Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI12914
Trapped Gene
Cacng7 (ENSMUSG00000069806)
Vector Insertion
Chr 7: 3339127 - 3365535
Public Clones XC212 (baygenomics) 3SE035B05 (ggtc) 5SD159B05 (ggtc) 5SE107B11 (ggtc)
5SD151E03 (ggtc) (cmhd) CMHD-GT_469B8-3 (cmhd) (cmhd)
(cmhd) CMHD-GT_355F5-3 (cmhd) (cmhd) (cmhd) PST768-1 (escells)
PST21320-NR (escells) IST13132B9 (tigm) IST10605F5 (tigm) IST14241B5 (tigm)
IST14543D8 (tigm) IST11073C11 (tigm) IST11779F5 (tigm) IST13965E3 (tigm)
IST11073C11 (tigm) IST12065C6 (tigm) IST10024C5 (tigm) IST10011A3 (tigm)
IST11396G10 (tigm) IST12393D5 (tigm) IST10184A1 (tigm) IST12397C5 (tigm)
IST12819E7BBF1 (tigm) IST12065C6 (tigm) IST12448F8 (tigm) IST12448F8 (tigm)
IST11182E6 (tigm) IST12393D5 (tigm)
Private Clones OST300327 (lexicon) OST275441 (lexicon) OST249410 (lexicon) OST197641 (lexicon)
OST196984 (lexicon) OST182444 (lexicon) OST93043 (lexicon)
Severity of mutation (?) Insertion after 52% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000677465 (Chr7:3338986..3339126 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
ACCATTCTTGCGTTCGTTTC Chr7:3339084..3339103 60.12 45 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000677465 (Chr7:3338986..3339126 +)
Downstram Exon
ENSMUSE00000578335 (Chr7:3365536..3365681 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
ACCATTCTTGCGTTCGTTTC Chr7:3339084..3339103 60.12 45 GTTCATGACCTCGTCGTTGA Chr7:3365600..3365619 59.68 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000677469 Chr7:3333055..3333136 No primer for this exon
upstream ENSMUSE00000677467 Chr7:3336656..3336880 AGACCACCGAGGTCAAGATG Chr7:3336821..3336840 60.11 55
upstream ENSMUSE00000677466 Chr7:3338545..3338631 CAACTTGGTGACGGAAAACA Chr7:3338597..3338616 59.58 45
upstream ENSMUSE00000677465 Chr7:3338986..3339126 ACCATTCTTGCGTTCGTTTC Chr7:3339084..3339103 60.12 45

*** Putative Vector Insertion (Chr 7: 3339127 - 3365535) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000578335 Chr7:3365536..3365681 GTTCATGACCTCGTCGTTGA Chr7:3365600..3365619 59.68 50
downstream ENSMUSE00000578334 Chr7:3366280..3367810 GAGATGGTCCGGGTACTTGA Chr7:3366516..3366535 59.93 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 CGTTCGTTTCTGGCATCTTT Chr7:3363095..3363115 60.25 45 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACTAACACTCCCTGCGTCGT Chr7:3363161..3363181 59.79 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000069806