Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI27862
Trapped Gene
Irak3 (ENSMUSG00000020227)
Vector Insertion
Chr 10: 119583686 - 119602148
Public Clones (sanger) E138G04 (ggtc) E138G04 (ggtc) IST12069D4 (tigm) IST10892H9 (tigm)
IST11646A8 (tigm) IST12069D4 (tigm) IST12841F8 (tigm) IST14762G11 (tigm)
IST11794D12 (tigm) IST11733B3 (tigm) IST10065C1 (tigm) IST14762G11 (tigm)
IST10079D7 (tigm) IST11733B3 (tigm)
Private Clones OST45562 (lexicon)
Severity of mutation (?) Insertion after 51% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000398454 (Chr10:119602149..119602267 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
No primer for this exon TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000398454 (Chr10:119602149..119602267 -)
Downstram Exon
ENSMUSE00000361517 (Chr10:119583487..119583685 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
No primer for this exon No primer for this exon

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000241567 Chr10:119638383..119638593 No primer for this exon
upstream ENSMUSE00000241560 Chr10:119619582..119619764 No primer for this exon
upstream ENSMUSE00000102008 Chr10:119615752..119615855 No primer for this exon
upstream ENSMUSE00000102004 Chr10:119615124..119615178 No primer for this exon
upstream ENSMUSE00000102005 Chr10:119613287..119613438 No primer for this exon
upstream ENSMUSE00000102003 Chr10:119607374..119607438 No primer for this exon
upstream ENSMUSE00000102001 Chr10:119603461..119603575 No primer for this exon
upstream ENSMUSE00000398454 Chr10:119602149..119602267 No primer for this exon

*** Putative Vector Insertion (Chr 10: 119583686 - 119602148) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000361517 Chr10:119583487..119583685 No primer for this exon
downstream ENSMUSE00000241629 Chr10:119582954..119583016 No primer for this exon
downstream ENSMUSE00000241622 Chr10:119582702..119582866 No primer for this exon
downstream ENSMUSE00000241613 Chr10:119578710..119580247 No primer for this exon

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ATCGTCAAGGTTGGGTTCAC Chr10:119596132..119596152 59.83 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ATCGTCAAGGTTGGGTTCAC Chr10:119596132..119596152 59.83 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 TGTTGCCATTGGTGAAACAG Chr10:119593227..119593247 60.55 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 ATGGACGTGACTGGGAAAAC Chr10:119593202..119593222 59.83 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000020227