Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI16355
Trapped Gene
Ldlrad3 (ENSMUSG00000048058)
Vector Insertion
Chr 2: 101910216 - 101953689
Public Clones 5SE287E02 (ggtc) IST14734B2 (tigm) IST12128G10 (tigm) IST12216B1 (tigm)
IST12342E1 (tigm) IST12346F10 (tigm) IST10482C8 (tigm) IST14531H5 (tigm)
Private Clones OST462464 (lexicon) OST404958 (lexicon) OST379461 (lexicon) OST332580 (lexicon)
OST313034 (lexicon) OST226715 (lexicon) OST222900 (lexicon) OST130021 (lexicon)
OST59261 (lexicon) OST58842 (lexicon) OST43402 (lexicon) OST34465 (lexicon)
OST30248 (lexicon)
Severity of mutation (?) Insertion after 11% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000564530 (Chr2:101953690..101953836 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
TTCACCAACGAGTGCAACAT Chr2:101953791..101953810 60.16 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000564530 (Chr2:101953690..101953836 -)
Downstram Exon
ENSMUSE00000643018 (Chr2:101910090..101910215 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
TTCACCAACGAGTGCAACAT Chr2:101953791..101953810 60.16 45 GTCGGGACAGTCCTCAAATC Chr2:101910090..101910109 59.51 55

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

*** Putative Vector Insertion (Chr 2: 101910216 - 101953689) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000643018 Chr2:101910090..101910215 GTCGGGACAGTCCTCAAATC Chr2:101910090..101910109 59.51 55
downstream ENSMUSE00000643016 Chr2:101898064..101898198 TGAAGCTCTTGTCGATGCAC Chr2:101898105..101898124 60.14 50
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 AGGTGACAGGATGTGTGGTG Chr2:101917671..101917691 59.41 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGCTTTCGTGACTGGGAAAA Chr2:101917624..101917644 59.85 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TTCTCATAATCGCCTTGCAG Chr2:101917772..101917792 59.02 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 TGGAGTGAGCTGGGCTTTTA Chr2:101917801..101917821 60.9 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048058