Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26087
Trapped Gene
Arrdc1 (ENSMUSG00000026972)
Vector Insertion
Chr 2: 24782248 - 24782433
Public Clones not available
Private Clones OST139184 (lexicon)
Severity of mutation (?) Insertion after 52% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000699233 (Chr2:24782434..24782546 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CCATCGACACTCCACGTTTT Chr2:24782473..24782492 60.95 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000699233 (Chr2:24782434..24782546 -)
Downstram Exon
ENSMUSE00000164970 (Chr2:24782065..24782247 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CCATCGACACTCCACGTTTT Chr2:24782473..24782492 60.95 50 ACCACATAGCCACGAAGGTC Chr2:24782125..24782144 60 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000164964 Chr2:24790548..24790685 CTTCGAGATCCGCCTGAGTC Chr2:24790629..24790648 62.4 60
upstream ENSMUSE00000660808 Chr2:24783249..24783359 TCAACAGCTCCCTGTCACTG Chr2:24783259..24783278 60.02 55
upstream ENSMUSE00000660807 Chr2:24782646..24782696 No primer for this exon
upstream ENSMUSE00000699233 Chr2:24782434..24782546 CCATCGACACTCCACGTTTT Chr2:24782473..24782492 60.95 50
upstream ENSMUSE00000164975 Chr2:24782398..24782552 AGCACCCACATCTTTTGAGG Chr2:24782529..24782548 60.11 50

*** Putative Vector Insertion (Chr 2: 24782248 - 24782433) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000164970 Chr2:24782065..24782247 ACCACATAGCCACGAAGGTC Chr2:24782125..24782144 60 55
downstream ENSMUSE00000660806 Chr2:24781792..24781965 GGTCCGCACATCATAGATCC Chr2:24781902..24781921 60.31 55
downstream ENSMUSE00000713251 Chr2:24781792..24781968 GGTCCGCACATCATAGATCC Chr2:24781902..24781921 60.31 55
downstream ENSMUSE00000721400 Chr2:24781792..24781968 GGTCCGCACATCATAGATCC Chr2:24781902..24781921 60.31 55
downstream ENSMUSE00000164966 Chr2:24781276..24781714 GAGTGGCTCTTGGTGGAGAG Chr2:24781475..24781494 59.99 60
downstream ENSMUSE00000699234 Chr2:24781276..24781714 GAGTGGCTCTTGGTGGAGAG Chr2:24781475..24781494 59.99 60
downstream ENSMUSE00000394229 Chr2:24780875..24781196 GCACCACAGCTCTGCTCATA Chr2:24781141..24781160 60.17 55
downstream ENSMUSE00000660805 Chr2:24780875..24781196 GCACCACAGCTCTGCTCATA Chr2:24781141..24781160 60.17 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CCCTTGAACCTGAACAGCAT Chr2:24782409..24782429 60.11 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 CCCTTGAACCTGAACAGCAT Chr2:24782409..24782429 60.11 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000026972