Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI679
Trapped Gene
Lrch4 (ENSMUSG00000029720)
Vector Insertion
Chr 5: 138070655 - 138074799
Public Clones (sanger) (sanger) (sanger) (sanger) (sanger) DC0368 (sanger)
(sanger) (sanger) (sanger) YHC204 (baygenomics) YHC203 (baygenomics)
D158H08 (ggtc) 3SE223C03 (ggtc) W270B07 (ggtc) P100G02 (ggtc) (ggtc)
W235F04 (ggtc) E051B09 (ggtc) 5SE223C03 (ggtc) A055F02 (ggtc) (ggtc)
PST7842-NR (escells) IST14155C9 (tigm) IST14649A3 (tigm) IST14886A2 (tigm)
IST14462A7 (tigm) IST14119A5 (tigm) IST14380A3 (tigm)
Private Clones OST422206 (lexicon) OST317851 (lexicon) OST299634 (lexicon) OST283580 (lexicon)
OST248998 (lexicon) OST234009 (lexicon) OST211075 (lexicon) OST206941 (lexicon)
Severity of mutation (?) Insertion after 11% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000192065 (Chr5:138070406..138070654 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCGCAGTTACGACTTGTCAG Chr5:138070620..138070639 59.51 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000192065 (Chr5:138070406..138070654 +)
Downstram Exon
ENSMUSE00000192071 (Chr5:138074800..138074944 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCGCAGTTACGACTTGTCAG Chr5:138070620..138070639 59.51 55 TTGAGGTAGGTGAGGGCTGT Chr5:138074941..138074960 59.72 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000192065 Chr5:138070406..138070654 CCGCAGTTACGACTTGTCAG Chr5:138070620..138070639 59.51 55

*** Putative Vector Insertion (Chr 5: 138070655 - 138074799) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000192071 Chr5:138074800..138074944 TTGAGGTAGGTGAGGGCTGT Chr5:138074941..138074960 59.72 55
downstream ENSMUSE00000192063 Chr5:138075077..138075203 AGATGTAGGGTGGCAACGAC Chr5:138075114..138075133 60 55
downstream ENSMUSE00000192069 Chr5:138075372..138075477 GCAGGGTACTGAGCTGGTTC Chr5:138075474..138075493 59.87 60
downstream ENSMUSE00000192068 Chr5:138077967..138078103 CTGTAGGGGGTTGCTATCCA Chr5:138078091..138078110 59.95 55
downstream ENSMUSE00000192059 Chr5:138078213..138078325 GCCAGCTTCCATTGTTAGGT Chr5:138078269..138078288 59.2 50
downstream ENSMUSE00000192070 Chr5:138078441..138078540 TAACGACGTCCCGGAAATAA Chr5:138078476..138078495 60.31 45
downstream ENSMUSE00000192061 Chr5:138078773..138078863 ATCCGGAAAGACAGCTCTGA Chr5:138078810..138078829 59.95 50
downstream ENSMUSE00000192064 Chr5:138078954..138079030 TCAGCTGCACTTCGATCTTC Chr5:138079032..138079051 59.27 50
downstream ENSMUSE00000192055 Chr5:138079133..138079194 TTCTCCACATCCCCTGCTAC Chr5:138079182..138079201 60.07 55
downstream ENSMUSE00000192062 Chr5:138079294..138079410 GCCACAACTGCAAAGTGTCT Chr5:138079352..138079371 58.94 50
downstream ENSMUSE00000192058 Chr5:138079521..138079589 No primer for this exon
downstream ENSMUSE00000192067 Chr5:138079667..138079770 CTCCCAGTTGGGTAGTGCTG Chr5:138079704..138079723 60.7 60
downstream ENSMUSE00000192057 Chr5:138079883..138079966 AAGAGGACCGGAAGAGGAAG Chr5:138079954..138079973 59.81 55
downstream ENSMUSE00000192056 Chr5:138080350..138080426 GCCGAGGTCTCAAAACAGAC Chr5:138080388..138080407 59.85 55
downstream ENSMUSE00000192066 Chr5:138080578..138080715 TCTGCCAGGTCCTCAGGTAG Chr5:138080627..138080646 60.4 60
downstream ENSMUSE00000192060 Chr5:138080806..138080883 TCCGACAGGCTTCTAGGAAA Chr5:138080869..138080888 59.95 50
downstream ENSMUSE00000590794 Chr5:138081176..138081373 AGGAGCCGAGTGTAGACGAC Chr5:138081366..138081385 59.48 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGATGGAGTAATCGCCTTGC Chr5:138073698..138073718 59.3 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCGCAGTTACGACTTGTCAG Chr5:138073621..138073641 59.51 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000029720