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCGATGGACTGCCATCTATT Chr4:44923099..44923118 60.07 50 TTGTCCAGAAGGGGTCTTTG Chr4:44938894..44938913 60.08 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000418496 Chr4:44769440..44769564 CGGCTTCCTTACCTCATTTG Chr4:44769476..44769495 59.7 50
upstream ENSMUSE00000412283 Chr4:44774722..44775346 ATTGAAGTCCAAGCGGAAGA Chr4:44775064..44775083 59.81 45
upstream ENSMUSE00000713624 Chr4:44774722..44775346 ATTGAAGTCCAAGCGGAAGA Chr4:44775064..44775083 59.81 45
upstream ENSMUSE00000418240 Chr4:44906405..44906442 No primer for this exon
upstream ENSMUSE00000286458 Chr4:44907788..44907913 AAAACTGCCCCTTACCACAA Chr4:44907894..44907913 59.47 45
upstream ENSMUSE00000286450 Chr4:44908691..44908861 AAACGATGTGACCGATGTGA Chr4:44908820..44908839 59.97 45
upstream ENSMUSE00000527451 Chr4:44921323..44924931 GCGATGGACTGCCATCTATT Chr4:44923099..44923118 60.07 50
upstream ENSMUSE00000674536 Chr4:44921323..44921358 TGGAGGCAGTATCACCTAACG Chr4:44921338..44921358 60.14 52.38

*** Putative Vector Insertion (Chr 4: 44924932 - 44938846) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000674532 Chr4:44937042..44938942 GCAGGCATAGGTGAGAGAGG Chr4:44938019..44938038 59.97 60
downstream ENSMUSE00000674534 Chr4:44938847..44938942 TTGTCCAGAAGGGGTCTTTG Chr4:44938894..44938913 60.08 50
downstream ENSMUSE00000286404 Chr4:44941990..44942107 TTCGCTTTATTCTCCGATCC Chr4:44942101..44942120 59.25 45
downstream ENSMUSE00000286396 Chr4:44943908..44945074 CAGAGACCACTCGGCTTAGG Chr4:44944349..44944368 60.01 60
downstream ENSMUSE00000674533 Chr4:44943908..44945087 CAGAGACCACTCGGCTTAGG Chr4:44944349..44944368 60.01 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTGTTATCCCCACCTCATGC Chr4:44924931..44924951 60.34 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTTCGTGACTGGGAAAACC Chr4:44924979..44924999 59.95 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035649