Tools for the biologist enabling optimized use of gene trap clones
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About
UniTrap UNI5543
Trapped Gene
Cdc5l (
ENSMUSG00000023932
)
Vector Insertion
Chr 17: 45561550 - 45562800
Public Clones
YTA190 (baygenomics)
IST10993G11 (tigm)
IST10993G11 (tigm)
Private Clones
OST422663 (lexicon)
Severity of mutation
(?)
Insertion after 18% of polypeptide chain
Suggested RT-PCR
(?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000389518 (Chr17:45562801..45562928 -)
Vector Sequence
Forward Primer
Location
Tm
%GC
LacZrt Reverse Primer
Location
CCCGATAGACATGGATGAGG
Chr17:45562801..45562820
60.29
55
TGGCGAAAGGGGGATGTG
Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000389518 (Chr17:45562801..45562928 -)
Downstram Exon
ENSMUSE00000543081 (Chr17:45561450..45561549 -)
Forward Primer
Location
Tm
%GC
Reverse Primer
Location
Tm
%GC
CCCGATAGACATGGATGAGG
Chr17:45562801..45562820
60.29
55
CCTCGGAGAGCATCTCAAGT
Chr17:45561504..45561523
59.56
55
Other possible Exon-Primers for RT-PCR
(?)
Exon ID
Exon location
Forward Primer
Primer location
Tm
%GC
upstream
ENSMUSE00000502094
Chr17:45570340..45570686
GCGCCGTTACTACTTTCTCG
Chr17:45570427..45570446
60.04
55
upstream
ENSMUSE00000136462
Chr17:45564888..45564991
GATTGCCTCATTGCTGCATA
Chr17:45564919..45564938
59.8
45
upstream
ENSMUSE00000402096
Chr17:45563469..45563630
No primer for this exon
upstream
ENSMUSE00000389518
Chr17:45562801..45562928
CCCGATAGACATGGATGAGG
Chr17:45562801..45562820
60.29
55
*** Putative Vector Insertion (Chr 17: 45561550 - 45562800) ***
Exon ID
Exon location
Reverse Primer
Primer location
Tm
%GC
downstream
ENSMUSE00000543081
Chr17:45561450..45561549
CCTCGGAGAGCATCTCAAGT
Chr17:45561504..45561523
59.56
55
downstream
ENSMUSE00000136475
Chr17:45556550..45556768
CTGCTCGAAGCTCTCGTCTT
Chr17:45556706..45556725
60.03
55
downstream
ENSMUSE00000367198
Chr17:45553894..45554038
CCACTGGTTTGGAGGATAGC
Chr17:45553924..45553943
59.55
55
downstream
ENSMUSE00000607325
Chr17:45552502..45552690
TTCTCAGAGCGATGCTGTTG
Chr17:45552518..45552537
60.29
50
downstream
ENSMUSE00000136467
Chr17:45550071..45550219
GTGGGGTATTAAGCCCACCT
Chr17:45550131..45550150
60.07
55
downstream
ENSMUSE00000394171
Chr17:45548777..45548939
GGGTGGCATTAGTGACTGGT
Chr17:45548844..45548863
59.85
55
downstream
ENSMUSE00000136466
Chr17:45547723..45547887
GTTCCTTCTCGGCATTTTCA
Chr17:45547766..45547785
60.19
45
downstream
ENSMUSE00000136463
Chr17:45545285..45545365
TCCTTTACACGCTCAGCATC
Chr17:45545315..45545334
59.03
50
downstream
ENSMUSE00000312815
Chr17:45544745..45544987
TTTCCAGATGGTTCGTAGGG
Chr17:45544826..45544845
59.93
50
downstream
ENSMUSE00000312798
Chr17:45541543..45541740
CCATGGCTCATTCCTTGTTT
Chr17:45541663..45541682
59.93
45
downstream
ENSMUSE00000396781
Chr17:45529942..45530154
TTCAAAAGTGCGTAGCTCCA
Chr17:45529965..45529984
59.61
45
downstream
ENSMUSE00000543072
Chr17:45528841..45529253
ACGGTGCTGGGTAACTTGTC
Chr17:45529027..45529046
60.03
55
Suggested Genomic-PCR
(?)
Forward
Forward location
Tm
%GC
Reverse name
Reverse
Reverse Location
PCR 1
GGGAGTGCTCAGCTCACTGT
Chr17:45562765..45562785
60.62
60
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 2
GGGAGTGCTCAGCTCACTGT
Chr17:45562765..45562785
60.62
60
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
PCR 3
CTAATCGCCTTGCAGCACAT
Chr17:45562859..45562879
61.32
50
L232
GATGTGCTGCAAGGCGATTA
Gene trap vector
PCR 4
CCCAAAGGGACAATGAAGAA
Chr17:45562896..45562916
59.9
45
LacZ
CCAGGGTTTTCCCAGTCACG
Gene trap vector
Come back to gene
ENSMUSG00000023932