Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI3335
Trapped Gene
Csnk1g1 (ENSMUSG00000032384)
Vector Insertion
Chr 9: 65867720 - 65880045
Public Clones AB0249 (sanger)
Private Clones not available
Severity of mutation (?) Insertion after 86% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000219284 (Chr9:65867609..65867719 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GAGGAGAGTGGGAAATCCAG Chr9:65867628..65867647 58.66 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000219284 (Chr9:65867609..65867719 +)
Downstram Exon
ENSMUSE00000584162 (Chr9:65880046..65880152 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GAGGAGAGTGGGAAATCCAG Chr9:65867628..65867647 58.66 55 CATCGACATTCAGCTCTCCA Chr9:65880085..65880104 59.94 50

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000394344 Chr9:65756817..65756975 AAGGGGTGGTTGAGAGAAGC Chr9:65756892..65756911 60.63 55
upstream ENSMUSE00000712627 Chr9:65757246..65757469 AGGGCTTGTAAGGGTTTCGT Chr9:65757415..65757434 60 50
upstream ENSMUSE00000361706 Chr9:65797823..65797871 No primer for this exon
upstream ENSMUSE00000396124 Chr9:65806136..65806528 GTTCGAGACCATCTGGCACT Chr9:65806421..65806440 60.27 55
upstream ENSMUSE00000714520 Chr9:65806136..65806528 GTTCGAGACCATCTGGCACT Chr9:65806421..65806440 60.27 55
upstream ENSMUSE00000219277 Chr9:65821286..65821326 No primer for this exon
upstream ENSMUSE00000219276 Chr9:65828710..65828779 CACGTGCTCCACAACTTCAT Chr9:65828723..65828742 59.75 50
upstream ENSMUSE00000245512 Chr9:65847202..65847353 CTTTGGACCATGTGGGAAGT Chr9:65847227..65847246 59.82 50
upstream ENSMUSE00000219283 Chr9:65849854..65850088 GTTTGACTGGAACTGCGAGA Chr9:65850038..65850057 59.01 50
upstream ENSMUSE00000584164 Chr9:65855547..65855632 CTACCCTGGCAAGGACTCAA Chr9:65855612..65855631 60.25 55
upstream ENSMUSE00000584163 Chr9:65857870..65857954 ACTCCCATCGAAGCTCTCTG Chr9:65857921..65857940 59.56 55
upstream ENSMUSE00000219275 Chr9:65858229..65858377 ATGCCTATGATTGGGTTGGA Chr9:65858349..65858368 60.15 45
upstream ENSMUSE00000219288 Chr9:65860554..65860661 GGTGCATCTGCAATAACTCG Chr9:65860587..65860606 59.3 50
upstream ENSMUSE00000219284 Chr9:65867609..65867719 GAGGAGAGTGGGAAATCCAG Chr9:65867628..65867647 58.66 55

*** Putative Vector Insertion (Chr 9: 65867720 - 65880045) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000584162 Chr9:65880046..65880152 CATCGACATTCAGCTCTCCA Chr9:65880085..65880104 59.94 50
downstream ENSMUSE00000532529 Chr9:65882857..65882880 No primer for this exon
downstream ENSMUSE00000331733 Chr9:65887384..65892821 TGCAATGTCTCAAGGACAGC Chr9:65890357..65890376 59.99 50
downstream ENSMUSE00000710842 Chr9:65887384..65890882 TGCAATGTCTCAAGGACAGC Chr9:65890357..65890376 59.99 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GATAATCGCCTTGCAGCACA Chr9:65876769..65876789 62.25 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGGACGTGACTGGGAAAACC Chr9:65876767..65876787 61.32 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032384