Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI5971
Trapped Gene
Elavl1 (ENSMUSG00000040028)
Vector Insertion
Chr 8: 4295562 - 4301684
Public Clones CSH360 (baygenomics) RRC083 (baygenomics)
Private Clones not available
Severity of mutation (?) Insertion after 44% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000229429 (Chr8:4301685..4301838 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GTTTGGGCGAATCATCAACT Chr8:4301712..4301731 59.94 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000229429 (Chr8:4301685..4301838 -)
Downstram Exon
ENSMUSE00000278547 (Chr8:4295336..4295561 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GTTTGGGCGAATCATCAACT Chr8:4301712..4301731 59.94 45 CTGCTTCTGACCGTTTGTCA Chr8:4295489..4295508 60.03 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000638320 Chr8:4324886..4325086 No primer for this exon
upstream ENSMUSE00000706646 Chr8:4324886..4324906 No primer for this exon
upstream ENSMUSE00000706645 Chr8:4312557..4312614 No primer for this exon
upstream ENSMUSE00000229444 Chr8:4311599..4311786 ACGAAGTCTGTTCAGCAGCA Chr8:4311644..4311663 59.78 50
upstream ENSMUSE00000229435 Chr8:4304927..4305030 CACACTGAACGGCTTGAGAC Chr8:4304947..4304966 59.47 55
upstream ENSMUSE00000229429 Chr8:4301685..4301838 GTTTGGGCGAATCATCAACT Chr8:4301712..4301731 59.94 45

*** Putative Vector Insertion (Chr 8: 4295562 - 4301684) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000278547 Chr8:4295336..4295561 CTGCTTCTGACCGTTTGTCA Chr8:4295489..4295508 60.03 50
downstream ENSMUSE00000638319 Chr8:4288347..4289924 ACAGAACCCCAAACGTCAAG Chr8:4288409..4288428 60.01 50
downstream ENSMUSE00000706644 Chr8:4288344..4289924 ACAGAACCCCAAACGTCAAG Chr8:4288409..4288428 60.01 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TTTGGGTTTGGTTTTGGTTT Chr8:4295674..4295694 59.2 35 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TTTGGGTTTGGTTTTGGTTT Chr8:4295674..4295694 59.2 35 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000040028