Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI36280
Trapped Gene
Prdm14 (ENSMUSG00000042414)
Vector Insertion
Chr 1: 13114443 - 13114754
Public Clones IST10265D3 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 43% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000316429 (Chr1:13114700..13114753 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CAAAGACTCCCTCCAGCTTC Chr1:13114706..13114725 59.01 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000316429 (Chr1:13114700..13114753 -)
Downstram Exon
ENSMUSE00000316422 (Chr1:13114444..13114601 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CAAAGACTCCCTCCAGCTTC Chr1:13114706..13114725 59.01 55 CATCCGAGAGTTGTCCCTGT Chr1:13114428..13114447 60.11 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000702730 Chr1:13117191..13117244 No primer for this exon
upstream ENSMUSE00000316434 Chr1:13115247..13115937 TCCCGAAGTACCACGATTTC Chr1:13115580..13115599 59.93 50
upstream ENSMUSE00000316429 Chr1:13114700..13114753 CAAAGACTCCCTCCAGCTTC Chr1:13114706..13114725 59.01 55
upstream ENSMUSE00000316422 Chr1:13114444..13114601 AGGGACAACTCTCGGATGTG Chr1:13114448..13114467 60.11 55

*** Putative Vector Insertion (Chr 1: 13114443 - 13114754) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000316412 Chr1:13112442..13112712 GGTTCCGCTGGATGTCTCTA Chr1:13112528..13112547 60.22 55
downstream ENSMUSE00000316401 Chr1:13108844..13109046 AACACCTTTCCACAGCGTTC Chr1:13108982..13109001 60.16 50
downstream ENSMUSE00000702728 Chr1:13106362..13106364 No primer for this exon
downstream ENSMUSE00000316395 Chr1:13105861..13105962 CACTGGTATGGCCTGTCTCC Chr1:13105855..13105874 60.53 60
downstream ENSMUSE00000630774 Chr1:13103509..13104568 GCACATAGTCGCTGGCTACA Chr1:13104056..13104075 60.04 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CAAAGACTCCCTCCAGCTTC Chr1:13114704..13114724 59.01 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAAAGACTCCCTCCAGCTTC Chr1:13114704..13114724 59.01 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000042414