Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27956
Trapped Gene
Clic4 (ENSMUSG00000037242)
Vector Insertion
Chr 4: 134773181 - 134774422
Public Clones IST14782D7 (tigm)
Private Clones OST43387 (lexicon)
Severity of mutation (?) Insertion after 79% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000496847 (Chr4:134774423..134774604 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ATTTTCCACACGTCGGTTTC Chr4:134774485..134774504 59.84 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000496847 (Chr4:134774423..134774604 -)
Downstram Exon
ENSMUSE00000497876 (Chr4:134772898..134773180 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ATTTTCCACACGTCGGTTTC Chr4:134774485..134774504 59.84 45 GAGGCGGAGCAGTCTGTTAG Chr4:134772925..134772944 60.16 60

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000264663 Chr4:134828433..134828678 TCATCGAGCTCTTCGTCAAG Chr4:134828433..134828452 59.27 50
upstream ENSMUSE00000524581 Chr4:134794777..134794886 GTGTCACAACCGTTGACCTG Chr4:134794782..134794801 60.05 55
upstream ENSMUSE00000264643 Chr4:134781939..134782064 AGCGAAGTCAAGACGGATGT Chr4:134781984..134782003 59.87 50
upstream ENSMUSE00000264631 Chr4:134779379..134779485 ACCCAGAGTCGAACACTGCT Chr4:134779443..134779462 59.91 55
upstream ENSMUSE00000496847 Chr4:134774423..134774604 ATTTTCCACACGTCGGTTTC Chr4:134774485..134774504 59.84 45

*** Putative Vector Insertion (Chr 4: 134773181 - 134774422) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000497876 Chr4:134772898..134773180 GAGGCGGAGCAGTCTGTTAG Chr4:134772925..134772944 60.16 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CTCACCAGTAATCGCCTTGC Chr4:134774359..134774379 60.8 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GAGAGGGGGCTCTTGAAAAC Chr4:134774578..134774598 60.19 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 3 GAGAGGGGGCTCTTGAAAAC Chr4:134774578..134774598 60.19 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037242