Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI28697
Trapped Gene
Ccdc57 (ENSMUSG00000048445)
Vector Insertion
Chr 11: 120721941 - 120722451
Public Clones not available
Private Clones OST23224 (lexicon) OST20757 (lexicon)
Severity of mutation (?) Insertion after 86% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000309042 (Chr11:120722452..120722583 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GGAAGAGTCAACCCCACTCA Chr11:120722521..120722540 60.09 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000309042 (Chr11:120722452..120722583 -)
Downstram Exon
ENSMUSE00000414877 (Chr11:120721715..120721940 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GGAAGAGTCAACCCCACTCA Chr11:120722521..120722540 60.09 55 AAGACGATCTGTGGGTACGG Chr11:120721786..120721805 59.99 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000512694 Chr11:120794030..120794186 CGGGAGACGAAGCTAATTCC Chr11:120794054..120794073 61.08 55
upstream ENSMUSE00000401898 Chr11:120782834..120783248 AGCTGGAGCGCTATGATGTT Chr11:120783013..120783032 60.01 50
upstream ENSMUSE00000366049 Chr11:120780787..120780895 TCGATGGTGAACTTGCTCTG Chr11:120780796..120780815 59.98 50
upstream ENSMUSE00000409661 Chr11:120765298..120765399 CGACATGAGCAACGTAGTCC Chr11:120765315..120765334 59.32 55
upstream ENSMUSE00000406389 Chr11:120764837..120764994 AGCTCTGAGAGACGCTGGAG Chr11:120764949..120764968 60.03 60
upstream ENSMUSE00000371022 Chr11:120764630..120764704 ACAGCTGGCCAAGAAGAAAG Chr11:120764652..120764671 59.62 50
upstream ENSMUSE00000414005 Chr11:120763189..120763389 TGAGTGCACAAGAGCAGAGG Chr11:120763220..120763239 60.33 55
upstream ENSMUSE00000367026 Chr11:120759123..120759281 GCCAGATTCCAACAGGACAT Chr11:120759129..120759148 59.93 50
upstream ENSMUSE00000407738 Chr11:120756571..120756733 TGGAGCGTGAACAGGTACAG Chr11:120756670..120756689 59.9 55
upstream ENSMUSE00000380530 Chr11:120755913..120756047 ACGTACACATGGGCTCCTTC Chr11:120755930..120755949 60 55
upstream ENSMUSE00000337249 Chr11:120747164..120747377 TGTTCAAATGCAGACCCTGA Chr11:120747196..120747215 60.24 45
upstream ENSMUSE00000383238 Chr11:120746547..120746699 GACCCTTGAAGCAGAAATGC Chr11:120746670..120746689 59.82 50
upstream ENSMUSE00000396036 Chr11:120743129..120743229 CTCTGGCAGACCAGACATCC Chr11:120743204..120743223 60.83 60
upstream ENSMUSE00000368661 Chr11:120740192..120740362 TCATCCAGGGAGCAGTTACA Chr11:120740199..120740218 59.24 50
upstream ENSMUSE00000356044 Chr11:120734900..120735113 ACCAGACGGAGTCCCCTACT Chr11:120735060..120735079 59.99 60
upstream ENSMUSE00000337295 Chr11:120727869..120727990 TTGCAGCCCTACTCAACAACT Chr11:120727872..120727892 59.93 47.62
upstream ENSMUSE00000309042 Chr11:120722452..120722583 GGAAGAGTCAACCCCACTCA Chr11:120722521..120722540 60.09 55

*** Putative Vector Insertion (Chr 11: 120721941 - 120722451) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000414877 Chr11:120721715..120721940 AAGACGATCTGTGGGTACGG Chr11:120721786..120721805 59.99 55
downstream ENSMUSE00000414924 Chr11:120687856..120688238 CTTTTGGCTGAGCTTCCATC Chr11:120688106..120688125 59.96 50

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 GCTCAGGTAGAGTGGGTGCT Chr11:120722436..120722456 59.48 60 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 GGATACCGTGACTGGGAAAA Chr11:120722386..120722406 59.79 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000048445