Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27392
Trapped Gene
Elf1 (ENSMUSG00000036461)
Vector Insertion
Chr 14: 79960735 - 79965268
Public Clones IST14960H12 (tigm)
Private Clones OST60868 (lexicon)
Severity of mutation (?) Insertion after 15% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000295543 (Chr14:79960554..79960734 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CGATGACGACATCACCCTTA Chr14:79960712..79960731 59.52 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000295543 (Chr14:79960554..79960734 +)
Downstram Exon
ENSMUSE00000295536 (Chr14:79965269..79965379 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CGATGACGACATCACCCTTA Chr14:79960712..79960731 59.52 50 GCAGCCTCAATGGTCTCAAT Chr14:79965323..79965342 60.23 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000512972 Chr14:79881001..79881444 CTTCGGCTCAGAACTTTCCA Chr14:79881274..79881293 60.51 50
upstream ENSMUSE00000647192 Chr14:79915481..79915577 CCAGAGGACGAAACCTGAAG Chr14:79915544..79915563 59.84 55
upstream ENSMUSE00000360302 Chr14:79935930..79936229 GGAAGCTGCTTAGGCCTTTT Chr14:79936108..79936127 59.99 50
upstream ENSMUSE00000295543 Chr14:79960554..79960734 CGATGACGACATCACCCTTA Chr14:79960712..79960731 59.52 50

*** Putative Vector Insertion (Chr 14: 79960735 - 79965268) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000295536 Chr14:79965269..79965379 GCAGCCTCAATGGTCTCAAT Chr14:79965323..79965342 60.23 50
downstream ENSMUSE00000554267 Chr14:79966957..79967121 TCTTTCTCTTGCGCTGCTCT Chr14:79967121..79967140 60.56 50
downstream ENSMUSE00000554263 Chr14:79969028..79969111 GTGTAGTCGTCGGGGAATCT Chr14:79969075..79969094 59.02 55
downstream ENSMUSE00000612853 Chr14:79970530..79970722 TCTCCCCATGGTCTCGTAGT Chr14:79970717..79970736 59.53 55
downstream ENSMUSE00000295500 Chr14:79972979..79973425 AGAATTCCCGGGCTTTAGAA Chr14:79973225..79973244 60.03 45
downstream ENSMUSE00000474019 Chr14:79979992..79982282 ACTTGGGTTCGCCTCCTTAT Chr14:79980736..79980755 59.96 50
downstream ENSMUSE00000647193 Chr14:79979992..79982283 ACTTGGGTTCGCCTCCTTAT Chr14:79980736..79980755 59.96 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCTAGGCCAGGGGGTTTAAT Chr14:79960770..79960790 59.79 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTTAGGACGTGACTGGGAAA Chr14:79960778..79960799 59.72 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036461