Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI1240
Trapped Gene
Ldlrad3 (ENSMUSG00000048058)
Vector Insertion
Chr 2: 101795332 - 101898063
Public Clones DD0948 (sanger) GST142 (baygenomics) XST123 (baygenomics) Ex186 (baygenomics)
RST448 (baygenomics) XA360 (baygenomics) RST373 (baygenomics)
Private Clones OST445445 (lexicon)
Severity of mutation (?) Insertion after 44% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000643016 (Chr2:101898064..101898198 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTGCATCGACAAGAGCTTCA Chr2:101898127..101898146 60.14 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000643016 (Chr2:101898064..101898198 -)
Downstram Exon
ENSMUSE00000643015 (Chr2:101794986..101795331 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTGCATCGACAAGAGCTTCA Chr2:101898127..101898146 60.14 50 AGGGTCATGAGGTTGTTTCG Chr2:101795147..101795166 59.97 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000378318 Chr2:102026437..102026515 No primer for this exon
upstream ENSMUSE00000687112 Chr2:102026437..102026534 No primer for this exon
upstream ENSMUSE00000687104 Chr2:101954318..101954341 TTGGGATTTTGCACCAATTT Chr2:101954320..101954339 60.17 35
upstream ENSMUSE00000687105 Chr2:101953786..101953836 TTCACCAACGAGTGCAACAT Chr2:101953791..101953810 60.16 45
upstream ENSMUSE00000564528 Chr2:101953690..101953861 TTCACCAACGAGTGCAACAT Chr2:101953791..101953810 60.16 45
upstream ENSMUSE00000564530 Chr2:101953690..101953836 TTCACCAACGAGTGCAACAT Chr2:101953791..101953810 60.16 45
upstream ENSMUSE00000643018 Chr2:101910090..101910215 TGGCATCCACTGTATCATCG Chr2:101910150..101910169 60.5 50
upstream ENSMUSE00000643016 Chr2:101898064..101898198 GTGCATCGACAAGAGCTTCA Chr2:101898127..101898146 60.14 50

*** Putative Vector Insertion (Chr 2: 101795332 - 101898063) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000643015 Chr2:101794986..101795331 AGGGTCATGAGGTTGTTTCG Chr2:101795147..101795166 59.97 50
downstream ENSMUSE00000470570 Chr2:101793221..101793332 AGGAAGGTCGTACCATGCAG Chr2:101793289..101793308 60.13 55
downstream ENSMUSE00000687103 Chr2:101793138..101793218 CTGCTGGCTTCCACACTCAG Chr2:101793158..101793177 62.17 60
downstream ENSMUSE00000461346 Chr2:101790360..101793332 TTTTGACCGGCTTAATTTGG Chr2:101792180..101792199 59.94 40
downstream ENSMUSE00000469702 Chr2:101790358..101793332 TTTTGACCGGCTTAATTTGG Chr2:101792180..101792199 59.94 40

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTGAACCTTTTGCCAAATCC Chr2:101829041..101829061 59.92 40 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTGAACCTTTTGCCAAATCC Chr2:101829041..101829061 59.92 40 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048058