Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28547
Trapped Gene
S100a1 (ENSMUSG00000044080)
Vector Insertion
Chr 3: 90315287 - 90315917
Public Clones CMHD-GT_440E10-3 (cmhd) CMHD-GT_401H8-3 (cmhd) CMHD-GT_400C5-3 (cmhd)
Private Clones OST28275 (lexicon) OST24588 (lexicon) OST17775 (lexicon) OST15914 (lexicon)
OST13825 (lexicon) OST1803 (lexicon)
Severity of mutation (?) Insertion after 50% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000333133 (Chr3:90315918..90316071 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCATGGAGACCCTCATCAAT Chr3:90316017..90316036 59.74 50 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000333133 (Chr3:90315918..90316071 -)
Downstram Exon
ENSMUSE00000672788 (Chr3:90314960..90315286 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCATGGAGACCCTCATCAAT Chr3:90316017..90316036 59.74 50 TCTGGACTGCCACTCTTGTG Chr3:90314974..90314993 60.02 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000380803 Chr3:90318123..90318186 GCCCTTCTGTCGAGAATCTG Chr3:90318148..90318167 59.95 55
upstream ENSMUSE00000672787 Chr3:90318123..90318200 GCCCTTCTGTCGAGAATCTG Chr3:90318148..90318167 59.95 55
upstream ENSMUSE00000333133 Chr3:90315918..90316071 CCATGGAGACCCTCATCAAT Chr3:90316017..90316036 59.74 50
upstream ENSMUSE00000672786 Chr3:90315901..90316071 CCATGGAGACCCTCATCAAT Chr3:90316017..90316036 59.74 50

*** Putative Vector Insertion (Chr 3: 90315287 - 90315917) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000672790 Chr3:90315189..90315277 TTGAAGTCCACTTCCCCATC Chr3:90315188..90315207 59.9 50
downstream ENSMUSE00000672788 Chr3:90314960..90315286 TCTGGACTGCCACTCTTGTG Chr3:90314974..90314993 60.02 55
downstream ENSMUSE00000373524 Chr3:90314959..90315286 TCTGGACTGCCACTCTTGTG Chr3:90314974..90314993 60.02 55
downstream ENSMUSE00000672789 Chr3:90314815..90314869 TTCGGACCCCTACATTTCTG Chr3:90314801..90314820 59.93 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TGAGGTACAGGGTGGAGGAA Chr3:90315883..90315903 60.5 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TGAGGTACAGGGTGGAGGAA Chr3:90315883..90315903 60.5 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000044080