Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI17993
Trapped Gene
Lypla1 (ENSMUSG00000025903)
Vector Insertion
Chr 1: 4831214 - 4835043
Public Clones IST12751B10 (tigm) IST12751B10 (tigm)
Private Clones OST432397 (lexicon)
Severity of mutation (?) Insertion after 92% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000154049 (Chr1:4831037..4831213 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TGATGCACAGCTCATGTCAG Chr1:4831191..4831210 59.55 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000154049 (Chr1:4831037..4831213 +)
Downstram Exon
ENSMUSE00000703290 (Chr1:4835044..4835433 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TGATGCACAGCTCATGTCAG Chr1:4831191..4831210 59.55 50 CAATGAAGTGCTTGACATCCA Chr1:4835073..4835093 59.71 42.86

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000154051 Chr1:4797943..4798063 No primer for this exon
upstream ENSMUSE00000703291 Chr1:4797992..4798063 No primer for this exon
upstream ENSMUSE00000154054 Chr1:4798536..4798567 CCTTCACGGATTGGGAGATA Chr1:4798544..4798563 59.89 50
upstream ENSMUSE00000154050 Chr1:4818665..4818730 GCAGAAGCCTTTGCAGGTAT Chr1:4818675..4818694 59.48 50
upstream ENSMUSE00000154052 Chr1:4820349..4820396 No primer for this exon
upstream ENSMUSE00000154053 Chr1:4822392..4822462 TGGAATTAAACAGGCAGCAG Chr1:4822437..4822456 58.92 45
upstream ENSMUSE00000154057 Chr1:4827082..4827155 No primer for this exon
upstream ENSMUSE00000154056 Chr1:4829468..4829569 ACTCAGTTGCTGGCTTCCAC Chr1:4829530..4829549 60.45 55
upstream ENSMUSE00000154049 Chr1:4831037..4831213 TGATGCACAGCTCATGTCAG Chr1:4831191..4831210 59.55 50

*** Putative Vector Insertion (Chr 1: 4831214 - 4835043) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000154055 Chr1:4835044..4836817 AAAAAGCCTGGTCTCCCAAT Chr1:4835679..4835698 59.94 45
downstream ENSMUSE00000703290 Chr1:4835044..4835433 CAATGAAGTGCTTGACATCCA Chr1:4835073..4835093 59.71 42.86

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCCAGAGTGGTAGGATGAGG Chr1:4834192..4834212 59.68 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GCCAGAGTGGTAGGATGAGG Chr1:4834192..4834212 59.68 60 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025903