Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI31779
Trapped Gene
Clk3 (ENSMUSG00000032316)
Vector Insertion
Chr 9: 57609522 - 57613325
Public Clones (sanger) IST14678D2 (tigm)
Private Clones not available
Severity of mutation (?) Insertion after 23% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000444579 (Chr9:57612881..57613324 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAAGAGACCTCCACCGATGT Chr9:57613091..57613110 59.1 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000444579 (Chr9:57612881..57613324 -)
Downstram Exon
ENSMUSE00000348008 (Chr9:57609523..57609674 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAAGAGACCTCCACCGATGT Chr9:57613091..57613110 59.1 55 TCGGGATGGGTATCGTAGTC Chr9:57609536..57609555 59.77 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000444579 Chr9:57612881..57613324 GAAGAGACCTCCACCGATGT Chr9:57613091..57613110 59.1 55
upstream ENSMUSE00000348008 Chr9:57609523..57609674 GGGAGCATGAAGGTCGACTA Chr9:57609573..57609592 60.22 55

*** Putative Vector Insertion (Chr 9: 57609522 - 57613325) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000218641 Chr9:57608631..57608847 CGATGTCGAGAACGTGAAGA Chr9:57608703..57608722 59.98 50
downstream ENSMUSE00000218647 Chr9:57606434..57606530 CTGCGCTTACTGCTCTGTTG Chr9:57606483..57606502 59.95 55
downstream ENSMUSE00000218639 Chr9:57606091..57606157 No primer for this exon
downstream ENSMUSE00000218644 Chr9:57603059..57603175 GCCCACATTACGGATGATCT Chr9:57603111..57603130 59.78 50
downstream ENSMUSE00000218646 Chr9:57602309..57602475 TGACCATGGAAGTTGAACCA Chr9:57602412..57602431 59.94 45
downstream ENSMUSE00000218650 Chr9:57601308..57601402 GGTCAGCTGGTTCTCGTGTAG Chr9:57601358..57601378 59.92 57.14
downstream ENSMUSE00000218640 Chr9:57601078..57601207 CCACAATGGTGGTGTGATGT Chr9:57601092..57601111 60.14 50
downstream ENSMUSE00000218648 Chr9:57600452..57600534 ATGCAGCCGATACTCCAGAC Chr9:57600467..57600486 60.25 55
downstream ENSMUSE00000218638 Chr9:57599922..57600001 CTGGTACGGTGGATCATGTG Chr9:57599900..57599919 59.83 55
downstream ENSMUSE00000218645 Chr9:57599544..57599634 AGCTGTTCTCATCCCAAACC Chr9:57599563..57599582 59.14 50
downstream ENSMUSE00000517721 Chr9:57598518..57598928 CTCCAACTCTTCGTGTGCTG Chr9:57598699..57598718 59.62 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 ACTCTGGATGGGTCAGCAAG Chr9:57610315..57610335 60.26 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 ACCTGATTGTGGCTCCTTTC Chr9:57610344..57610364 59.14 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032316