Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI18793
Trapped Gene
Actl6a (ENSMUSG00000027671)
Vector Insertion
Chr 3: 32607803 - 32610789
Public Clones (sanger) D072F02 (ggtc) D128A08 (ggtc) D106A06 (ggtc) CMHD-GT_500G5-3 (cmhd)
CMHD-GT_462A3-3 (cmhd) IST10601E12 (tigm) IST10601E12 (tigm)
Private Clones OST414244 (lexicon) OST408777 (lexicon) OST113903 (lexicon)
Severity of mutation (?) Insertion after 2% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000172002 (Chr3:32607650..32607802 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGTCACGCCGCTGTTATCTT Chr3:32607717..32607736 59.9 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000172002 (Chr3:32607650..32607802 +)
Downstram Exon
ENSMUSE00000171995 (Chr3:32610790..32610866 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGTCACGCCGCTGTTATCTT Chr3:32607717..32607736 59.9 50 AACAAGAGCGCCAACTTCAT Chr3:32610812..32610831 59.88 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000172002 Chr3:32607650..32607802 AGTCACGCCGCTGTTATCTT Chr3:32607717..32607736 59.9 50

*** Putative Vector Insertion (Chr 3: 32607803 - 32610789) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000171995 Chr3:32610790..32610866 AACAAGAGCGCCAACTTCAT Chr3:32610812..32610831 59.88 45
downstream ENSMUSE00000172004 Chr3:32611023..32611197 TGCCATTCTTGAGTGGTGAG Chr3:32611197..32611216 59.83 50
downstream ENSMUSE00000172013 Chr3:32613439..32613539 TGCTTCCGACATGAGAACAG Chr3:32613539..32613558 59.98 50
downstream ENSMUSE00000171999 Chr3:32614338..32614435 CAGGGATGCTGTAGTGCTCA Chr3:32614404..32614423 60.01 55
downstream ENSMUSE00000172006 Chr3:32616953..32617047 CAGCCCAGTAGAACGACCAT Chr3:32616983..32617002 60.13 55
downstream ENSMUSE00000172000 Chr3:32617290..32617396 CCAGAGGGGATTTCACAATG Chr3:32617313..32617332 60.31 50
downstream ENSMUSE00000171997 Chr3:32617489..32617578 TTGTAACCTGGGGCAGTTTC Chr3:32617555..32617574 59.97 50
downstream ENSMUSE00000171994 Chr3:32618823..32618884 TCGTCGTAGGTGGAGTCTGA Chr3:32618884..32618903 59.42 55
downstream ENSMUSE00000172012 Chr3:32619108..32619222 GTAGTGGACGGTTGGCATCT Chr3:32619141..32619160 60 55
downstream ENSMUSE00000172007 Chr3:32619357..32619437 ATCGTGTTCCCAGACAGTCC Chr3:32619379..32619398 59.97 55
downstream ENSMUSE00000171998 Chr3:32621542..32621637 GCTACGATCACACTGCCGTA Chr3:32621570..32621589 59.9 55
downstream ENSMUSE00000172011 Chr3:32624169..32624255 CCAATCCATGAGCTGAACCT Chr3:32624236..32624255 60.07 50
downstream ENSMUSE00000477018 Chr3:32625444..32625891 ACACACTGCTTCCCTCCTTC Chr3:32625508..32625527 59.31 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GTACGGCGGAGGTGAGTGAG Chr3:32610793..32610813 63.15 65 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCTTCAGCGTGACTGGGAAA Chr3:32610784..32610804 61.92 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000027671