Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI8828
Trapped Gene
Csnk1g1 (ENSMUSG00000032384)
Vector Insertion
Chr 9: 65828780 - 65847201
Public Clones TEA218 (baygenomics)
Private Clones OST40048 (lexicon)
Severity of mutation (?) Insertion after 23% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000219276 (Chr9:65828710..65828779 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
CACGTGCTCCACAACTTCAT Chr9:65828723..65828742 59.75 50 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000219276 (Chr9:65828710..65828779 +)
Downstram Exon
ENSMUSE00000245512 (Chr9:65847202..65847353 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
CACGTGCTCCACAACTTCAT Chr9:65828723..65828742 59.75 50 AACGTTCGGTCACAGAGGTC Chr9:65847319..65847338 60.16 55

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

*** Putative Vector Insertion (Chr 9: 65828780 - 65847201) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000245512 Chr9:65847202..65847353 AACGTTCGGTCACAGAGGTC Chr9:65847319..65847338 60.16 55
downstream ENSMUSE00000219283 Chr9:65849854..65850088 CTTGTCGGCCAATCAAGAAG Chr9:65849938..65849957 60.77 50
downstream ENSMUSE00000584164 Chr9:65855547..65855632 CATATGGCCTAAGGCTTCCA Chr9:65855590..65855609 60.05 50
downstream ENSMUSE00000584163 Chr9:65857870..65857954 CAGAGAGCTTCGATGGGAGT Chr9:65857943..65857962 59.56 55
downstream ENSMUSE00000219275 Chr9:65858229..65858377 ATAGGCCTTCCAACCCAATC Chr9:65858379..65858398 60.15 50
downstream ENSMUSE00000219288 Chr9:65860554..65860661 ATCCCTGTGTGTGTGGCTTT Chr9:65860631..65860650 60.43 50
downstream ENSMUSE00000219284 Chr9:65867609..65867719 CGGCGCTCTGATGATGTAGT Chr9:65867631..65867650 61.37 55
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 AGCTTGGCAGTGCAGGTAAG Chr9:65828766..65828786 60.59 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGCTTGGCAGTGCAGGTAAG Chr9:65828766..65828786 60.59 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000032384