Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI6459
Trapped Gene
Zfhx2 (ENSMUSG00000040721)
Vector Insertion
Chr 14: 55686119 - 55686321
Public Clones CSA151 (baygenomics) PST5418-NL (escells)
Private Clones not available
Severity of mutation (?) Insertion after 42% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000648712 (Chr14:55686322..55686448 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATGACCTTCGCAACCAAAAT Chr14:55686414..55686433 59.43 40 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000648712 (Chr14:55686322..55686448 -)
Downstram Exon
ENSMUSE00000454262 (Chr14:55682642..55686118 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATGACCTTCGCAACCAAAAT Chr14:55686414..55686433 59.43 40 CAGTCTCGCCTTCCTTGAAC Chr14:55685458..55685477 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000648718 Chr14:55710845..55710885 No primer for this exon
upstream ENSMUSE00000616120 Chr14:55692050..55694121 TGTTGTCCCACGATACCTCA Chr14:55693515..55693534 59.96 50
upstream ENSMUSE00000648717 Chr14:55691384..55691901 CGCTGCAACATCTGTGACTT Chr14:55691460..55691479 60.06 50
upstream ENSMUSE00000648716 Chr14:55690696..55690936 AGCCTTGCTGCAACACCTAC Chr14:55690828..55690847 60.46 55
upstream ENSMUSE00000648715 Chr14:55689398..55689472 TGACACCCCCTTAGCTCAAC Chr14:55689443..55689462 60.11 55
upstream ENSMUSE00000648714 Chr14:55688976..55689034 TCCGAAGTGACAGAGGACAG Chr14:55689013..55689032 58.96 55
upstream ENSMUSE00000648713 Chr14:55686945..55687145 ACCAGGTGAGGGTCCATACA Chr14:55687083..55687102 60.24 55
upstream ENSMUSE00000648712 Chr14:55686322..55686448 ATGACCTTCGCAACCAAAAT Chr14:55686414..55686433 59.43 40

*** Putative Vector Insertion (Chr 14: 55686119 - 55686321) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000454262 Chr14:55682642..55686118 CAGTCTCGCCTTCCTTGAAC Chr14:55685458..55685477 59.99 55
downstream ENSMUSE00000319241 Chr14:55680498..55682408 AGCCTCCCGTTTGGTTAGTT Chr14:55680917..55680936 60 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AAGTAATCGCCTTGCAGCAC Chr14:55686253..55686273 60.42 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATCAAGCGTGACTGGGAAAA Chr14:55686256..55686276 60.64 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TGCTTCCTGGACCCATAATC Chr14:55686393..55686413 59.89 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TTTCCCTACCCCACAGTCAC Chr14:55686464..55686484 59.82 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040721