Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI9170
Trapped Gene
Elf1 (ENSMUSG00000036461)
Vector Insertion
Chr 14: 79973426 - 79979991
Public Clones RRE117 (baygenomics) IST12329G12 (tigm) IST11909A12 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 66% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000295500 (Chr14:79972979..79973425 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATCAAGTCGGAATCAAGCA Chr14:79973131..79973150 59.8 45 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000295500 (Chr14:79972979..79973425 +)
Downstram Exon
ENSMUSE00000474019 (Chr14:79979992..79982282 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATCAAGTCGGAATCAAGCA Chr14:79973131..79973150 59.8 45 ACTTGGGTTCGCCTCCTTAT Chr14:79980736..79980755 59.96 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
upstream ENSMUSE00000295536 Chr14:79965269..79965379 TAGATTCTCCCAGCCCTCCT Chr14:79965338..79965357 60.17 55
upstream ENSMUSE00000554267 Chr14:79966957..79967121 AGAGCAGCGCAAGAGAAAGA Chr14:79967099..79967118 60.56 50
upstream ENSMUSE00000554263 Chr14:79969028..79969111 No primer for this exon
upstream ENSMUSE00000612853 Chr14:79970530..79970722 ACTACGAGACCATGGGGAGA Chr14:79970695..79970714 59.53 55
upstream ENSMUSE00000295500 Chr14:79972979..79973425 CATCAAGTCGGAATCAAGCA Chr14:79973131..79973150 59.8 45

*** Putative Vector Insertion (Chr 14: 79973426 - 79979991) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
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 CAGGAGGAAGCAGCAAATTC Chr14:79973389..79973409 59.96 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CAGGAGGAAGCAGCAAATTC Chr14:79973389..79973409 59.96 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000036461