Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI13881
Trapped Gene
Rg9mtd3 (ENSMUSG00000035601)
Vector Insertion
Chr 4: 45327279 - 45327883
Public Clones CMHD-GT_213B4-3 (cmhd)
Private Clones not available
Severity of mutation (?) Insertion after 89% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000285886 (Chr4:45327155..45327278 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CATTTCAAAAAGCCCGAGAA Chr4:45327162..45327181 60.18 40 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000285886 (Chr4:45327155..45327278 +)
Downstram Exon
ENSMUSE00000674476 (Chr4:45327884..45328014 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CATTTCAAAAAGCCCGAGAA Chr4:45327162..45327181 60.18 40 GCTTCAGGCCAGTTACGAGT Chr4:45327935..45327954 59.5 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000285946 Chr4:45310040..45310067 No primer for this exon
upstream ENSMUSE00000285941 Chr4:45313289..45313499 TTCAGGAACCAGACGGACTC Chr4:45313366..45313385 60.24 55
upstream ENSMUSE00000674480 Chr4:45313306..45313499 TTCAGGAACCAGACGGACTC Chr4:45313366..45313385 60.24 55
upstream ENSMUSE00000285934 Chr4:45314108..45314222 GCAGGAAAGAGAACGAAGGA Chr4:45314173..45314192 59.55 50
upstream ENSMUSE00000674478 Chr4:45314108..45314216 GCAGGAAAGAGAACGAAGGA Chr4:45314173..45314192 59.55 50
upstream ENSMUSE00000285924 Chr4:45317136..45317260 CACAGCAAACGCTTTTTGAA Chr4:45317150..45317169 60.03 40
upstream ENSMUSE00000285916 Chr4:45318616..45318768 AACGACGGGTTTTCTGCTTA Chr4:45318745..45318764 59.75 45
upstream ENSMUSE00000285907 Chr4:45320764..45320842 TTCCTCTGGAAACCCTTGTG Chr4:45320798..45320817 60.08 50
upstream ENSMUSE00000285897 Chr4:45321369..45321436 No primer for this exon
upstream ENSMUSE00000285886 Chr4:45327155..45327278 CATTTCAAAAAGCCCGAGAA Chr4:45327162..45327181 60.18 40

*** Putative Vector Insertion (Chr 4: 45327279 - 45327883) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000285877 Chr4:45327884..45329003 GCAGGTGGTAAGAGCTGAGG Chr4:45328825..45328844 60.01 60
downstream ENSMUSE00000674476 Chr4:45327884..45328014 GCTTCAGGCCAGTTACGAGT Chr4:45327935..45327954 59.5 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGGAAATATTGGCCATCAAC Chr4:45327256..45327276 60.15 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CGGAAATATTGGCCATCAAC Chr4:45327256..45327276 60.15 45 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000035601